Loop dependence of the stability and dynamics of nucleic acid hairpins (Q33311658)

25 July 2017

title

Loop dependence of the stability and dynamics of nucleic acid hairpins (English)

1 reference

25 July 2017

Sarah A Woodson

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Serguei V Kuznetsov

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25 July 2017

Cha-Chi Ren

series ordinal

1 reference

25 July 2017

Anjum Ansari

series ordinal

1 reference

25 July 2017

language of work or name

English

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publication date

20 December 2007

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25 July 2017

published in

Nucleic Acids Research

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25 July 2017

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25 July 2017

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25 July 2017

page(s)

1098-1112

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Optimization by Simulated Annealing

25 July 2017

cites work

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14 July 2018

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Loop formation in unfolded polypeptide chains on the picoseconds to microseconds time scale

14 July 2018

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Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid

14 July 2018

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The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force

14 July 2018

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Is hairpin formation in single-stranded polynucleotide diffusion-controlled?

14 July 2018

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The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy

14 July 2018

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Effects of denaturants on the dynamics of loop formation in polypeptides

14 July 2018

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Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins

14 July 2018

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Hairpin RNA: a secondary structure of primary importance

14 July 2018

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14 July 2018

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Exploring the complex folding kinetics of RNA hairpins: II. Effect of sequence, length, and misfolded states

14 July 2018

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14 July 2018

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14 July 2018

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Does water play a structural role in the folding of small nucleic acids?

14 July 2018

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Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate

14 July 2018

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Evidence that folding of an RNA tetraloop hairpin is less cooperative than its DNA counterpart

14 July 2018

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RNA folding and unfolding

14 July 2018

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Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy

14 July 2018

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RNA interference and human disease

14 July 2018

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Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments?

14 July 2018

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Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations

14 July 2018

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Killing the messenger: short RNAs that silence gene expression

14 July 2018

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Single-Strand Stacking Free Energy from DNA Beacon Kinetics

14 July 2018

1 reference

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Selection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg),d(cCNNGg), and d(gCNNGc).

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Effects of magnesium ions on the stabilization of RNA oligomers of defined structures

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

RNA hairpin-folding kinetics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

A semiflexible polymer model applied to loop formation in DNA hairpins

14 July 2018

1 reference

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Force-induced denaturation of RNA

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions

14 July 2018

1 reference

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Monitoring the conformational fluctuations of DNA hairpins using single-pair fluorescence resonance energy transfer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Non-Arrhenius kinetics for the loop closure of a DNA hairpin.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching

14 July 2018

1 reference

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Conformation and dynamics of abasic sites in DNA investigated by time-resolved fluorescence of 2-aminopurine

14 July 2018

1 reference

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Replication by a single DNA polymerase of a stretched single-stranded DNA

14 July 2018

1 reference

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Measuring the rate of intramolecular contact formation in polypeptides

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Small angle X-ray scattering reveals a compact intermediate in RNA folding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Single-molecule studies of the effect of template tension on T7 DNA polymerase activity.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Heat capacity effects on the melting of DNA. 1. General aspects.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Themes in RNA-protein recognition.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

The speed limit for protein folding measured by triplet-triplet energy transfer.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Nucleic acid duplex stability: influence of base composition on cation effects

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Single-pair fluorescence resonance energy transfer on freely diffusing molecules: observation of Förster distance dependence and subpopulations

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Kinetics of conformational fluctuations in DNA hairpin-loops

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

DNA condensation by multivalent cations

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Global flexibility of tertiary structure in RNA: yeast tRNAPhe as a model system

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Folding dynamics and mechanism of β-hairpin formation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Hierarchy and dynamics of RNA folding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Ionic effects on the elasticity of single DNA molecules

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Regulating the fate of mRNA: the control of cellular iron metabolism

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Condensation of supercoiled DNA induced by MnCl2.

