A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics (scientific article)

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Q42670802	Equilibrium analysis of the efficiency of an autonomous molecular computer
Q40783955	Equilibrium gels of trivalent DNA-nanostars: Effect of the ionic strength on the dynamics
Q54540612	Escherichia coli DnaA protein loads a single DnaB helicase at a DnaA box hairpin.
Q33922353	Evaluating oligonucleotide properties for DNA microarray probe design
Q42737581	Evidence for DNA hairpin recognition by Zta at the Epstein-Barr virus origin of lytic replication
Q28178625	Evidence for an important role of perilipin in the regulation of human adipocyte lipolysis
Q35677790	Evidence of positive selection on a class I ADH locus
Q64935133	Evolutionary advantage of directional symmetry breaking in self-replicating polymers.
Q28650495	Evolutionary dynamics of hAT DNA transposon families in Saccharomycetaceae
Q34180258	Excitonic heterodimer formation in an HIV-1 oligonucleotide labeled with a donor-acceptor pair used for fluorescence resonance energy transfer
Q47994680	Experimental measurement of binding energy, selectivity, and allostery using fluctuation theorems
Q33302865	Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays.
Q35547868	Experimental phase diagram of negatively supercoiled DNA measured by magnetic tweezers and fluorescence
Q33989761	Exploitation of plasmid pMRC01 to direct transfer of mobilizable plasmids into commercial lactococcal starter strains
Q50991342	Exploiting Receptor Competition to Enhance Nanoparticle Binding Selectivity.
Q34353188	Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis.
Q34353197	Exploring the complex folding kinetics of RNA hairpins: II. Effect of sequence, length, and misfolded states
Q33237751	Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions
Q44801528	Expression profiling using a hexamer-based universal microarray
Q42154106	Extendable blocking probe in reverse transcription for analysis of RNA variants with superior selectivity.
Q35145469	Extensive relationship between antisense transcription and alternative splicing in the human genome.
Q78564320	External-loop free energy affects dye-labeled terminators premature terminations in DNA cycle-sequencing reactions
Q30620427	FARE, a new family of foldback transposons in Arabidopsis.
Q21285080	Family-specific degenerate primer design: a tool to design consensus degenerated oligonucleotides
Q51595908	Fast large scale oligonucleotide selection using the longest common factor approach.
Q34459399	Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization
Q52632384	First characterization of a biphasic, switch-like DNA amplification.
Q58611614	Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif
Q41125874	Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs
Q34502500	Flexible and efficient genome tiling design with penalized uniqueness score
Q99237983	Fluorescence Resonant Energy Transfer-Based Quantum Dot Sensor for the Detection of Calcium Ions
Q37644386	Fluorescent probes and delivery methods for single-molecule experiments.
Q34193908	Folding-upon-binding and signal-on electrochemical DNA sensor with high affinity and specificity
Q91963225	Force-Dependent Binding Constants
Q42124918	Force-driven separation of short double-stranded DNA.
Q34175002	Force-induced melting of the DNA double helix. 2. Effect of solution conditions
Q30924732	Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure
Q28757627	Formation of the open complex by bacterial RNA polymerase--a quantitative model
Q37426610	Free energy calculation of modified base-pair formation in explicit solvent: A predictive model
Q33534038	Free energy estimation of short DNA duplex hybridizations
Q36742536	Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes
Q38306514	Free energy of DNA duplex formation on short oligonucleotide microarrays
Q34400829	From genes to machines: DNA nanomechanical devices
Q37192001	G clustering is important for the initiation of transcription-induced R-loops in vitro, whereas high G density without clustering is sufficient thereafter
Q30373930	G-quadruplex aptamer targeting Protein A and its capability to detect Staphylococcus aureus demonstrated by ELONA.
Q33566263	G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration
Q35212962	GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR.
Q34174022	GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group
Q28727129	Gauging triple stores with actual biological data.
Q27303508	Gender and Obesity Specific MicroRNA Expression in Adipose Tissue from Lean and Obese Pigs
Q33957241	Gene Assembly from Chip-Synthesized Oligonucleotides.
Q36145681	Gene Deletion by Synthesis in Yeast.
Q50856690	Gene synthesis by circular assembly amplification.
Q34447143	Gene-gene interaction and functional impact of polymorphisms on innate immune genes in controlling Plasmodium falciparum blood infection level.
Q41010791	Gene2Oligo: oligonucleotide design for in vitro gene synthesis.
Q98386190	Generation of Cry11 Variants of Bacillus thuringiensis by Heuristic Computational Modeling
Q24684546	Generation of non-genomic oligonucleotide tag sequences for RNA template-specific PCR
Q38316375	Genetic targeting of individual cells with a voltage-sensitive dye through enzymatic activation of membrane binding
Q36828390	Genetic variation in sialidase and linkage to N-acetylneuraminate catabolism in Mycoplasma synoviae
Q35021831	Genome Size Evolution in Pufferfish: A Comparative Analysis of Diodontid and Tetraodontid Pufferfish Genomes
Q35036891	Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots
Q35417828	Genomic signal processing methods for computation of alignment-free distances from DNA sequences
Q35790079	Genotyping of human platelet antigens 1 to 6 and 15 by high-resolution amplicon melting and conventional hybridization probes
Q41886476	Global assessment of cross-hybridization for oligonucleotide arrays.
Q31047047	GnRH binding RNA and DNA Spiegelmers: a novel approach toward GnRH antagonism
Q48514442	GoArrays: highly dynamic and efficient microarray probe design.
Q30846768	Gorilla MHC class I gene and sequence variation in a comparative context
Q37069465	Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray.
Q59051232	Guiding the folding pathway of DNA origami
Q24628718	HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome
Q61795097	Hachimoji DNA and RNA: A genetic system with eight building blocks
Q42679292	Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds
Q54640665	Haplotyping of TNFalpha gene promoter using melting temperature analysis: detection of a novel -856(G/A) mutation.
Q36375057	Heat capacity changes associated with nucleic acid folding
Q34172029	Heat capacity effects on the melting of DNA. 1. General aspects.
Q34172037	Heat capacity effects on the melting of DNA. 2. Analysis of nearest-neighbor base pair effects
Q34977386	High levels of PROM1 (CD133) transcript are a potential predictor of poor prognosis in medulloblastoma
Q54516608	High resolution melting analysis of almond SNPs derived from ESTs.
