Base-stacking and base-pairing contributions into thermal stability of the DNA double helix (Q22065979)

6 July 2017

Base-stacking and base-pairing contributions into thermal stability of the DNA double helix (English)

1 reference

Maxim D. Frank-Kamenetskii

6 July 2017

series ordinal

3

object named as

Maxim D Frank-Kamenetskii

author given names

Maxim D

author last names

Frank-Kamenetskii

1 reference

6 July 2017

Peter Yakovchuk

1

Peter

Yakovchuk

1 reference

PubMed ID

16449200

6 July 2017

Ekaterina Protozanova

series ordinal

2

author given names

Ekaterina

author last names

Protozanova

1 reference

PubMed ID

16449200

6 July 2017

language of work or name

English

0 references

publication date

31 January 2006

1 reference

6 July 2017

Nucleic Acids Research

1 reference

6 July 2017

34

1 reference

6 July 2017

564-574

1 reference

6 July 2017

2

1 reference

Isothermal reactions for the amplification of oligonucleotides

6 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

A nicked duplex decamer DNA with a PEG(6) tether

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Molecular structure of nicked DNA: a substrate for DNA repair enzymes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Stacked-unstacked equilibrium at the nick site of DNA

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

The thermodynamics of DNA structural motifs

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Multiplexed genotyping with sequence-tagged molecular inversion probes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

The physical basis of nucleic acid base stacking in water

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Improved free-energy parameters for predictions of RNA duplex stability

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Gapped DNA and cyclization of short DNA fragments.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Gapped DNA is anisotropically bent.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Force spectroscopy of single DNA and RNA molecules

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Rolling-circle amplification under topological constraints.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

DNA ligases in the repair and replication of DNA.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Thermodynamic parameters for DNA sequences with dangling ends

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Conformations of nicked and gapped DNA structures by NMR and molecular dynamic simulations in water

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

A free energy analysis of nucleic acid base stacking in aqueous solution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

DNA sequencing: modular primers assembled from a library of hexamers or pentamers

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Conformational analysis of a 139 base-pair DNA fragment containing a single-stranded break and its interaction with human poly(ADP-ribose) polymerase

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Enhanced DNA sequencing by hybridization

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Detection of localized DNA flexibility

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Conformational transitions of duplex and triplex nucleic acid helices: thermodynamic analysis of effects of salt concentration on stability using preferential interaction coefficients

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Padlock probes: circularizing oligonucleotides for localized DNA detection

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Conformational and thermodynamic consequences of the introduction of a nick in duplexed DNA fragments: an NMR study augmented by biochemical experiments

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

The thermodynamic advantage of DNA oligonucleotide 'stacking hybridization' reactions: energetics of a DNA nick

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Poly(ADP-ribose) polymerase: a molecular nick-sensor

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Thermodynamic analysis of stacking hybridization of oligonucleotides with DNA template.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Beyond the hydrophobic effect: attractions involving heteroaromatic rings in aqueous solution.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Opposite effect of counterions on the persistence length of nicked and non-nicked DNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Energetics of DNA twisting. I. Relation between twist and cyclization probability.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Characterization of the structure and melting of DNAs containing backbone nicks and gaps

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Stacking energies in DNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Sequence-dependent base pair opening in DNA double helix

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Efficiency of Coaxial Stacking Depends on the DNA Duplex Structure

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Monitoring of single nicks in duplex DNA by gel electrophoretic mobility-shift assay

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

A nick-sensing DNA 3'-repair enzyme from Arabidopsis.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

In situ strand displacement amplification: an improved technique for the detection of low copy nucleic acids

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Structural Polymorphism and Dynamism in the DNA Segment GATCTTCCCCCCGGAA: NMR Investigations of Hairpin, Dumbbell, Nicked Duplex, Parallel Strands, and i-Motif

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1360284

Sequence-dependent DNA structure. The role of base stacking interactions

29 November 2018

1 reference

12 December 2020

Studies of DNA dumbbells VII: evaluation of the next-nearest-neighbor sequence-dependent interactions in duplex DNA

1 reference

12 December 2020

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

1 reference

12 December 2020

Melting behavior of a covalently closed, single-stranded, circular DNA

1 reference

12 December 2020

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

1 reference

12 December 2020

Nature of the stacking of nucleic acid bases in water: a Monte Carlo simulation

1 reference

12 December 2020

Electrophoretic evidence that single-stranded regions of one or more nucleotides dramatically increase the flexibility of DNA

1 reference

12 December 2020

How the double helix breathes

1 reference

12 December 2020

Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops: evaluation of the nearest-neighbor stacking interactions in DNA

1 reference

12 December 2020

Improved nearest-neighbor parameters for predicting DNA duplex stability

1 reference

12 December 2020

Sequence-dependent DNA structure: dinucleotide conformational maps

1 reference

12 December 2020

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs

1 reference

12 December 2020

Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp

1 reference

12 December 2020

Proton magnetic resonance melting studies of CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp

1 reference

12 December 2020

A single mode of DNA base-pair opening drives imino proton exchange

1 reference

12 December 2020

Allowance for heterogeneous stacking in the DNA helix-coil transition theory

1 reference

12 December 2020

Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKJ454

1 reference

release_qs2d4lfkjzd2jdndufwvu4dlim

6 July 2017

0 references

OpenCitations bibliographic resource ID

989888

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

6 July 2017

1 reference

PubMed ID

16449200