scholarly journals Toward a Designed, Functioning Genetic System with Expanded-Size Base Pairs:  Solution Structure of the Eight-Base xDNA Double Helix

2006 ◽  
Vol 128 (45) ◽  
pp. 14704-14711 ◽  
Author(s):  
Stephen R. Lynch ◽  
Haibo Liu ◽  
Jianmin Gao ◽  
Eric T. Kool
Keyword(s):  
Solution Structure ◽  
Double Helix ◽  
Genetic System ◽  
Base Pairs

scholarly journals Solution structure of a DNA double helix with consecutive metal-mediated base pairs

2010 ◽  
Vol 2 (3) ◽  
pp. 229-234 ◽  
Author(s):  
Silke Johannsen ◽  
Nicole Megger ◽  
Dominik Böhme ◽  
Roland K. O. Sigel ◽  
Jens Müller
Keyword(s):  
Solution Structure ◽  
Double Helix ◽  
Base Pairs ◽  
Dna Double Helix

Developing a Genetic System in Deinococcus radiodurans for Analyzing Mutations

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 661-668
Author(s):  
Mandy Kim ◽  
Erika Wolff ◽  
Tiffany Huang ◽  
Lilit Garibyan ◽  
Ashlee M Earl ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Deinococcus Radiodurans ◽  
Genetic System ◽  
Base Change ◽  
Base Substitution ◽  
Wild Type ◽  
Base Pairs ◽  
E Coli ◽  
Radiation Induced ◽  
Induced Mutagenesis

Abstract We have applied a genetic system for analyzing mutations in Escherichia coli to Deinococcus radiodurans, an extremeophile with an astonishingly high resistance to UV- and ionizing-radiation-induced mutagenesis. Taking advantage of the conservation of the β-subunit of RNA polymerase among most prokaryotes, we derived again in D. radiodurans the rpoB/Rif r system that we developed in E. coli to monitor base substitutions, defining 33 base change substitutions at 22 different base pairs. We sequenced >250 mutations leading to Rif r in D. radiodurans derived spontaneously in wild-type and uvrD (mismatch-repair-deficient) backgrounds and after treatment with N-methyl-N′-nitro-N-nitrosoguanidine (NTG) and 5-azacytidine (5AZ). The specificities of NTG and 5AZ in D. radiodurans are the same as those found for E. coli and other organisms. There are prominent base substitution hotspots in rpoB in both D. radiodurans and E. coli. In several cases these are at different points in each organism, even though the DNA sequences surrounding the hotspots and their corresponding sites are very similar in both D. radiodurans and E. coli. In one case the hotspots occur at the same site in both organisms.

scholarly journals Base pairing structure in the poly d(G-T) double helix: wobble base pairs

1978 ◽  
Vol 5 (6) ◽  
pp. 1955-1970 ◽  
Author(s):  
Thomas A. Early ◽  
John Olmsted ◽  
David R. Kearns ◽  
Axel G. Lezius
Keyword(s):  
Double Helix ◽  
Base Pairing ◽  
Base Pairs

The unique structure of A-tracts and intrinsic DNA bending

2009 ◽  
Vol 42 (1) ◽  
pp. 41-81 ◽  
Author(s):  
Tali E. Haran ◽  
Udayan Mohanty
Keyword(s):  
Current Knowledge ◽  
Double Helix ◽  
Dna Bending ◽  
Helical Axis ◽  
Base Pairs ◽  
Regulatory Regions ◽  
Unique Structure ◽  
Distinct Structure ◽  
Global Curvature ◽  
Dna Double Helix

AbstractShort runs of adenines are a ubiquitous DNA element in regulatory regions of many organisms. When runs of 4–6 adenine base pairs (‘A-tracts’) are repeated with the helical periodicity, they give rise to global curvature of the DNA double helix, which can be macroscopically characterized by anomalously slow migration on polyacrylamide gels. The molecular structure of these DNA tracts is unusual and distinct from that of canonical B-DNA. We review here our current knowledge about the molecular details of A-tract structure and its interaction with sequences flanking them of either side and with the environment. Various molecular models were proposed to describe A-tract structure and how it causes global deflection of the DNA helical axis. We review old and recent findings that enable us to amalgamate the various findings to one model that conforms to the experimental data. Sequences containing phased repeats of A-tracts have from the very beginning been synonymous with global intrinsic DNA bending. In this review, we show that very often it is the unique structure of A-tracts that is at the basis of their widespread occurrence in regulatory regions of many organisms. Thus, the biological importance of A-tracts may often be residing in their distinct structure rather than in the global curvature that they induce on sequences containing them.

X-ray Crystal Structure of a Metalled Double-Helix Generated by Infinite and Consecutive C*-AgI -C* (C*:N1 -Hexylcytosine) Base Pairs through Argentophilic and Hydrogen Bond Interactions

2017 ◽  
Vol 23 (9) ◽  
pp. 2103-2108 ◽  
Author(s):  
Angel Terrón ◽  
Blas Moreno-Vachiano ◽  
Antonio Bauzá ◽  
Angel García-Raso ◽  
Juan Jesús Fiol ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Double Helix ◽  
Base Pairs ◽  
X Ray ◽  
Hydrogen Bond Interactions

Protein Recognition of Base Pairs in a Double Helix

1977 ◽  
pp. 361-374 ◽  
Author(s):  
ALEXANDER RICH ◽  
N ADRIAN C. SEEMAN ◽  
JOH.M. ROSENBERG
Keyword(s):  
Double Helix ◽  
Protein Recognition ◽  
Base Pairs

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.

scholarly journals Crystal structure of d(CCGGGGTACCCCGG)2at 1.4 Å resolution

2017 ◽  
Vol 73 (5) ◽  
pp. 259-265
Author(s):  
Selvam Karthik ◽  
Arunachalam Thirugnanasambandam ◽  
Pradeep Kumar Mandal ◽  
Namasivayam Gautham
Keyword(s):  
Crystal Structure ◽  
Metal Ion ◽  
Double Helix ◽  
Barium Chloride ◽  
Base Pairs ◽  
X Ray ◽  
Density Map ◽  
Solvent Molecules ◽  
Electron Density Map ◽  
Phosphate Groups

The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG)2is reported at 1.4 Å resolution in the tetragonal space groupP41212. 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.

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