Q33392932	High throughput single molecule detection for monitoring biochemical reactions
Q40537609	High-resolution DNA melting curve analysis to establish HLA genotypic identity
Q77975033	High-resolution calorimetric and optical melting profiles of DNA plasmids: resolving contributions from intrinsic melting domains and specifically designed inserts
Q31105364	High-throughput detection of pathogenic yeasts of the genus trichosporon
Q39063986	High-throughput thermal stability assessment of DNA hairpins based on high resolution melting
Q24537607	Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules
Q28709958	Highly informative ancient DNA 'snippets' for New Zealand moa
Q42378966	Highly sensitive and specific Alu-based quantification of human cells among rodent cells
Q36681978	Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments
Q83228197	Homology sensing via non-linear amplification of sequence-dependent pausing by RecQ helicase
Q55710893	How Well Can DNA Rupture DNA? Shearing and Unzipping Forces inside DNA Nanostructures.
Q53530969	How a short double-stranded DNA bends.
Q58042555	How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model
Q36537717	Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides.
Q40282451	Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs
Q39735230	Hybridization kinetics and thermodynamics of molecular beacons
Q33525165	Hybridization thermodynamics of NimbleGen microarrays.
Q38324106	Hydration changes upon DNA folding studied by osmotic stress experiments
Q41966841	Hyperthermophilic Aquifex aeolicus initiates primer synthesis on a limited set of trinucleotides comprised of cytosines and guanines
Q24646200	IDT SciTools: a suite for analysis and design of nucleic acid oligomers
Q99557365	IMPROvER: the Integral Membrane Protein Stability Selector
Q50683837	IWO Algorithm Based on Niche Crowding for DNA Sequence Design.
Q30456379	Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis
Q51904621	Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability.
Q41618041	Identification of Diatraea spp. (Lepidoptera: Crambidae) based on cytochrome oxidase II.
Q35857611	Identification of PCR products using PNA amphiphiles in micellar electrokinetic chromatography.
Q55018220	Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy.
Q33287053	Identification of sequence motifs significantly associated with antisense activity
Q29395646	Identification of species by multiplex analysis of variable-length sequences
Q33691580	Identifying Fishes through DNA Barcodes and Microarrays
Q91699413	Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model
Q35622142	Identifying the last bloodmeal of questing sheep tick nymphs (Ixodes ricinus L.) using high resolution melting analysis.
Q47779992	Imbalance of G and C contents influences the sensitivity of single-strand conformation polymorphism.
Q42360815	Immuno Affinity SELEX for Simple, Rapid, and Cost-Effective Aptamer Enrichment and Identification against Aflatoxin B1.
Q58048567	Impact of DNA physical properties on local sequence bias of human mutation
Q59349667	Impact of primer dimers and self-amplifying hairpins on reverse transcription loop-mediated isothermal amplification detection of viral RNA
Q47989062	Impact of the terminal bulges of HIV-1 cTAR DNA on its stability and the destabilizing activity of the nucleocapsid protein NCp7.
Q36942630	Importance of diffuse metal ion binding to RNA
Q51763166	Improved Cardiovascular Function in Old Mice after N-Acetyl Cysteine and Glycine Supplemented Diet: Inflammation and Mitochondrial Factors.
Q36777792	Improved assay-dependent searching of nucleic acid sequence databases
Q35563550	Improved lower bounds of DNA tags based on a modified genetic algorithm
Q34771864	Improving signal/noise resolution in single-molecule experiments using molecular constructs with short handles
Q28829179	In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization
Q33674951	In silico analyses of primers used to detect the pathogenicity genes of Vibrio cholerae
Q91330218	In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription
Q36538858	In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water
Q30406029	In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A.
Q33365071	In vitro antibacterial effects of antilipopolysaccharide DNA aptamer-C1qrs complexes
Q34108039	In vitro assembly of cubic RNA-based scaffolds designed in silico
Q34479451	In vitro selection of a single-stranded DNA molecular recognition element specific for bromacil
Q55080492	In vitro synthesis of gene-length single-stranded DNA.
Q92890535	In-silico Design of DNA Oligonucleotides: Challenges and Approaches
Q30531073	Incorporation of a cationic aminopropyl chain in DNA hairpins: thermodynamics and hydration
Q60192121	Increased Flexibility between Stems of Intramolecular Three-Way Junctions by the Insertion of Bulges
Q91173497	Independent control of the thermodynamic and kinetic properties of aptamer switches
Q51944017	Inference of DNA sequences from mechanical unzipping: an ideal-case study.
Q31105544	Inferring DNA sequences from mechanical unzipping data: the large-bandwidth case
Q40161732	Influence of DNA sequence on the structure of minicircles under torsional stress
Q41808427	Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides
Q35837385	Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization
Q36492142	Influence of the N-terminal domain and divalent cations on self-association and DNA binding by the Saccharomyces cerevisiae TATA binding protein
Q49784609	Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics.
Q50611609	Information management in DNA replication modeled by directional, stochastic chains with memory.
Q33286173	Inhibiting gene expression with locked nucleic acids (LNAs) that target chromosomal DNA.
Q27486247	Inhibition of Hepatitis C Virus (HCV) RNA Polymerase by DNA Aptamers: Mechanism of Inhibition of In Vitro RNA Synthesis and Effect on HCV-Infected Cells
Q41184183	Insight into the sequence specificity of a probe on an Affymetrix GeneChip by titration experiments using only one oligonucleotide.
Q38014471	Integrating fragmented software applications into holistic solutions: focus on drug discovery
Q38302626	Interactions of the cold shock protein CspB from Bacillus subtilis with single-stranded DNA. Importance of the T base content and position within the template
Q34408746	Intrinsic disorder as a generalizable strategy for the rational design of highly responsive, allosterically cooperative receptors
Q30104396	Introduction on Using the FastPCR Software and the Related Java Web Tools for PCR and Oligonucleotide Assembly and Analysis
Q38477262	Invader plus method detects herpes simplex virus in cerebrospinal fluid and simultaneously differentiates types 1 and 2.
Q33411034	Inverse Langmuir method for oligonucleotide microarray analysis
Q37066566	Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs
Q30379297	Investigating the dynamics of surface-immobilized DNA nanomachines
Q53558171	Investigation of the Melting Behavior of DNA Three-Way Junctions in the Closed and Open States.
Q36238166	Ion-mediated RNA structural collapse: effect of spatial confinement.
Q42826519	Irreducible representation for nucleotide sequence physical properties and self-consistency of nearest-neighbor dimer sets
Q53084505	J-factors of short DNA molecules.
Q33899367	Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis
Q24530528	Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots
Q43229711	Kinetic control of Mg2+-dependent melting of duplex DNA ends by Escherichia coli RecBC.
Q47592838	Kinetic theory for DNA melting with vibrational entropy
Q47424724	Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size.
