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Pesquisa : D13.444.308.130 [Categoria DeCS]
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[PMID]:28471357
[Au] Autor:Karthik S; Thirugnanasambandam A; Mandal PK; Gautham N
[Ad] Endereço:CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.
[Ti] Título:Crystal structure of d(CCGGGGTACCCCGG) at 1.4 Šresolution.
[So] Source:Acta Crystallogr F Struct Biol Commun;73(Pt 5):259-265, 2017 May 01.
[Is] ISSN:2053-230X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG) is reported at 1.4 Šresolution in the tetragonal space group P4 2 2. The sequence was designed to fold as a four-way junction. However, it forms an A-type double helix in the presence of barium chloride. The metal ion could not be identified in the electron-density map. The crystallographic asymmetric unit consists of one A-type double helix with 12 base pairs per turn, in contrast to 11 base pairs per turn for canonical A-DNA. A large number of solvent molecules have been identified in both the grooves of the duplex and around the backbone phosphate groups.
[Mh] Termos MeSH primário: DNA Forma A/química
Oligodesoxirribonucleotídeos/química
[Mh] Termos MeSH secundário: Compostos de Bário/química
Pareamento de Bases
Cloretos/química
Modelos Moleculares
Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Barium Compounds); 0 (Chlorides); 0 (DNA, A-Form); 0 (Oligodeoxyribonucleotides); 0VK51DA1T2 (barium chloride)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:171204
[Lr] Data última revisão:
171204
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1107/S2053230X17004770


  2 / 82 MEDLINE  
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[PMID]:28576665
[Au] Autor:Kulkarni M; Mukherjee A
[Ad] Endereço:Department of Chemistry, Indian Institute of Science Education and Research, Pune, 411008, Maharashtra, India.
[Ti] Título:Understanding B-DNA to A-DNA transition in the right-handed DNA helix: Perspective from a local to global transition.
[So] Source:Prog Biophys Mol Biol;128:63-73, 2017 Sep.
[Is] ISSN:1873-1732
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The right-handed DNA helix exhibits two major conformations, A-DNA and B-DNA, depending on the environmental conditions. The B-DNA to A-DNA (B→A) transition is sequence specific, cooperative, and reversible. The reduced water activity due to the addition of solvents like ethanol or the presence of protein or drug molecules causes B→A transition. In several biological cases, B→A transition occurs at a local level where small fragments of a long DNA sequence undergoes B→A transition. In this review, we have discussed various aspects of B→A transition such as the role of water, sequence specificity, mechanism of B→A transition, etc. The review primarily focuses on the B→A mechanism involved at a local level, and finally its connection to the global transition in theoretical and experimental studies.
[Mh] Termos MeSH primário: DNA Forma A/química
DNA de Forma B/química
Conformação de Ácido Nucleico
[Mh] Termos MeSH secundário: Solventes/química
Termodinâmica
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (DNA, A-Form); 0 (DNA, B-Form); 0 (Solvents)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170906
[Lr] Data última revisão:
170906
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170604
[St] Status:MEDLINE


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[PMID]:28387634
[Au] Autor:Karthik S; Thirugnanasambandam A; Mandal PK; Gautham N
[Ad] Endereço:a CAS in Crystallography and Biophysics , University of Madras , Guindy Campus, Chennai , Tamil Nadu , India.
[Ti] Título:Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG) at 1.7 Å resolution.
[So] Source:Nucleosides Nucleotides Nucleic Acids;36(5):343-354, 2017 May 04.
[Is] ISSN:1532-2335
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:We present here a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG) all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. However, in the presence of zinc, magnesium, and in the absence of any metal ion, it does not take up the junction structure, but forms an A-type double helix. This allowed us to study possible conformational changes in the double helix due to the presence of metal ions. Upon addition of the zinc ion, there is a change in the space group from P4 2 2 to P4 . The overall conformation of the duplex remains the same. There are small changes in the interaction of the metal ions with the DNA. In the zinc-bound structure, there are two zinc ions that show direct interaction with the N7 atoms of terminal G bases at either end of the molecule. There are small changes in the interhelical contacts. The consequence of these differences is to break some of the symmetry and change the space group.
[Mh] Termos MeSH primário: DNA/química
Oligodesoxirribonucleotídeos/química
[Mh] Termos MeSH secundário: Sequência de Bases
Cristalografia por Raios X
DNA Forma A/química
Magnésio/química
Modelos Moleculares
Conformação de Ácido Nucleico
Zinco/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, A-Form); 0 (Oligodeoxyribonucleotides); 9007-49-2 (DNA); I38ZP9992A (Magnesium); J41CSQ7QDS (Zinc)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170906
[Lr] Data última revisão:
170906
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170408
[St] Status:MEDLINE
[do] DOI:10.1080/15257770.2017.1287378


