DNA conformations and their sequence preferences. (Q39633989)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18477633%20AND%20SRC:MED&resulttype=core&format=json

7 January 2020

title

DNA conformations and their sequence preferences (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18477633%20AND%20SRC:MED&resulttype=core&format=json

7 January 2020

1

1 reference

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7 January 2020

Jan Kalina

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18477633%20AND%20SRC:MED&resulttype=core&format=json

7 January 2020

Marek Omelka

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18477633%20AND%20SRC:MED&resulttype=core&format=json

7 January 2020

Bohdan Schneider

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18477633%20AND%20SRC:MED&resulttype=core&format=json

7 January 2020

language of work or name

English

0 references

publication date

13 May 2008

1 reference

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7 January 2020

published in

Nucleic Acids Research

1 reference

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7 January 2020

volume

36

1 reference

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7 January 2020

issue

11

1 reference

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7 January 2020

page(s)

3690-3706

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18477633%20AND%20SRC:MED&resulttype=core&format=json

RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

7 January 2020

cites work

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DNA stretching and extreme kinking in the nucleosome core

14 September 2017

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A genomic code for nucleosome positioning

14 September 2017

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Describing RNA structure by libraries of clustered nucleotide doublets

14 September 2017

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How sequence defines structure: a crystallographic map of DNA structure and conformation.

14 September 2017

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Molecular recognition of the nucleosomal "supergroove".

14 September 2017

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RNA conformational classes

14 September 2017

1 reference

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Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions

14 September 2017

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RNA backbone is rotameric

14 September 2017

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Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes

14 September 2017

1 reference

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Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes

14 September 2017

1 reference

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Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes

14 September 2017

1 reference

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The structure of DNA in the nucleosome core

14 September 2017

1 reference

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Conformational and hydration effects of site-selective sodium, calcium and strontium ion binding to the DNA Holliday junction structure d(TCGGTACCGA)(4)

14 September 2017

1 reference

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Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands

14 September 2017

1 reference

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Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG.

14 September 2017

1 reference

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Crystal structure of the potassium form of an Oxytricha nova G-quadruplex

14 September 2017

1 reference

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Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Structural characterization of a new crystal form of the four-way Holliday junction formed by the DNA sequence d(CCGGTACCGG)2: sequence versus lattice?

14 September 2017

2 references

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14 September 2017

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The influence of different structure representations on the clustering of an RNA nucleotides data set.

21 January 2018

1 reference

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A standard reference frame for the description of nucleic acid base-pair geometry.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

A crystallographic map of the transition from B-DNA to A-DNA.

14 September 2017

1 reference

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Geometric nomenclature and classification of RNA base pairs

14 September 2017

1 reference

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Structures of helical junctions in nucleic acids

14 September 2017

1 reference

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A-form conformational motifs in ligand-bound DNA structures

14 September 2017

1 reference

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The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions

14 September 2017

1 reference

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The structure of a stable intermediate in the A left-right-arrow B DNA helix transition

14 September 2017

1 reference

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TATA element recognition by the TATA box-binding protein has been conserved throughout evolution

14 September 2017

1 reference

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Crystal structure of a DNA Holliday junction

14 September 2017

1 reference

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Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse

14 September 2017

1 reference

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An A-DNA structure with two independent duplexes in the asymmetric unit

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Structure-based prediction of DNA target sites by regulatory proteins.

14 September 2017

1 reference

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Stabilization of the i-motif by intramolecular adenine-adenine-thymine base triple in the structure of d(ACCCT)

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Structure of the d(CGCCCGCGGGCG) dodecamer: a kinked A-DNA molecule showing some B-DNA features

14 September 2017

1 reference

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DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

14 September 2017

1 reference

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Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination.

14 September 2017

1 reference

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Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 A resolution

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT)

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

DNA bending: the prevalence of kinkiness and the virtues of normality

14 September 2017

1 reference

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Flexibility of the B-DNA backbone: effects of local and neighbouring sequences on pyrimidine-purine steps

14 September 2017

1 reference

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Crystal structure of the nucleosome core particle at 2.8 A resolution

14 September 2017

1 reference

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Solution structure of the CpG containing d(CTTCGAAG)2 oligonucleotide: NMR data and energy calculations are compatible with a BI/BII equilibrium at CpG.