Q21284338	LAVA: an open-source approach to designing LAMP (loop-mediated isothermal amplification) DNA signatures
Q39815600	Label-free detection of DNA single-base mismatches using a simple reflectance-based optical technique
Q33568193	Large scale analysis of positional effects of single-base mismatches on microarray gene expression data
Q53083702	Lattice model of oligonucleotide hybridization in solution. I. Model and thermodynamics.
Q51401183	Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity.
Q95642685	Light Forge: A Microfluidic DNA Melting-based Tuberculosis Test
Q33853941	Linear-After-The-Exponential (LATE)-PCR: primer design criteria for high yields of specific single-stranded DNA and improved real-time detection
Q36604138	Linear-after-the-exponential (LATE)-PCR: an advanced method of asymmetric PCR and its uses in quantitative real-time analysis
Q38331754	Linkage between proton binding and folding in RNA: a thermodynamic framework and its experimental application for investigating pKa shifting
Q34756999	Linkage mapping in the oilseed crop Jatropha curcas L. reveals a locus controlling the biosynthesis of phorbol esters which cause seed toxicity
Q34297090	Linking class-switch recombination with somatic hypermutation
Q50992453	LncTar: a tool for predicting the RNA targets of long noncoding RNAs.
Q46265054	Local cooperativity mechanism in the DNA melting transition
Q33716412	Localization of denaturation bubbles in random DNA sequences
Q33698593	Lomofungin and dilomofungin: inhibitors of MBNL1-CUG RNA binding with distinct cellular effects
Q54118286	Long Fragment Polymerase Chain Reaction.
Q81342468	Long oligonucleotide microarrays in wheat: evaluation of hybridization signal amplification and an oligonucleotide-design computer script
Q79160494	Long-range correlations in the helix free energy distribution in DNA
Q24799498	Low density DNA microarray for detection of most frequent TP53 missense point mutations
Q36088519	MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity
Q33860611	MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering.
Q36240627	MPD: multiplex primer design for next-generation targeted sequencing
Q33542864	MPprimer: a program for reliable multiplex PCR primer design
Q36676477	MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCR.
Q38302023	Macroscopic self-assembly based on complementary interactions between nucleobase pairs.
Q42138811	Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength.
Q34316080	Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides.
Q30983384	Mapping the intrinsic curvature and flexibility along the DNA chain.
Q38610344	Massively parallel and multiparameter titration of biochemical assays with droplet microfluidics
Q51920179	Master equation approach to DNA breathing in heteropolymer DNA.
Q51851825	Mathematical algorithms for high-resolution DNA melting analysis.
Q34445615	Mathematical tools to optimize the design of oligonucleotide probes and primers.
Q30483370	Measurement of the effect of monovalent cations on RNA hairpin stability
Q52604128	Measuring DNA hybridization using fluorescent DNA-stabilized silver clusters to investigate mismatch effects on therapeutic oligonucleotides.
Q30466742	Measuring the folding landscape of a harmonically constrained biopolymer
Q41790436	Mechanical properties of high-G.C content DNA with a-type base-stacking
Q34181000	Mechanically probing the folding pathway of single RNA molecules
Q52638162	Mechanically unzipping dsDNA with built-in sequence inhomogeneities and bound proteins.
Q37363001	Mechanism of strand-specific smooth muscle alpha-actin enhancer interaction by purine-rich element binding protein B (Purbeta).
Q37701458	Mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization.
Q41837841	Melting of DNA oligomers: dynamical models and comparison with experimental results
Q39687074	Melting studies of dangling-ended DNA hairpins: effects of end length, loop sequence and biotinylation of loop bases
Q36400257	Melting thermodynamics of reversible DNA/ligand complexes at interfaces
Q48310775	Melting transition in lipid vesicles functionalised by mobile DNA linkers
Q24498105	Mfold web server for nucleic acid folding and hybridization prediction
Q37724950	MicroRNAs in leukemias: emerging diagnostic tools and therapeutic targets
Q36580129	Microarray oligonucleotide probes
Q37518218	Microarray probes and probe sets
Q35136600	Microdroplet temperature calibration via thermal dissociation of quenched DNA oligomers
Q89307327	Microrheology of DNA hydrogel gelling and melting on cooling
Q56759953	Microrheology of DNA hydrogels
Q46468107	Microscopic implications of S-DNA.
Q30895597	Mismatch and G-stack modulated probe signals on SNP microarrays
Q34646792	Mismatches and bubbles in DNA.
Q37697999	Mismatches improve the performance of strand-displacement nucleic Acid circuits
Q34278779	Mitochondrial DNA deletions are associated with non-B DNA conformations
Q35794812	Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis
Q56931081	Mobile Linkers on DNA-Coated Colloids: Valency without Patches
Q33786802	Mode of action and application of Scorpion primers to mutation detection
Q58042565	Model for melting of confined DNA
Q38357932	Model-based probe set optimization for high-performance microarrays
Q34250442	Model-guided ligation strategy for optimal assembly of DNA libraries
Q33634112	Modeling DNA thermodynamics under torsional stress
Q38289127	Modeling background intensity in DNA microarrays.
Q34297824	Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics
Q30803659	Modeling of DNA microarray data by using physical properties of hybridization
Q44021054	Modeling translocation dynamics of strand displacement DNA synthesis by DNA polymerase I.
Q50782455	Modelling DNA origami self-assembly at the domain level.
Q89578673	Molecular Characterization of the Dwarf53 Gene Homolog in Dasypyrum villosum
Q38355565	Molecular beacons for detecting DNA binding proteins: mechanism of action
Q46401986	Molecular characterization and phylogenetic analysis of Plasmodium vivax, Plasmodium falciparum, Plasmodium ovale, Plasmodium malariae and Plasmodium cynomolgi
Q24816490	Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it.
Q34542982	Molecular diagnostics on the toxigenic potential of Fusarium spp. plant pathogens.
Q30482104	Molecular force balance measurements reveal that double-stranded DNA unbinds under force in rate-dependent pathways
Q37328191	Molecular geometry of CsrA (RsmA) binding to RNA and its implications for regulated expression
Q35020416	Molecular recognition of 6'-N-5-hexynoate kanamycin A and RNA 1x1 internal loops containing CA mismatches
Q33234895	Molecular targets for rapid identification of Brucella spp.
Q41083340	Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations
Q104624107	Morphology of obligate ectosymbionts reveals Paralaxus gen. nov.: A new circumtropical genus of marine stilbonematine nematodes
Q52889984	MsLDR-creator: a web service to design msLDR assays.
Q73435389	Multiplex PCR by multicolor fluorimetry and fluorescence melting curve analysis
Q48259309	Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci
Q33622660	Multiplex analysis of mitochondrial DNA pathogenic and polymorphic sequence variants.