14 July 2018

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Trinucleotide repeats that expand in human disease form hairpin structures in vitro

14 July 2018

1 reference

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RNA hairpin loop stability depends on closing base pair

14 July 2018

1 reference

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Transcription termination at intrinsic terminators: the role of the RNA hairpin

14 July 2018

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14 July 2018

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Thermodynamics and kinetics of G·C base pairing in the isolated extra arm of serine-specific transfer RNA from yeast

14 July 2018

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Free energy of imperfect nucleic acid helices. II. Small hairpin loops

14 July 2018

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Diffusion in a rough potential

14 July 2018

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14 July 2018

RNA structure prediction

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Analysis of melting transitions of the DNA hairpins formed from the oligomer sequences d[GGATAC(X)4GTATCC] (X = A, T, G, C).

14 July 2018

1 reference

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Structural Features that Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA Loops

14 July 2018

1 reference

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Solution structure of an unusually stable RNA hairpin, 5GGAC(UUCG)GUCC

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Tetraloops and RNA folding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Nucleotide sequence of a region of human mitochondrial DNA containing the precisely identified origin of replication

14 July 2018

1 reference

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The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides

14 July 2018

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Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Kinetics of interior loop formation in semiflexible chains

14 July 2018

1 reference

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Structural and energetic consequences of expanding a highly cooperative stable DNA hairpin loop

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Force-extension behavior of folding polymers

31 October 2018

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Kinetics of end-to-end collision in short single-stranded nucleic acids

31 October 2018

1 reference

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Folding of a stable DNA motif involves a highly cooperative network of interactions.

31 October 2018

1 reference

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Thermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs

31 October 2018

1 reference

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RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop

31 October 2018

1 reference

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A fluorescence-based method for direct measurement of submicrosecond intramolecular contact formation in biopolymers: an exploratory study with polypeptides

31 October 2018

1 reference

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Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics

31 October 2018

1 reference

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Reversible unfolding of single RNA molecules by mechanical force

31 October 2018

1 reference

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Single-molecule studies of DNA mechanics

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2275088

Stabilization of RNA structure by Mg ions. Specific and non-specific effects.

31 October 2018

1 reference

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Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations

31 October 2018

1 reference

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Elastic properties of a single-stranded charged homopolymeric ribonucleotide

31 October 2018

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12 December 2020

Folding and unfolding kinetics of DNA hairpins in flowing solution by multiparameter fluorescence correlation spectroscopy

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12 December 2020

Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA)

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12 December 2020

Cation-induced toroidal condensation of DNA studies with Co3+(NH3)6

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12 December 2020

Misfolded loops decrease the effective rate of DNA hairpin formation

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12 December 2020

Monomolecular condensation of λ-DNA induced by cobalt hexammine

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12 December 2020

Exploring the energy landscape of a small RNA hairpin

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12 December 2020

Dynamics of chain closure: approximate treatment of nonlocal interactions

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12 December 2020

Hairpin formation in synthetic oligonucleotides

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12 December 2020

Conformation of polyribouridylic acid in solution

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12 December 2020

E. coli SSB activates N4 virion RNA polymerase promoters by stabilizing a DNA hairpin required for promoter recognition

1 reference

12 December 2020

V(D)J recombination: broken DNA molecules with covalently sealed (hairpin) coding ends in scid mouse thymocytes

1 reference

12 December 2020

Structure and dynamics of double helices in solution: modes of DNA bending

1 reference

12 December 2020

X-ray diffraction studies on cation-collapsed DNA

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12 December 2020

Hairpin formation and elongation of biomolecules

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12 December 2020

Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering

1 reference

12 December 2020

Thermodynamic and kinetic parameters of an oligonucleotide hairpin helix

1 reference

12 December 2020

Sequence dependent rigidity of single stranded DNA

1 reference

12 December 2020

A three-state mechanism for DNA hairpin folding characterized by multiparameter fluorescence fluctuation spectroscopy

1 reference

12 December 2020

Melting studies of short DNA hairpins: influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability

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12 December 2020

Studies of the temperature-dependent conformation and phase separation of polyriboadenylic acid solutions at neutral pH

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12 December 2020

A collapsed non-native RNA folding state

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12 December 2020

Predicting thermodynamic properties of RNA

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12 December 2020

Stretching single stranded DNA, a model polyelectrolyte

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKM1083

1 reference

25 July 2017

1 reference

25 July 2017

1 reference