A semiflexible polymer model applied to loop formation in DNA hairpins (Q34176855)

31 July 2017

title

A semiflexible polymer model applied to loop formation in DNA hairpins (English)

1 reference

31 July 2017

Kuznetsov SV

1 reference

31 July 2017

Shen Y

series ordinal

1 reference

31 July 2017

Benight AS

series ordinal

1 reference

31 July 2017

Ansari A

series ordinal

1 reference

31 July 2017

language of work or name

English

0 references

publication date

1 November 2001

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

31 July 2017

page(s)

2864-2875

1 reference

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

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Effect of pH on the overstretching transition of double-stranded DNA: evidence of force-induced DNA melting

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Mechanical stability of single DNA molecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Melting studies of short DNA hairpins containing the universal base 5-nitroindole

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Adenine base unstacking dominates the observed enthalpy and heat capacity changes for the Escherichia coli SSB tetramer binding to single-stranded oligoadenylates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

RecA binding to a single double-stranded DNA molecule: a possible role of DNA conformational fluctuations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Kinetics of conformational fluctuations in DNA hairpin-loops

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Thermal stability of DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Folding dynamics and mechanism of β-hairpin formation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Studies of DNA dumbbells. VI. Analysis of optical melting curves of dumbbells with a sixteen-base pair duplex stem and end-loops of variable size and sequence

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Thermodynamics of DNA hairpins: contribution of loop size to hairpin stability and ethidium binding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Influence of 5'-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Simple model of protein folding kinetics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Bent helix formation between RNA hairpins with complementary loops

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

DNA flexibility studied by covalent closure of short fragments into circles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Helix formation by d(TA) oligomers. 3. Electrostatic effects.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Duplex-hairpin transitions in DNA: NMR studies on CGCGTATACGCG.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Spin glasses and the statistical mechanics of protein folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Influence of loop residues on the relative stabilities of DNA hairpin structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Characterization of RNA hairpin loop stability

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Melting of a self-complementary DNA minicircle. Comparison of optical melting theory with exchange broadening of the nuclear magnetic resonance spectrum

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

On loop folding in nucleic acid hairpin-type structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

On finding all suboptimal foldings of an RNA molecule

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Studies of DNA dumbbells. III. Theoretical analysis of optical melting curves of dumbbells with a 16 base-pair duplex stem and Tn end loops (n = 2, 3, 4, 6, 8, 10, 14)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

The 3′ terminus of 16S rRNA: secondary structure and interaction with ribosomal protein S1

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Reversible unfolding of single RNA molecules by mechanical force

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Activation of the leu-500 promoter by a reversed polarity tetA gene. Response to global plasmid supercoiling

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Conformational relaxation and ligand binding in myoglobin.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Helix formation by d(TA) oligomers. II. Analysis of the helix-coli transitions of linear and circular oligomers

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301751

Misfolded loops decrease the effective rate of DNA hairpin formation

28 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Hairpin formation in Tn5 transposition

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Relaxation kinetics of dimer formation by self complementary oligonucleotides

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Analysis of the ring-closure probabilities of isotropic wormlike chains: application to duplex DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Hairpin formation in synthetic oligonucleotides

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Conformation of polyribouridylic acid in solution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Tn10 transposition via a DNA hairpin intermediate

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Experimental thermodynamics of the helix-random coil transition. IV. Influence of the base composition of DNA on the transition enthalpy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Stability and structure of DNA oligonucleotides containing non-specific base analogues

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

An Algorithm for Least-Squares Estimation of Nonlinear Parameters

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Equation of State Calculations by Fast Computing Machines

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Hairpin formation and elongation of biomolecules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Co-operative non-enzymatic base recognition III. Kinetics of the helix—coil transition of the oligoribouridylic · oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Improved parameters for the prediction of RNA hairpin stability

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Predicting thermodynamic properties of RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Persistence Length of Single-Stranded DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Stability of RNA hairpin loops: A6-Cm-U6

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

Thermal denaturation of DNA molecules: A comparison of theory with experiment

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2975927-9

10.1016/S0006-3495(01)75927-9

7 January 2021

Identifiers

DOI

1 reference

31 July 2017

1 reference

31 July 2017

1 reference