Q42121229	Multiplex quantitative real-time reverse transcriptase PCR for F+-specific RNA coliphages: a method for use in microbial source tracking
Q54299602	Multiplexed protein detection using an affinity aptamer amplification assay.
Q38790169	Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches
Q43773973	Multitemperature single-strand conformation polymorphism
Q38714591	Mutant enrichment with 3'-modified oligonucleotides a practical PCR method for detecting trace mutant DNAs
Q45933685	Mutation detection by electrocatalysis at DNA-modified electrodes.
Q30839225	Mutations underlying Episodic Ataxia type-1 antagonize Kv1.1 RNA editing
Q27674953	Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1 × 1 Nucleotide UU Internal Loop Conformations
Q41775337	NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon
Q33600780	NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
Q40635816	Nanomechanical DNA origami 'single-molecule beacons' directly imaged by atomic force microscopy.
Q34597333	Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins
Q64387824	Nanomechanics of Diaminopurine-Substituted DNA
Q33264203	Nanopore Detector based analysis of single-molecule conformational kinetics and binding interactions
Q34187685	Nanopore unzipping of individual DNA hairpin molecules.
Q42541307	Native characterization of nucleic acid motif thermodynamics via non-covalent catalysis.
Q42589910	Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotides
Q24813538	Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes
Q33719396	New approach to real-time nucleic acids detection: folding polymerase chain reaction amplicons into a secondary structure to improve cleavage of Forster resonance energy transfer probes in 5'-nuclease assays
Q35476770	New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey
Q34438616	New prediction model for probe specificity in an allele-specific extension reaction for haplotype-specific extraction (HSE) of Y chromosome mixtures
Q42264115	Non-specific binding of Na+ and Mg2+ to RNA determined by force spectroscopy methods
Q39443686	Nonspaced inverted DNA repeats are preferential targets for homology-directed gene repair in mammalian cells.
Q28743150	Normalization and centering of array-based heterologous genome hybridization based on divergent control probes
Q24653203	Novel microarray design strategy to study complex bacterial communities
Q41579710	Novel primer-probe sets for detection and identification of mycobacteria by PCR-microarray assay.
Q37857036	Nucleic acid based molecular devices
Q78632482	Nucleic acid conformational changes essential for HIV-1 nucleocapsid protein-mediated inhibition of self-priming in minus-strand transfer
Q33641842	Nucleic acid evolution and minimization by nonhomologous random recombination
Q34354064	Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length
Q34131851	Nucleic acid sequence design via efficient ensemble defect optimization
Q43037770	Nucleic acid unwinding by hepatitis C virus and bacteriophage t7 helicases is sensitive to base pair stability
Q35253781	Nucleic acid-triggered catalytic drug release
Q56931221	Numerical study of DNA-functionalized microparticles and nanoparticles: Explicit pair potentials and their implications for phase behavior
Q54223184	Oli2go: an automated multiplex oligonucleotide design tool.
Q38395379	OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS) to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands
Q30727963	OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
Q42431955	OligoCalc: an online oligonucleotide properties calculator.
Q24575548	OligoDesign: optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling
Q49790428	OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.
Q38297533	Oligonucleotide mapping of the core genomic RNA dimer linkage in human T-cell leukaemia virus type-1.
Q38357954	Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment.
Q39706856	On Correlation Effect of the Van-der-Waals and Intramolecular Forces for the Nucleotide Chain - Metallic Nanoparticles - Carbon Nanotube Binding.
Q37528778	On the biophysics and kinetics of toehold-mediated DNA strand displacement
Q30541427	On the mechanism of recombination hotspot scanning during double-stranded DNA break resection
Q25255781	On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes
Q34379902	On-demand droplet fusion: a strategy for stimulus-responsive biosensing in solution
Q35024820	One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy.
Q40406162	Optical absorption assay for strand-exchange reactions in unlabeled nucleic acids.
Q41588606	Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence
Q36845329	Optimal probe length and target location for electrochemical detection of selected uropathogens at ambient temperature
Q33389559	Optimised padlock probe ligation and microarray detection of multiple (non-authorised) GMOs in a single reaction
Q47710973	Optimization method for obtaining nearest-neighbour DNA entropies and enthalpies directly from melting temperatures
Q33667847	Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes
Q47415665	Optothermally Reversible Carbon Nanotube-DNA Supramolecular Hybrid Hydrogels
Q37564595	Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays.
Q24795993	PATTERNFINDER: combined analysis of DNA regulatory sequences and double-helix stability
Q30965995	PDEGEM: Modeling non-uniform read distribution in RNA-Seq data
Q41816412	PHUSER (Primer Help for USER): a novel tool for USER fusion primer design
Q24613802	Paradigms for computational nucleic acid design
Q24547239	Partition function and base pairing probabilities of RNA heterodimers
Q93087104	Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features
Q41866245	Patho-Genes.org: a website dedicated to gene sequences of potential bioterror bacteria and PCR primers used to amplify them
Q41925416	Pausing kinetics dominates strand-displacement polymerization by reverse transcriptase.
Q36446056	Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers
Q34183348	PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity.
Q52351485	Photoswitching of DNA Hybridization Using a Molecular Motor.
Q92640112	Phylogeny of Paullinia L. (Paullinieae: Sapindaceae), a diverse genus of lianas with dynamic fruit evolution
Q33580410	Physico-chemical fingerprinting of RNA genes
Q47200333	Plastic-adherent DNA aptamer-magnetic bead and quantum dot sandwich assay for Campylobacter detection
Q36414798	Polygamous particles
Q35808921	Population structure of Pseudomonas aeruginosa
Q33388531	Position dependent mismatch discrimination on DNA microarrays - experiments and model
Q24812603	Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations
Q40904618	Position-dependent effects of locked nucleic acid (LNA) on DNA sequencing and PCR primers
Q38300639	Positioning the 3'-DNA terminus for topoisomerase II-mediated religation
Q41500111	Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering
Q35168806	PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling
Q42627614	Predicting DNA-mediated colloidal pair interactions
Q40093186	Predicting Ion Effects in an RNA Conformational Equilibrium.
Q33243971	Predicting Shine-Dalgarno sequence locations exposes genome annotation errors
Q37206342	Predicting and understanding the stability of G-quadruplexes
Q34714253	Predicting crossover generation in DNA shuffling.
Q36920517	Predicting electrostatic forces in RNA folding
Q34099007	Predicting ion binding properties for RNA tertiary structures
Q42326406	Predicting ion-nucleic acid interactions by energy landscape-guided sampling
Q33658469	Predicting loop-helix tertiary structural contacts in RNA pseudoknots
Q24539440	Predicting oligonucleotide affinity to nucleic acid targets
Q31134755	Predicting oligonucleotide-directed mutagenesis failures in protein engineering
Q38302258	Predicting the rupture probabilities of molecular bonds in series.