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[PMID]:28334863
[Au] Autor:Molt RW; Georgiadis MM; Richards NGJ
[Ad] Endereço:Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
[Ti] Título:Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 µs molecular dynamics simulations.
[So] Source:Nucleic Acids Res;45(7):3643-3653, 2017 Apr 20.
[Is] ISSN:1362-4962
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Z: Little is known about the influence of multiple consecutive 'non-standard' ( , 6-amino-5-nitro-2(1H)-pyridone, and , 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one) nucleobase pairs on the structural parameters of duplex DNA. nucleobase pairs follow standard rules for Watson-Crick base pairing but have rearranged hydrogen bonding donor and acceptor groups. Using the X-ray crystal structure as a starting point, we have modeled the motions of a DNA duplex built from a self-complementary oligonucleotide (5΄-CTTATPPPZZZATAAG-3΄) in water over a period of 50 µs and calculated DNA local parameters, step parameters, helix parameters, and major/minor groove widths to examine how the presence of multiple, consecutive nucleobase pairs might impact helical structure. In these simulations, the -containing DNA duplex exhibits a significantly wider major groove and greater average values of stagger, slide, rise, twist and h-rise than observed for a 'control' oligonucleotide in which nucleobase pairs are replaced by . The molecular origins of these structural changes are likely associated with at least two differences between and . First, the electrostatic properties of differ from in terms of density distribution and dipole moment. Second, differences are seen in the base stacking of pairs in dinucleotide steps, arising from energetically favorable stacking of the nitro group in with π-electrons of the adjacent base.
[Mh] Termos MeSH primário: DNA/química
Simulação de Dinâmica Molecular
[Mh] Termos MeSH secundário: Pareamento de Bases
DNA Forma A/química
DNA de Forma B/química
Ligações de Hidrogênio
Conformação de Ácido Nucleico
Oligonucleotídeos/química
Eletricidade Estática
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, A-Form); 0 (DNA, B-Form); 0 (Oligonucleotides); 9007-49-2 (DNA)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170825
[Lr] Data última revisão:
170825
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170324
[St] Status:MEDLINE
[do] DOI:10.1093/nar/gkx144


  5 / 82 MEDLINE  
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[PMID]:28129992
[Au] Autor:Watkins D; Gong C; Kellish P; Arya DP
[Ad] Endereço:NUBAD, LLC, Greenville, SC 29607, USA.
[Ti] Título:Probing A-form DNA: A fluorescent aminosugar probe and dual recognition by anthraquinone-neomycin conjugates.
[So] Source:Bioorg Med Chem;25(4):1309-1319, 2017 Feb 15.
[Is] ISSN:1464-3391
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Nucleic acids adopt a broad array of hydrogen-bonded structures that enable their diverse roles in the cell; even the familiar DNA double helix displays subtle architectural nuances that are sequence dependent. While there have been many approaches for recognition of B-form nucleic acids, A-form DNA recognition has lagged behind. Here, using a tight binding fluorescein-neomycin (F-neo) conjugate that can probe the electrostatic environment of A-form DNA major groove, we developed a fluorescent displacement assay to be used as a screen for DNA duplex-binding compounds. As opposed to intercalating dyes that can significantly perturb DNA structure, the groove binding F-neo allows the probing of native DNA conformation. In combination with the assay development and probing of DNA grooves, we also report the synthesis and binding of a series of neomycin-anthraquinone conjugates, two units with a known preference for binding GC rich DNA. The assay can be used to identify duplex DNA-binding compounds, as well as probe structural features of a target DNA duplex, and can easily be scaled up for high throughput screening of compound libraries.
[Mh] Termos MeSH primário: DNA Forma A/análise
Fluoresceína/química
Corantes Fluorescentes/análise
Neomicina/química
[Mh] Termos MeSH secundário: Simulação de Acoplamento Molecular
Estrutura Molecular
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, A-Form); 0 (Fluorescent Dyes); 1404-04-2 (Neomycin); TPY09G7XIR (Fluorescein)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170808
[Lr] Data última revisão:
170808
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170129
[St] Status:MEDLINE


