(Q24817026)

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Role of stacking interactions in the binding sequence preferences of DNA bis-intercalators: insight from thermodynamic integration free energy simulations.

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16282585%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

Role of stacking interactions in the binding sequence preferences of DNA bis-intercalators: insight from thermodynamic integration free energy simulations (English)

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16282585%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

F. Javier Luque

3

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Europe PubMed Central

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9 January 2020

4

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9 January 2020

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Esther Marco

1

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9 January 2020

Ana Negri

2

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9 January 2020

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publication date

10 November 2005

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Europe PubMed Central

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9 January 2020

Nucleic Acids Research

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9 January 2020

33

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9 January 2020

19

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9 January 2020

6214-6224

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16282585%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

Solution structure of a complex between [N-MeCys3,N-MeCys7]TANDEM and [d(GATATC)]2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

7 April 2017

Sequence specificity of quinoxaline antibiotics. 1. Solution structure of a 1:1 complex between triostin A and [d(GACGTC)]2 and comparison with the solution structure of the [N-MeCys3,N-MeCys7]TANDEM-[d(GATATC)]2 complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

7 April 2017

Designed sequence-specific minor groove ligands

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

7 April 2017

Classical electrostatics in biology and chemistry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

7 April 2017

Molecular determinants of topoisomerase I poisoning by lamellarins: comparison with camptothecin and structure-activity relationships

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Energetics of echinomycin binding to DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Simulations of nucleic acids and their complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Intercalators as anticancer drugs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Sequence recognition of DNA by lexitropsins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Structural studies of atom-specific anticancer drugs acting on DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Footprinting of echinomycin and actinomycin D on DNA molecules asymmetrically substituted with inosine and/or 2,6-diaminopurine

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Structure-affinity relationships for the binding of actinomycin D to DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

DNA sequence-specific reading by echinomycin: role of hydrogen bonding and stacking interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

NMR investigation of Hoogsteen base pairing in quinoxaline antibiotic--DNA complexes: comparison of 2:1 echinomycin, triostin A and [N-MeCys3,N-MeCys7] TANDEM complexes with DNA oligonucleotides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Phosphorescence and optically detected magnetic resonance studies of echinomycin-DNA complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

The DNA sequence at echinomycin binding sites determines the structural changes induced by drug binding: NMR studies of echinomycin binding to [d(ACGTACGT)]2 and [d(TCGATCGA)]2.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Optically detected triplet-state magnetic resonance studies of the DNA complexes of the bisquinoline analogue of echinomycin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Proton NMR studies of [N-MeCys3,N-MeCys7]TANDEM binding to DNA oligonucleotides: sequence-specific binding at the TpA site

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

The 2-amino group of guanine is absolutely required for specific binding of the anti-cancer antibiotic echinomycin to DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Bifunctional intercalator [N-MeCys3, N-MeCys7]TANDEM binds to the dinucleotide TpA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 September 2017

Stacking interactions and intercalative DNA binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

31 May 2018

DNA recognition by quinoxaline antibiotics: use of base-modified DNA molecules to investigate determinants of sequence-specific binding of triostin A and TANDEM

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

31 May 2018

Statistical analysis of DNA duplex structural features

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

31 May 2018

Dissociation of the AT-specific bifunctional intercalator [N-MeCys3,N-MeCys7]TANDEM from TpA sites in DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

31 May 2018

Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 November 2018

Structures of complexes between echinomycin and duplex DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 November 2018

Atomic force microscopy study of the structural effects induced by echinomycin binding to DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 November 2018

Understanding the basis of resistance in the irksome Lys103Asn HIV-1 reverse transcriptase mutant through targeted molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 November 2018

Preferred binding sites for [N-MeCYs(3), N-MeCys(7)]TANDEM determined using a universal footprinting substrate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 November 2018

Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 November 2018

Sequence specificity of quinoxaline antibiotics. 2. NMR studies of the binding of [N-MeCys3,N-MeCys7]TANDEM and triostin A to DNA containing a CpI step

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1283521

28 November 2018

Structure of TANDEM and its implication for bifunctional intercalation into DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/16282585

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Optimised parameters for A-DNA and B-DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/16282585

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Sequence preferences in the binding to DNA of triostin A and TANDEM as reported by DNase I footprinting

1 reference

https://pubmed.ncbi.nlm.nih.gov/16282585

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Netropsin binding to poly[d(IC)].poly[IC)] and poly[d(GC].poly[d(GC)]: a computer simulation

1 reference

https://pubmed.ncbi.nlm.nih.gov/16282585

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Recognition elements that determine affinity and sequence-specific binding to DNA of 2QN, a biosynthetic bis-quinoline analogue of echinomycin

1 reference

https://pubmed.ncbi.nlm.nih.gov/16282585

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The molecular structure of a DNA-triostin A complex

1 reference

https://pubmed.ncbi.nlm.nih.gov/16282585

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKI916

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16282585%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16282585%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16282585%20AND%20SRC:MED&resulttype=core&format=json

9 January 2020

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