Q39689852	Predicting the success of primer extension genotyping assays using statistical modeling
Q33988594	Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling
Q33538211	Prediction of RNA multiloop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure model
Q34186238	Prediction of hybridization and melting for double-stranded nucleic acids
Q38317266	Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models.
Q92955119	Prediction of the secondary structure of short DNA aptamers
Q64931020	Predictive Model for the Sequence-Dependent Fluorogenic Response of Forced-Intercalation Peptide Nucleic Acid.
Q35207959	Primer Design Assistant (PDA): A web-based primer design tool
Q29614816	Primer3--new capabilities and interfaces
Q35631144	PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update
Q33600700	PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification
Q27350248	PrimerMapper: high throughput primer design and graphical assembly for PCR and SNP detection
Q42552471	PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome
Q35810211	Primerize: automated primer assembly for transcribing non-coding RNA domains
Q33301227	Primique: automatic design of specific PCR primers for each sequence in a family
Q34459448	Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts
Q48076464	Probe selection for DNA microarrays using OligoWiz.
Q36160579	Probe selection for high-density oligonucleotide arrays
Q104486515	ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization
Q45932820	Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips.
Q82213320	Probing DNA base pairing energy profiles using a nanopore
Q28267999	Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond
Q47208120	Probing interfacial equilibration in microsphere crystals formed by DNA-directed assembly
Q37359445	Probing the conformational distributions of subpersistence length DNA.
Q38296375	Probing the structure of DNA aptamers with a classic heterocycle
Q35904077	Processive ATP-driven substrate disassembly by the N-ethylmaleimide-sensitive factor (NSF) molecular machine
Q58221798	Programming colloidal phase transitions with DNA strand displacement
Q40800225	Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations
Q33242489	Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress
Q54613749	Protein-inspired modified DNAzymes: dramatic effects of shortening side-chain length of 8-imidazolyl modified deoxyadenosines in selecting RNaseA mimicking DNAzymes.
Q37533474	Pulsed IR heating studies of single-molecule DNA duplex dissociation kinetics and thermodynamics
Q37399351	Pyramidal and chiral groupings of gold nanocrystals assembled using DNA scaffolds
Q33381878	QuantPrime--a flexible tool for reliable high-throughput primer design for quantitative PCR.
Q60163810	Quantifying how DNA stretches, melts and changes twist under tension
Q40138129	Quantitative analysis of the nanopore translocation dynamics of simple structured polynucleotides
Q36154488	Quantitative experimental determination of primer-dimer formation risk by free-solution conjugate electrophoresis
Q28834147	Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?
Q42232925	RF-Cloning.org: an online tool for the design of restriction-free cloning projects.
Q40606140	RNA aptamers selected against the receptor activator of NF-kappaB acquire general affinity to proteins of the tumor necrosis factor receptor family
Q36275406	RNA challenges for computational chemists
Q28139158	RNA expression analysis using a 30 base pair resolution Escherichia coli genome array
Q35753774	RNA helix stability in mixed Na+/Mg2+ solution
Q37301668	RNA structure and modeling: progress and techniques
Q30778578	RNAsoft: A suite of RNA secondary structure prediction and design software tools
Q46521618	Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel
Q33960560	Rapid identification of carbapenemase genes in gram-negative bacteria with an oligonucleotide microarray-based assay
Q54758652	Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups.
Q40967620	Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora
Q37509316	Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs
Q33474085	Rational design of ligands targeting triplet repeating transcripts that cause RNA dominant disease: application to myotonic muscular dystrophy type 1 and spinocerebellar ataxia type 3.
Q37363821	Re-entrant DNA gels.
Q53219419	Real-Time Observation of Backtracking by Bacterial RNA Polymerase.
Q47842609	Real-time RT-PCR quantification of mRNA encoding cytokines and chemokines in histologically normal canine nasal, bronchial and pulmonary tissue
Q50679706	Real-time quantitative nicking endonuclease-mediated isothermal amplification with small molecular beacons.
Q38348355	Realtime exonuclease-mediated allelic discrimination (READ): a simple homogeneous genotyping assay for SNPs at the ABC gene loci
Q30597624	Recent amplification of miniature inverted-repeat transposable elements in the vector mosquito Culex pipiens: characterization of the Mimo family
Q58828853	Recent progress on the mechanics of sharply bent DNA
Q61719133	Receptor modulation and functional activation of human CD34+Lin−-derived immature NK cells in vitro by Mycobacterium bovisBacillus Calmette-Guerin (BCG)
Q24288657	Recombinase Polymerase Amplification Assay for Rapid Diagnostics of Dengue Infection
Q38922941	Redox-active and DNA-binding coordination complexes of clotrimazole
Q51150222	Refining the Results of a Classical SELEX Experiment by Expanding the Sequence Data Set of an Aptamer Pool Selected for Protein A.
Q38256396	Relationship between digital information and thermodynamic stability in bacterial genomes.
Q41853296	Relationship between gene expression and observed intensities in DNA microarrays--a modeling study
Q35280421	Relationship between promoter sequence and its strength in gene expression
Q38357429	Relevance of sequence and structure elements for deletion events in the dystrophin gene major hot-spot
Q90618095	Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters
Q28769097	Resistance to gap repair of the transposon Tam3 in Antirrhinum majus: a role of the end regions
Q54263037	Retrospective monitoring of minimal residual disease using hairpin-shaped clone specific primers in B-cell lymphoma affected dogs.
Q61813607	Revealing the Presence of a Symbolic Sequence Representing Multiple Nucleotides Based on K-Means Clustering of Oligonucleotides
Q36673121	Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry
Q33212702	Reversible self-assembly and directed assembly of DNA-linked micrometer-sized colloids
Q36363476	Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA
Q98219406	Ribo-Pop: Simple, cost-effective, and widely applicable ribosomal RNA depletion
Q36375500	Ribonucleotide Reduction in Mycobacterium tuberculosis : Function and Expression of Genes Encoding Class Ib and Class II Ribonucleotide Reductases
Q40414773	Robust and accurate single nucleotide polymorphism genotyping by dynamic allele-specific hybridization (DASH): design criteria and assay validation
Q33959358	Robustness and modularity properties of a non-covalent DNA catalytic reaction
Q44522123	SAGE surveys C. elegans carbohydrate metabolism: evidence for an anaerobic shift in the long-lived dauer larva
Q42574260	Salerno's model of DNA re-analysed: could breather solitons have biological significance?
Q35079364	Salt contribution to RNA tertiary structure folding stability
Q45739309	Salt contribution to the flexibility of single-stranded nucleic acid offinite length
Q24650345	Salt dependence of nucleic acid hairpin stability
Q51010767	Scaling up an electrochemical signal with a catalytic hairpin assembly coupling nanocatalyst label for DNA detection.