  6 / 82 MEDLINE  
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[PMID]:26984848
[Au] Autor:Sobell HM
[Ad] Endereço:Departments of Chemistry and Molecular Biophysics, University of Rochester, Rochester, NY, 14642, USA. sobell@localnet.com.
[Ti] Título:Premeltons in DNA.
[So] Source:J Struct Funct Genomics;17(1):17-31, 2016 Mar.
[Is] ISSN:1570-0267
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Premeltons are examples of emergent-structures (i.e., structural-solitons) that arise spontaneously in DNA due to the presence of nonlinear-excitations in its structure. They are of two kinds: B-B (or A-A) premeltons form at specific DNA-regions to nucleate site-specific DNA melting. These are stationary and, being globally-nontopological, undergo breather-motions that allow drugs and dyes to intercalate into DNA. B-A (or A-B) premeltons, on the other hand, are mobile, and being globally-topological, act as phase-boundaries transforming B- into A-DNA during the structural phase-transition. They are not expected to undergo breather motions. A key feature of both types of premeltons is the presence of an intermediate structural-form in their central regions (proposed as being a transition-state intermediate in DNA-melting and in the B- to A-transition), which differs from either A- or B-DNA. Called beta-DNA, this is both metastable and hyperflexible--and contains an alternating sugar-puckering pattern along the polymer backbone combined with the partial unstacking (in its lower energy-forms) of every-other base-pair. Beta-DNA is connected to either B- or to A-DNA on either side by boundaries possessing a gradation of nonlinear structural-change, these being called the kink and the antikink regions. The presence of premeltons in DNA leads to a unifying theory to understand much of DNA physical chemistry and molecular biology. In particular, premeltons are predicted to define the 5' and 3' ends of genes in naked-DNA and DNA in active-chromatin, this having important implications for understanding physical aspects of the initiation, elongation and termination of RNA-synthesis during transcription. For these and other reasons, the model will be of broader interest to the general-audience working in these areas. The model explains a wide variety of data, and carries with it a number of experimental predictions--all readily testable--as will be described in this review.
[Mh] Termos MeSH primário: DNA/química
Substâncias Intercalantes/química
Modelos Moleculares
Conformação de Ácido Nucleico
[Mh] Termos MeSH secundário: Sítios de Ligação
Fenômenos Químicos
DNA/genética
DNA/metabolismo
DNA Forma A/química
DNA Forma A/genética
DNA Forma A/metabolismo
DNA de Forma B/química
DNA de Forma B/genética
DNA de Forma B/metabolismo
Substâncias Intercalantes/metabolismo
Biologia Molecular/métodos
Desnaturação de Ácido Nucleico
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (DNA, A-Form); 0 (DNA, B-Form); 0 (Intercalating Agents); 9007-49-2 (DNA)
[Em] Mês de entrada:1701
[Cu] Atualização por classe:170104
[Lr] Data última revisão:
170104
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160318
[St] Status:MEDLINE
[do] DOI:10.1007/s10969-016-9202-4


