Energetic signatures of single base bulges: thermodynamic consequences and biological implications. (Q33566378)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

title

Energetic signatures of single base bulges: thermodynamic consequences and biological implications (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

Rian Dickstein

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

Kenneth J Breslauer

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

language of work or name

English

0 references

publication date

27 November 2009

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

volume

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

issue

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

page(s)

97-116

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

Recognition of abasic sites and single base bulges in DNA by a metalloinsertor

12 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

UNAFold: software for nucleic acid folding and hybridization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Bulged adenosine influence on the RNA duplex conformation in solution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

A continuous hyperchromicity assay to characterize the kinetics and thermodynamics of DNA lesion recognition and base excision

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) Genome: a high frequency of deletions in tandem duplicates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

THE ACCOMMODATION OF NONCOMPLEMENTARY BASES IN HELICAL POLYRIBONUCLEOTIDES AND DEOXYRIBONUCLEIC ACIDS.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Mechanism of a genetic glissando: structural biology of indel mutations.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Heat capacity changes associated with nucleic acid folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

DINAMelt web server for nucleic acid melting prediction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

The thermodynamics of template-directed DNA synthesis: base insertion and extension enthalpies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Some factors in the interpretation of protein denaturation

21 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

21 June 2018

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Energetics of lesion recognition by a DNA repair protein: thermodynamic characterization of formamidopyrimidine-glycosylase (Fpg) interactions with damaged DNA duplexes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Heat capacity effects on the melting of DNA. 2. Analysis of nearest-neighbor base pair effects

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Calorimetry of proteins and nucleic acids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

On the mechanism of frameshift (deletion) mutagenesis in vitro.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

DNA adduct-induced stabilization of slipped frameshift intermediates within repetitive sequences: implications for mutagenesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

DNA lesions. A thermodynamic perspective

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

NMR evidence of the stabilisation by the carcinogen N-2-acetylaminofluorene of a frameshift mutagenesis intermediate

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

The thermodynamics of DNA structures that contain lesions of guanine tetrads

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Mechanisms of spontaneous and induced frameshift mutation in bacteriophage T4.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Predicting DNA duplex stability from the base sequence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Methyl-directed repair of frameshift mutations in heteroduplex DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Influence of abasic and anucleosidic sites on the stability, conformation, and melting behavior of a DNA duplex: correlations of thermodynamic and structural data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Methyl-directed repair of frameshift heteroduplexes in cell extracts from Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

A single nucleotide deletion in codon 123 of the beta-globin gene causes an inclusion body beta-thalassaemia trait: a novel elongated globin chain beta Makabe

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Carcinogen-induced frameshift mutagenesis in repetitive sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Misalignment-mediated DNA synthesis errors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Three-dimensional structures of bulge-containing DNA fragments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Influence of an exocyclic guanine adduct on the thermal stability, conformation, and melting thermodynamics of a DNA duplex

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Reading-frame restoration with an apolipoprotein B gene frameshift mutation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2800203

Conformation of a bulge-containing oligomer from a hot-spot sequence by NMR and energy minimization

21 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Structural model for an oligonucleotide containing a bulged guanosine by NMR and energy minimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Proton nuclear magnetic resonance studies on bulge-containing DNA oligonucleotides from a mutational hot-spot sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

The effect of base sequence on the stability of RNA and DNA single base bulges.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Thermodynamic parameters based on a nearest-neighbor model for DNA sequences with a single-bulge loop

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Correlation between sequence-dependent glycosylase repair and the thermal stability of oligonucleotide duplexes containing 1, N6-ethenoadenine

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: role of thermodynamic stability imposed by neighbor bases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Sequence context- and temperature-dependent nucleotide excision repair of a benzo[a]pyrene diol epoxide-guanine DNA adduct catalyzed by thermophilic UvrABC proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Photocross-linking of the NH2-terminal Region of Taq MutS Protein to the Major Groove of a Heteroduplex DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Nuclear magnetic resonance investigation of primer--template models: formation of a pyrimidine bulge upon misincorporation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKP1036

Conformational transitions in cytidine bulge-containing deoxytridecanucleotide duplexes: extra cytidine equilibrates between looped out (low temperature) and stacked (elevated temperature) conformations in solution

21 January 2018

1 reference

12 December 2020

Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes. Role of flanking sequence and temperature in modulating the equilibrium between looped out and stacked thymidine bulge states

1 reference

12 December 2020

Effects of bulge composition and flanking sequence on the kinking of DNA by bulged bases

1 reference

12 December 2020

Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence

1 reference

12 December 2020

The impact of a bistrand abasic lesion on DNA duplex properties

1 reference

12 December 2020

Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices

1 reference

12 December 2020

Conformation of adenosine bulge-containing deoxytridecanucleotide duplexes in solution. Extra adenosine stacks into duplex independent of flanking sequence and temperature

1 reference

12 December 2020

Influence of neighboring base pairs on the stability of single base bulges and base pairs in a DNA fragment

1 reference

12 December 2020

Free energy of imperfect nucleic acid helices. I. The bulge defect

1 reference

12 December 2020

Improved nearest-neighbor parameters for predicting DNA duplex stability

1 reference

12 December 2020

Energetics of nucleic acid stability: the effect of DeltaCP

1 reference

12 December 2020

The impact of an exocyclic cytosine adduct on DNA duplex properties: significant thermodynamic consequences despite modest lesion-induced structural alterations

1 reference

12 December 2020

Stability of DNA duplexes containing GG, CC, AA, and TT mismatches

1 reference

12 December 2020

Kinetics for exchange of imino protons in the d(C-G-C-G-A-A-T-T-C-G-C-G) double helix and in two similar helices that contain a G.cntdot.T base pair, d(C-G-T-G-A-A-T-T-C-G-C-G), and an extra adenine, d(C-G-C-A-G-A-A-T-T-C-G-C-G)

1 reference

12 December 2020

Positional effect of single bulge nucleotide on PNA(peptide nucleic acid)/DNA hybrid stability

1 reference

12 December 2020

Extra adenosine stacks into the self-complementary d(CGCAGAATTCGCG) duplex in solution

1 reference

12 December 2020

Differential hydration of dA.dT base pairing and dA and dT bulges in deoxyoligonucleotides

1 reference

12 December 2020

The energetics of HMG box interactions with DNA: thermodynamic description of the target DNA duplexes

1 reference

12 December 2020

NMR studies of a deoxyribodecanucleotide containing an extrahelical thymidine surrounded by an oligo(dA).oligo(dT) tract

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKP1036

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

PubMed publication ID

19946018

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19946018%20AND%20SRC:MED&resulttype=core&format=json