Q43674505	Scatter: a novel family of miniature inverted-repeat transposable elements in the fungus Botrytis cinerea
Q51590608	Screening CYP3A single nucleotide polymorphisms in a Han Chinese population with a genotyping chip.
Q34716306	Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison
Q64386799	Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: implications for DNA hybridization
Q38298508	Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.
Q28469065	Selection acts on DNA secondary structures to decrease transcriptional mutagenesis
Q37139585	Selection and characterization of single stranded DNA aptamers for the hormone abscisic Acid
Q58127979	Selection criteria for SNP loci to maximize robustness of high-resolution melting analysis for plant breeding
Q36977319	Selection for 3'-end triplets for polymerase chain reaction primers
Q38295506	Selection of Nucleic Acid Aptamers Specific for Mycobacterium tuberculosis
Q30774795	Selection of genomic sequences that bind tightly to Ff gene 5 protein: primer-free genomic SELEX.
Q24816228	Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation.
Q36118916	Selective inhibitory DNA aptamers of the human RNase H1
Q61198338	Self-assembly of DNA nanotubes with controllable diameters
Q37631118	Sequence Affects the Cyclization of DNA Minicircles
Q40387879	Sequence analysis of the mobile genome island pKLC102 of Pseudomonas aeruginosa C
Q55496660	Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes.
Q37132714	Sequence context effect for hMSH2-hMSH6 mismatch-dependent activation
Q51931691	Sequence sensitivity of breathing dynamics in heteropolymer DNA.
Q35089454	Sequence-based design of bioactive small molecules that target precursor microRNAs
Q45944041	Sequence-based information-theoretic features for gene essentiality prediction.
Q40216502	Sequence-dependent DNA curvature and flexibility from scanning force microscopy images.
Q43221464	Sequence-dependent base pair opening in DNA double helix
Q36889452	Sequence-dependent base pair stepping dynamics in XPD helicase unwinding.
Q35225466	Sequence-dependent gating of an ion channel by DNA hairpin molecules
Q46727149	Sequence-dependent thermodynamics of a coarse-grained DNA model.
Q36311017	Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast
Q30471598	Sequence-specific ultrasonic cleavage of DNA
Q33944524	Serum inverts and improves the fluorescence response of an aptamer beacon to various vitamin D analytes
Q24562042	Sfold web server for statistical folding and rational design of nucleic acids
Q34298129	Shielding effect of monovalent and divalent cations on solid-phase DNA hybridization: surface plasmon resonance biosensor study
Q37578899	Short RNA indicator sequences are not completely degraded by autoclaving.
Q34336741	Similar gene expression patterns characterize aging and oxidative stress in Drosophila melanogaster
Q41950178	Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites.
Q38668918	Simultaneous A8344G heteroplasmy and mitochondrial DNA copy number quantification in myoclonus epilepsy and ragged-red fibers (MERRF) syndrome by a multiplex molecular beacon based real-time fluorescence PCR.
Q46072694	Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array
Q54504446	Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing.
Q41464146	Single molecule high-throughput footprinting of small and large DNA ligands
Q40236192	Single-Strand Stacking Free Energy from DNA Beacon Kinetics
Q34351841	Single-molecule FRET studies of important intermediates in the nucleocapsid-protein-chaperoned minus-strand transfer step in HIV-1 reverse transcription
Q34100246	Single-molecule derivation of salt dependent base-pair free energies in DNA
Q37706259	Single-molecule fluorescence reveals the unwinding stepping mechanism of replicative helicase.
Q56891097	Single-molecule study of the DNA denaturation phase transition in the force-torsion space
Q33824619	Single-pair fluorescence resonance energy transfer (spFRET) for the high sensitivity analysis of low-abundance proteins using aptamers as molecular recognition elements
Q48921888	Single-stranded DNA aptamer targeting and neutralization of anti-D alloantibody: a potential therapeutic strategy for haemolytic diseases caused by Rhesus alloantibody.
Q37398206	Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes
Q30373264	Site-specific recombinational cloning using gateway and in-fusion cloning schemes
Q45177467	Slow closure of denaturation bubbles in DNA: twist matters
Q36867716	Small Molecule Targeting of a MicroRNA Associated with Hepatocellular Carcinoma
Q52848093	Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars.
Q41807900	Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates
Q27639162	Solution structure of dAATAA and dAAUAA DNA bulges
Q41867302	Spatial control of DNA reaction networks by DNA sequence
Q31021076	Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers
Q39094349	Specific detection of DNA and RNA targets using a novel isothermal nucleic acid amplification assay based on the formation of a three-way junction structure
Q51638041	Speed-up of DNA melting algorithm with complete nearest neighbor properties.
Q102389112	Spin-enhanced nanodiamond biosensing for ultrasensitive diagnostics
Q36909305	Stability and kinetics of G-quadruplex structures
Q24634415	Stability and mismatch discrimination of locked nucleic acid-DNA duplexes
Q47716317	Stability domains of actin genes and genomic evolution
Q51821280	Stability of a surface-bound oligonucleotide duplex inferred from molecular dynamics: a study of single nucleotide defects using DNA microarrays.
Q34100111	Stability of double-stranded oligonucleotide DNA with a bulged loop: a microarray study
Q50984322	Stability of radiation-damaged DNA after multiple strand breaks.
Q36580865	Standards in gene expression microarray experiments
Q42734593	Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction
Q45946342	Statistical mechanics of base stacking and pairing in DNA melting.
Q24797672	Statistical modeling for selecting housekeeper genes
Q51877320	Statistical physics of the melting of inhomogeneous DNA.
Q56892799	Statistical properties of metastable intermediates in DNA unzipping
Q35128982	Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions
Q30912623	Stem loop sequences specific to transposable element IS605 are found linked to lipoprotein genes in Borrelia plasmids.
Q24812725	Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles
Q51890514	Stochastic dynamics and denaturation of thermalized DNA.
Q56750198	Strand design for biomolecular computation
Q36554331	Stretching and bending fluctuations of short DNA molecules
Q90333240	Structural Characterization of Bubbles Formed in DNA Melting: A Monte Carlo Simulation Study
Q35684183	Structural Insights Reveal the Dynamics of the Repeating r(CAG) Transcript Found in Huntington's Disease (HD) and Spinocerebellar Ataxias (SCAs)
Q35052775	Structural and affinity analyses of g-quadruplex DNA aptamers for camptothecin derivatives
Q52213858	Structural and dynamical properties of two DNA oligomers with the same base composition and different sequence.