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[PMID]:26872482
[Au] Autor:Porschke D
[Ad] Endereço:Max Planck Institut für biophysikalische Chemie, 37077, Göttingen, Germany. dpoersc@gwdg.de.
[Ti] Título:Boundary conditions for free A-DNA in solution and the relation of local to global DNA structures at reduced water activity.
[So] Source:Eur Biophys J;45(5):413-21, 2016 Jul.
[Is] ISSN:1432-1017
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:Because of repeated claims that A-DNA cannot exist without aggregation or condensation, the state of DNA restriction fragments with 84-859 bp has been analyzed in aqueous solutions upon reduction of the water activity. Rotational diffusion times τ (d) measured by electric dichroism at different water activities with a wide variation of viscosities are normalized to values τ (c) at the viscosity of water, which indicate DNA structures at a high sensitivity. For short helices (chain lengths [Formula: see text] ≤ persistence length p), cooperative formation of A-DNA is reflected by the expected reduction of the hydrodynamic length; the transition to the A-form is without aggregation or condensation upon addition of ethanol at monovalent salt ≤1 mM. The aggregation boundary, indicated by a strong increase of τ (c), is shifted to higher monovalent salt (≥4 mM) when ethanol is replaced by trifluoroethanol. The BA transition is not indicated anymore by a cooperative change of τ (c) for [Formula: see text] ¼ p; τ (c) values for these long chains decrease upon reduction of the water activity continuously over the full range, including the BA transition interval. This suggests a non-cooperative BC transition, which induces DNA curvature. The resulting wide distribution of global structures hides changes of local length during the BA transition. Free A-DNA without aggregation/condensation is found at low-salt concentrations where aggregation is inhibited and/or very slow. In an intermediate range of solvent conditions, where the A-form starts to aggregate, a time window remains that can be used for analysis of free A-DNA in a quasi-equilibrium state.
[Mh] Termos MeSH primário: DNA Forma A/química
Água/química
[Mh] Termos MeSH secundário: Pareamento de Bases
Difusão
Cinética
Rotação
Soluções
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, A-Form); 0 (Solutions); 059QF0KO0R (Water)
[Em] Mês de entrada:1702
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160214
[St] Status:MEDLINE
[do] DOI:10.1007/s00249-015-1110-1


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[PMID]:26789754
[Au] Autor:Perera RT; Fleming AM; Peterson AM; Heemstra JM; Burrows CJ; White HS
[Ad] Endereço:Department of Chemistry, University of Utah, Salt Lake City, Utah.
[Ti] Título:Unzipping of A-Form DNA-RNA, A-Form DNA-PNA, and B-Form DNA-DNA in the α-Hemolysin Nanopore.
[So] Source:Biophys J;110(2):306-14, 2016 Jan 19.
[Is] ISSN:1542-0086
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Unzipping of double-stranded nucleic acids by an electric field applied across a wild-type α-hemolysin (αHL) nanopore provides structural information about different duplex forms. In this work, comparative studies on A-form DNA-RNA duplexes and B-form DNA-DNA duplexes with a single-stranded tail identified significant differences in the blockage current and the unzipping duration between the two helical forms. We observed that the B-form duplex blocks the channel 1.9 ± 0.2 pA more and unzips ∼15-fold more slowly than an A-form duplex at 120 mV. We developed a model to describe the dependence of duplex unzipping on structure. We demonstrate that the wider A-form duplex (d = 2.4 nm) is unable to enter the vestibule opening of αHL on the cis side, leading to unzipping outside of the nanopore with higher residual current and faster unzipping times. In contrast, the smaller B-form duplexes (d = 2.0 nm) enter the vestibule of αHL, resulting in decreased current blockages and slower unzipping. We investigated the effects of varying the length of the single-stranded overhang, and studied A-form DNA-PNA duplexes to provide additional support for the proposed model. This study identifies key differences between A- and B-form duplex unzipping that will be important in the design of future probe-based methods for detecting DNA or RNA.
[Mh] Termos MeSH primário: Toxinas Bacterianas/química
Pareamento de Bases
DNA Forma A/química
DNA de Forma B/química
Proteínas Hemolisinas/química
Nanoporos
RNA/química
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Toxinas Bacterianas/metabolismo
Sequência de Bases
DNA Forma A/metabolismo
DNA de Forma B/metabolismo
DNA de Cadeia Simples/química
DNA de Cadeia Simples/metabolismo
Proteínas Hemolisinas/metabolismo
Dados de Sequência Molecular
Ligação Proteica
RNA/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Bacterial Toxins); 0 (DNA, A-Form); 0 (DNA, B-Form); 0 (DNA, Single-Stranded); 0 (Hemolysin Proteins); 0 (staphylococcal alpha-toxin); 63231-63-0 (RNA)
[Em] Mês de entrada:1610
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160121
[St] Status:MEDLINE


