scholarly journals Antitumor drug SN6999 perturbs the DNA double helix and O6-ethyl-G:C base pair: crystal structure of the d[CGC(O6-ethyl-G)AATTCGCG]-SN6999 complex

1993 ◽  
Vol 49 (s1) ◽  
pp. c135-c136
Author(s):  
Y.-G. Gao ◽  
M. Sriram ◽  
W. Denny ◽  
A. H.-J. Wang
Keyword(s):  
Crystal Structure ◽  
Base Pair ◽  
Double Helix ◽  
Antitumor Drug ◽  
Dna Double Helix

scholarly journals Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Shu-ichi Nakano ◽  
Masayuki Fujii ◽  
Naoki Sugimoto
Keyword(s):  
Nucleic Acid ◽  
Base Pair ◽  
Double Helix ◽  
Nucleoside Analogs ◽  
Structural Analog ◽  
Base Pairs ◽  
Nucleic Acid Analogs ◽  
Dna Double Helix ◽  
Nucleic Acid Interactions ◽  
Site Selective

Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

The Extension of a DNA Double Helix by an Additional Watson-Crick Base Pair on the Same Backbone

ChemBioChem ◽  
2013 ◽  
Vol 14 (9) ◽  
pp. 1072-1074 ◽  
Author(s):  
Pawan Kumar ◽  
Pawan K. Sharma ◽  
Charlotte S. Madsen ◽  
Michael Petersen ◽  
Poul Nielsen
Keyword(s):  
Base Pair ◽  
Double Helix ◽  
Dna Double Helix

scholarly journals Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea

PLoS ONE ◽  
2016 ◽  
Vol 11 (9) ◽  
pp. e0163361 ◽  
Author(s):  
Lei Tian ◽  
Zhenfeng Zhang ◽  
Hanqian Wang ◽  
Mohan Zhao ◽  
Yuhui Dong ◽  
...  
Keyword(s):  
Base Pair ◽  
Double Helix ◽  
Chromatin Protein ◽  
Sequence Dependent ◽  
Dna Double Helix ◽  
Base Pair Opening

scholarly journals Sequence dependency of canonical base pair opening in the DNA double helix

2017 ◽  
Vol 13 (4) ◽  
pp. e1005463 ◽  
Author(s):  
Viveca Lindahl ◽  
Alessandra Villa ◽  
Berk Hess
Keyword(s):  
Base Pair ◽  
Double Helix ◽  
Canonical Base ◽  
Canonical Base Pair ◽  
Dna Double Helix ◽  
Base Pair Opening

Protamine-DNA interaction

1978 ◽  
Vol 36 (2) ◽  
pp. 200-201
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Small Volume ◽  
Double Helix ◽  
Dna Interaction ◽  
Dark Field ◽  
Sperm Head ◽  
Nuclear Proteins ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Dna Double Helix ◽  
Positively Charged

Dark field electron microscopy has been used for the study of the structure of individual macromolecules with a resolution to at least the 5Å level. The use of this technique has been extended to the investigation of structure of interacting molecules, particularly the interaction between DNA and fish protamine, a class of basic nuclear proteins of molecular weight 4,000 daltons.Protamine, which is synthesized during spermatogenesis, binds to chromatin, displaces the somatic histones and wraps up the DNA to fit into the small volume of the sperm head. It has been proposed that protamine, existing as an extended polypeptide, winds around the minor groove of the DNA double helix, with protamine's positively-charged arginines lining up with the negatively-charged phosphates of DNA. However, viewing protamine as an extended protein is inconsistent with the results obtained in our laboratory.

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