Q73195463	Structural and thermodynamic strategies for site-specific DNA binding proteins
Q81209789	Structural factors determining DNA length limitations in conformation-sensitive mutation detection methods
Q34363753	Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription
Q51527238	Structural features of DNA are conserved in the promoter region of orthologous genes across different strains of H. pylori.
Q24810289	Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes
Q24803215	Structural roles of CTG repeats in slippage expansion during DNA replication
Q94463899	Structure and diversity of 13S globulin zero-repeat subunit, the trypsin-resistant storage protein of common buckwheat (Fagopyrum esculentum M.) seeds
Q37071508	Structure-function correlations derived from faster variants of a RNA ligase deoxyribozyme
Q42381125	Structures of the kinetically trapped i-motif DNA intermediates.
Q51123081	Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies.
Q90322942	Super-beacons: Open-source probes with spontaneous tuneable blinking compatible with live-cell super-resolution microscopy
Q51970792	Surface and bulk dissolution properties, and selectivity of DNA-linked nanoparticle assemblies.
Q46789572	Surface-driven DNA assembly of binary cubic 3D nanocrystal superlattices
Q52656982	Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs.
Q34105242	Synthesis and evaluation of new spacers for use as dsDNA end-caps
Q36002428	Synthesis of crystals with a programmable kinetic barrier to nucleation
Q38319128	Synthesis of oligodeoxynucleotides with 5'-caps binding RNA targets
Q52910405	Synthesis, Characterization, and Biological Activities of Pendant Arm-Pyridyltetrazole Copper(II) Complexes: DNA Binding/Cleavage Activity and Cytotoxic Studies.
Q46426365	Systematic evaluation of single mismatch stability predictors for fluorescence in situ hybridization
Q34529467	TT-seq maps the human transient transcriptome
Q73938830	Tagging DNA mismatches by selective 2'-amine acylation
Q42277508	Targeted resequencing of HIV variants by microarray thermodynamics.
Q34879217	Targeting the r(CGG) repeats that cause FXTAS with modularly assembled small molecules and oligonucleotides
Q52596844	Temperature and pressure spikes in ion-beam cancer therapy.
Q34609298	Temperature dependence of DNA persistence length
Q74318470	Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation
Q87963470	Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs
Q42036435	Temperature effects on DNA chip experiments from surface plasmon resonance imaging: isotherms and melting curves
Q42275333	Temperature- and flow-enhanced detection specificity of mutated DNA against the wild type with reporter microspheres.
Q39514406	Tension on dsDNA bound to ssDNA-RecA filaments may play an important role in driving efficient and accurate homology recognition and strand exchange.
Q33889394	Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments.
Q24658277	The 3'-flap pocket of human flap endonuclease 1 is critical for substrate binding and catalysis
Q36351119	The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation
Q35165241	The Arcanobacterium pyogenes collagen-binding protein, CbpA, promotes adhesion to host cells
Q39504763	The Brucella suis homologue of the Agrobacterium tumefaciens chromosomal virulence operon chvE is essential for sugar utilization but not for survival in macrophages
Q92810052	The Business of DNA Nanotechnology: Commercialization of Origami and Other Technologies
Q24673673	The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci
Q39115723	The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease.
Q43263643	The Na-K-ATPase is a target for an EDHF displaying characteristics similar to potassium ions in the porcine renal interlobar artery
Q35590418	The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems
Q28504551	The Sμ Tandem Repeat Region Is Critical for Ig Isotype Switching in the Absence of Msh2
Q24646014	The Vienna RNA websuite
Q28475013	The Werner syndrome helicase/exonuclease processes mobile D-loops through branch migration and degradation
Q30807609	The analysis of microarray data
Q48044589	The collective behavior of spring-like motifs tethered to a DNA origami nanostructure.
Q42662801	The complete mitochondrial DNA sequence of the guanaco (Lama guanicoe): comparative analysis with the vicuña (Vicugna vicugna) genome.
Q51902684	The dynamics of intermittent strand separation in double-stranded DNA.
Q83321520	The effect of promoter strength, supercoiling and secondary structure on mutation rates in Escherichia coli
Q37396778	The effects of hairpin loops on ligand-DNA interactions
Q28237580	The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters
Q38935449	The energetic basis of the DNA double helix: a combined microcalorimetric approach
Q42060631	The energetic contribution of induced electrostatic asymmetry to DNA bending by a site-specific protein
Q36106977	The eukaryotic initiation factor eIF4H facilitates loop-binding, repetitive RNA unwinding by the eIF4A DEAD-box helicase
Q29304892	The evolution and population genetics of the ALDH2 locus: random genetic drift, selection, and low levels of recombination
Q47832738	The evolution of the genetic code revisited
Q37298559	The flexibility of locally melted DNA
Q34218486	The genome of bacteriophage phiKMV, a T7-like virus infecting Pseudomonas aeruginosa
Q33285035	The human genomic melting map.
Q40226199	The importance of thermodynamic equilibrium for high throughput gene expression arrays.
Q39725917	The mechanism of actinomycin D-mediated inhibition of HIV-1 reverse transcription
Q42610190	The mitochondrial genome of Strongyloides stercoralis (Nematoda) - idiosyncratic gene order and evolutionary implications
Q48321612	The mitochondrial genomes of the human hookworms, Ancylostoma duodenale and Necator americanus (Nematoda: Secernentea).
Q34327481	The newly discovered Q motif of DEAD-box RNA helicases regulates RNA-binding and helicase activity
Q24798491	The over-representation of binary DNA tracts in seven sequenced chromosomes
Q48072170	The post-SCF quantum chemistry characteristics of inter- and intra-strand stacking interactions in d(CpG) and d(GpC) steps found in B-DNA, A-DNA and Z-DNA crystals
Q35259226	The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA
Q39310951	The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity.
Q36669669	The role of ATP-dependent machines in regulating genome topology
Q44983925	The thermodynamic patterns of eukaryotic genes suggest a mechanism for intron-exon recognition.
Q34384012	The thermodynamics of template-directed DNA synthesis: base insertion and extension enthalpies
Q30596224	The transition mechanism of DNA overstretching: a microscopic view using molecular dynamics.
Q33322220	The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays
Q36494846	Theoretical study of sequence-dependent nanopore unzipping of DNA
Q38728170	Theory and simulation of DNA-coated colloids: a guide for rational design
Q36494746	There and (slowly) back again: entropy-driven hysteresis in a model of DNA overstretching
Q42648731	Thermal denaturation of fluctuating finite DNA chains: the role of bending rigidity in bubble nucleation
Q41926183	Thermal fluctuation spectroscopy of DNA thermal denaturation
Q50042066	Thermally reversible nanoparticle gels with tuneable porosity showing structural colour.