  9 / 82 MEDLINE  
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[PMID]:26538133
[Au] Autor:Kulkarni M; Mukherjee A
[Ad] Endereço:Department of Chemistry, Indian Institute of Science Education and Research, Pune-, 411008, India.
[Ti] Título:Computational Approach to Explore the B/A Junction Free Energy in DNA.
[So] Source:Chemphyschem;17(1):147-54, 2016 Jan 04.
[Is] ISSN:1439-7641
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:Protein-DNA interactions induce conformational changes in DNA such as B- to A-form transitions at a local level. Such transitions are associated with a junction free energy cost at the boundary of two different conformations in a DNA molecule. In this study, we performed umbrella sampling simulations to find the free energy values of the B-A transition at the dinucleotide and trinucleotide level of DNA. Using a combination of dinucleotide and trinucleotide free energy costs obtained from simulations, we calculated the B/A junction free energy. Our study shows that the B/A junction free energy is 0.52 kcal mol(-1) for the A-philic GG step and 1.59 kcal mol(-1) for the B-philic AA step. This observation is in agreement with experimentally derived values. After excluding junction effects, we obtained an absolute free energy cost for the B- to A-form conversion for all the dinucleotide steps. These absolute free energies may be used for predicting the propensity of structural transitions in DNA.
[Mh] Termos MeSH primário: DNA Forma A/química
DNA de Forma B/química
[Mh] Termos MeSH secundário: Sequência de Bases
Transferência de Energia
Modelos Químicos
Água/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, A-Form); 0 (DNA, B-Form); 059QF0KO0R (Water)
[Em] Mês de entrada:1610
[Cu] Atualização por classe:161230
[Lr] Data última revisão:
161230
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151106
[St] Status:MEDLINE
[do] DOI:10.1002/cphc.201500690


  10 / 82 MEDLINE  
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[PMID]:26642982
[Au] Autor:Cabeza de Vaca I; Lucas MF; Guallar V
[Ad] Endereço:Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , c/Jordi Girona 29, 08034 Barcelona, Barcelona, Spain.
[Ti] Título:New Monte Carlo Based Technique To Study DNA-Ligand Interactions.
[So] Source:J Chem Theory Comput;11(12):5598-605, 2015 Dec 08.
[Is] ISSN:1549-9626
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:We present a new all-atom Monte Carlo technique capable of performing quick and accurate DNA-ligand conformational sampling. In particular, and using the PELE software as a frame, we have introduced an additional force field, an implicit solvent, and an anisotropic network model to effectively map the DNA energy landscape. With these additions, we successfully generated DNA conformations for a test set composed of six DNA fragments of A-DNA and B-DNA. Moreover, trajectories generated for cisplatin and its hydrolysis products identified the best interacting compound and binding site, producing analogous results to microsecond molecular dynamics simulations. Furthermore, a combination of the Monte Carlo trajectories with Markov State Models produced noncovalent binding free energies in good agreement with the published molecular dynamics results, at a significantly lower computational cost. Overall our approach will allow a quick but accurate sampling of DNA-ligand interactions.
[Mh] Termos MeSH primário: DNA/química
Ligantes
[Mh] Termos MeSH secundário: Algoritmos
Sequência de Bases
Sítios de Ligação
Cisplatino/química
Cisplatino/metabolismo
DNA/metabolismo
DNA Forma A/química
DNA de Forma B/química
Cadeias de Markov
Simulação de Dinâmica Molecular
Método de Monte Carlo
Conformação de Ácido Nucleico
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, A-Form); 0 (DNA, B-Form); 0 (Ligands); 9007-49-2 (DNA); Q20Q21Q62J (Cisplatin)
[Em] Mês de entrada:1609
[Cu] Atualização por classe:151208
[Lr] Data última revisão:
151208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151209
[St] Status:MEDLINE
[do] DOI:10.1021/acs.jctc.5b00838



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