14 September 2017

1 reference

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The crystal structure of the trigonal decamer C-G-A-T-C-G-6meA-T-C-G: a B-DNA helix with 10.6 base-pairs per turn

14 September 2017

1 reference

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The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments

14 September 2017

1 reference

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Crystal structure of a yeast TBP/TATA-box complex

14 September 2017

1 reference

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Coupling of local folding to site-specific binding of proteins to DNA

14 September 2017

1 reference

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Solution structure of a parallel-stranded G-quadruplex DNA

14 September 2017

1 reference

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"...the tyranny of the lattice...".

14 September 2017

1 reference

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Refined solution structure of the dimeric quadruplex formed from the Oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG)

14 September 2017

1 reference

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Crystal structure of a four-stranded intercalated DNA: d(C4)

14 September 2017

1 reference

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Molecular structure of the octamer d(G-G-C-C-G-G-C-C): modified A-DNA

14 September 2017

1 reference

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Structure of a B-DNA dodecamer: conformation and dynamics

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C)

14 September 2017

1 reference

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14 September 2017

Parallel stranded DNA.

1 reference

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Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGTACAC)

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

The molecular structure of the left-handed Z-DNA double helix at 1.0-A atomic resolution. Geometry, conformation, and ionic interactions of d(CGCGCG)

14 September 2017

1 reference

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The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair reversals

14 September 2017

1 reference

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Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees

14 September 2017

1 reference

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DNA structure from A to Z.

14 September 2017

1 reference

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The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

14 September 2017

1 reference

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Sequence-specific recognition of double helical nucleic acids by proteins

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Molecular structure of a left-handed double helical DNA fragment at atomic resolution

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Stereochemical basis of DNA bending by transcription factors

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

DNA recognition code of transcription factors

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules

25 September 2017

1 reference

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Crystal studies of B-DNA: the answers and the questions

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Protein-DNA interactions: A structural analysis

25 September 2017

1 reference

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Helix bending as a factor in protein/DNA recognition.

17 June 2018

1 reference

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Two distinct modes of protein-induced bending in DNA.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles

17 June 2018

1 reference

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Further analysis of the altered secondary structure of superhelical DNA. Sensitivity to methylmercuric hydroxide a chemical probe for unpaired bases.

17 June 2018

1 reference

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Protein-DNA interaction. No code for recognition

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

Conformations of the sugar-phosphate backbone in helical DNA crystal structures

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

The role of DNA deformation energy at individual base steps for the identification of DNA-protein binding sites

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2441783

From crystal statics to chemical dynamics

21 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKN260

FORMATION OF A THREE-STRANDED POLYNUCLEOTIDE MOLECULE

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKN260

Coexistence of A- and B-form DNA in a single crystal lattice

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKN260

Model for DNA replication by Kornberg's DNA polymerase

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/18477633

12 December 2020

Structural behavior of the CpG step in two related oligonucleotides reflects its malleability in solution

1 reference

https://pubmed.ncbi.nlm.nih.gov/18477633

12 December 2020

Binding geometry of alpha-helices that recognize DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/18477633

12 December 2020

A complete conformational map for RNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/18477633

12 December 2020

Left-handed double helical DNA: variations in the backbone conformation

1 reference

https://pubmed.ncbi.nlm.nih.gov/18477633

12 December 2020

Approaches to predicting effects of single amino acid substitutions on the function of a protein

1 reference

https://pubmed.ncbi.nlm.nih.gov/18477633

12 December 2020

Sequence-dependent DNA structure: dinucleotide conformational maps

1 reference

https://pubmed.ncbi.nlm.nih.gov/18477633

12 December 2020

Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition?

1 reference

https://pubmed.ncbi.nlm.nih.gov/18477633

12 December 2020

Identifiers

DOI

10.1093/NAR/GKN260

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18477633%20AND%20SRC:MED&resulttype=core&format=json

7 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18477633%20AND%20SRC:MED&resulttype=core&format=json

7 January 2020

PubMed publication ID

18477633

1 reference