Q41853608	ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing
Q52048589	Thermodynamic analysis of stacking hybridization of oligonucleotides with DNA template.
Q34798289	Thermodynamic basis for engineering high-affinity, high-specificity binding-induced DNA clamp nanoswitches
Q37310615	Thermodynamic basis for the optimization of binding-induced biomolecular switches and structure-switching biosensors
Q35186100	Thermodynamic calculations and statistical correlations for oligo-probes design.
Q34699840	Thermodynamic contributions of single internal rA·dA, rC·dC, rG·dG and rU·dT mismatches in RNA/DNA duplexes
Q39959025	Thermodynamic criteria for high hit rate antisense oligonucleotide design
Q39545871	Thermodynamic parameters for DNA sequences with dangling ends
Q34386322	Thermodynamic treatment of oligonucleotide duplex-simplex equilibria
Q24811207	Thermodynamically based DNA strand design.
Q36050670	Thermodynamically optimal whole-genome tiling microarray design and validation
Q47162939	Thermodynamics and kinetics of DNA nanotube polymerization from single-filament measurements
Q34246814	Thermodynamics of RNA duplexes modified with unlocked nucleic acid nucleotides.
Q37263332	Thermodynamics of forming a parallel DNA crossover
Q39724036	Thermodynamics of internal C.T mismatches in DNA.
Q51605938	Thermodynamics of twisted DNA with solvent interaction.
Q53513931	Thinking inside the box: designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding.
Q24814683	Topological constraints in nucleic acid hybridization kinetics
Q54986541	Torque spectroscopy of DNA: base-pair stability, boundary effects, backbending, and breathing dynamics.
Q33366975	Touchdown PCR for increased specificity and sensitivity in PCR amplification
Q90625647	Toward a Rational Approach to Design Split G-Quadruplex Probes
Q38334075	TraA and its N-terminal relaxase domain of the Gram-positive plasmid pIP501 show specific oriT binding and behave as dimers in solution
Q37442981	Tracking neuronal marker expression inside living differentiating cells using molecular beacons
Q47130241	Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase
Q92665067	Transcriptome sequencing, de novo assembly, characterisation of wild accession of blackgram (Vigna mungo var. silvestris) as a rich resource for development of molecular markers and validation of SNPs by high resolution melting (HRM) analysis
Q41987037	Transcriptomic responses of Solanum dulcamara to natural and simulated herbivory
Q38256914	Transient kinetics measured with force steps discriminate between double-stranded DNA elongation and melting and define the reaction energetics
Q34864970	Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching
Q47722980	Translational Entropy and DNA Duplex Stability
Q33680395	Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing
Q35663496	Trinucleotide repeat DNA alters structure to minimize the thermodynamic impact of 8-oxo-7,8-dihydroguanine
Q38330259	Troubleshooting fine-tuning procedures for qPCR system design.
Q35991471	Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements.
Q33499621	Two-dimensional combinatorial screening and the RNA Privileged Space Predictor program efficiently identify aminoglycoside-RNA hairpin loop interactions
Q33527092	Two-dimensional combinatorial screening of a bacterial rRNA A-site-like motif library: defining privileged asymmetric internal loops that bind aminoglycosides
Q34810481	UNAFold: software for nucleic acid folding and hybridization
Q34309267	URPD: a specific product primer design tool.
Q35393728	Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array
Q37247742	Ultrasensitive genotypic detection of antiviral resistance in hepatitis B virus clinical isolates
Q36901545	Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes
Q36100489	Universal fingerprinting chip server
Q38352682	Unusual intercalation of acridin-9-ylthiourea into the 5'-GA/TC DNA base step from the minor groove: implications for the covalent DNA adduct profile of a novel platinum-intercalator conjugate
Q37738344	Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression
Q30503568	Unzipping DNA with optical tweezers: high sequence sensitivity and force flips
Q78751417	Unzipping dynamics of long DNAs
Q34549610	Use of base modifications in primers and amplicons to improve nucleic acids detection in the real-time snake polymerase chain reaction
Q37271094	Use of extremely short Förster resonance energy transfer probes in real-time polymerase chain reaction
Q50894568	Using DNA sequencing electrophoresis compression artifacts as reporters of stable mRNA structures affecting gene expression.
Q58221794	Using DNA to program the self-assembly of colloidal nanoparticles and microparticles
Q86487387	Using synthetic RNAs as scaffolds and regulators
Q38271624	ValFold: Program for the aptamer truncation process
Q64056562	Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters
Q42607876	Vertebrate helentrons and other novel Helitrons.
Q28131816	Vienna RNA secondary structure server
Q43124858	Volatility in mRNA secondary structure as a design principle for antisense.
Q30625885	Volume and porosity thermal regulation in lipid mesophases by coupling mobile ligands to soft membranes
Q86827768	WITHDRAWN: Versatility of different melting temperature (Tm) calculator software for robust PCR and Real-time PCR oligonucleotide design: A practical guide
Q37854480	Walking molecules
Q21256653	Webtag: a new web tool providing tags/anchors for RT-PCR experiments with prokaryotes
Q30975313	Zaba: a novel miniature transposable element present in genomes of legume plants
Q33217461	Zn2+-dependent deoxyribozymes that form natural and unnatural RNA linkages
Q47803229	beta-Globin mutation detection by tagged single-base extension and hybridization to universal glass and flow-through microarrays
Q33957807	chipD: a web tool to design oligonucleotide probes for high-density tiling arrays
Q24812268	dnaMATE: a consensus melting temperature prediction server for short DNA sequences
Q31063252	eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments
Q93550660	easyPAC: A Tool for Fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from Alignments or Consensus Sequences
Q48116275	hATpin, a family of MITE-like hAT mobile elements conserved in diverse plant species that forms highly stable secondary structures
Q50058736	miPrimer: An empirical-based qPCR primer design method for small non-coding microRNA.
Q39179182	miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico
Q42687686	ptRNApred: computational identification and classification of post-transcriptional RNA
Q30999126	uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application

P819	ADS bibcode	1998PNAS...95.1460S
P356	DOI	10.1073/PNAS.95.4.1460
P3181	OpenCitations bibliographic resource ID	171749
P932	PMC publication ID	19045
P698	PubMed publication ID	9465037
P5875	ResearchGate publication ID	13765910

P2093	author name string	J SantaLucia
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P433	issue	4
P407	language of work or name	English	Q1860
P921	main subject	thermodynamics	Q11473
		nearest neighbour algorithm	Q1374523
P304	page(s)	1460-5
P577	publication date	1998-02-17
P1433	published in	Proceedings of the National Academy of Sciences of the United States of America	Q1146531
P1476	title	A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
P478	volume	95

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

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