Enzymatic incorporation of a new base pair into DNA and RNA

1989 ◽  
Vol 111 (21) ◽  
pp. 8322-8323 ◽  
Author(s):  
Christopher Switzer ◽  
Simon E. Moroney ◽  
Steven A. Benner
Keyword(s):  
Base Pair ◽  
Dna And Rna

scholarly journals Publisher Correction: Detection of genetic variation and base modifications at base-pair resolution on both DNA and RNA

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Zhen Wang ◽  
Jérôme Maluenda ◽  
Laurène Giraut ◽  
Thibault Vieille ◽  
Andréas Lefevre ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Base Pair ◽  
Dna And Rna ◽  
Base Modifications

A Correction to this paper has been published: https://doi.org/10.1038/s42003-021-01894-9

scholarly journals Symmetry in Nucleic-Acid Double Helices

Symmetry ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 737
Author(s):  
Udo Heinemann ◽  
Yvette Roske
Keyword(s):  
Nucleic Acid ◽  
Base Pair ◽  
Rna Structure ◽  
Test Tube ◽  
Base Pairs ◽  
Dna And Rna ◽  
Left Handed ◽  
Double Helices ◽  
Rna Duplexes ◽  
The Right

In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. Focusing on double helices, we describe the crucial role played by symmetry in shaping DNA and RNA structure. The base pairs in nucleic-acid double helices display rotational pseudo-symmetry. In the Watson–Crick base pairs found in naturally occurring DNA and RNA duplexes, the symmetry axis lies in the base-pair plane, giving rise to two different helical grooves. In contrast, anti-Watson–Crick base pairs have a dyad axis perpendicular to the base-pair plane and identical grooves. In combination with the base-pair symmetry, the syn/anti conformation of paired nucleotides determines the parallel or antiparallel strand orientation of double helices. DNA and RNA duplexes in nature are exclusively antiparallel. Watson–Crick base-paired DNA or RNA helices display either right-handed or left-handed helical (pseudo-) symmetry. Genomic DNA is usually in the right-handed B-form, and RNA double helices adopt the right-handed A-conformation. Finally, there is a higher level of helical symmetry in superhelical DNA in which B-form double strands are intertwined in a right- or left-handed sense.

Amplify this! DNA and RNA get a third base pair

2006 ◽  
Vol 3 (9) ◽  
pp. 667-668 ◽  
Author(s):  
Aaron M Leconte ◽  
Floyd E Romesberg
Keyword(s):  
Base Pair ◽  
Dna And Rna

Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet

Nature ◽  
1990 ◽  
Vol 343 (6253) ◽  
pp. 33-37 ◽  
Author(s):  
Joseph A. Piccirilli ◽  
Steven A. Benner ◽  
Tilman Krauch ◽  
Simon E. Moroney ◽  
Steven A. Benner
Keyword(s):  
Base Pair ◽  
Dna And Rna ◽  
Genetic Alphabet

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

2014 ◽  
Vol 10 (8) ◽  
pp. 3177-3189 ◽  
Author(s):  
Marie Zgarbová ◽  
Michal Otyepka ◽  
Jiří Šponer ◽  
Filip Lankaš ◽  
Petr Jurečka
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Base Pair ◽  
Dna And Rna ◽  
Dynamics Simulations

An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA

2006 ◽  
Vol 3 (9) ◽  
pp. 729-735 ◽  
Author(s):  
Ichiro Hirao ◽  
Michiko Kimoto ◽  
Tsuneo Mitsui ◽  
Tsuyoshi Fujiwara ◽  
Rie Kawai ◽  
...  
Keyword(s):  
Base Pair ◽  
Nucleotide Analogs ◽  
Site Specific ◽  
Dna And Rna

scholarly journals Optimization of Single-Base-Pair Mismatch Discrimination in Oligonucleotide Microarrays

2003 ◽  
Vol 69 (5) ◽  
pp. 2848-2856 ◽  
Author(s):  
Hidetoshi Urakawa ◽  
Said El Fantroussi ◽  
Hauke Smidt ◽  
James C. Smoot ◽  
Erik H. Tribou ◽  
...  
Keyword(s):  
Base Pair ◽  
Dna Microarrays ◽  
Perfect Match ◽  
Analytical Framework ◽  
Single Base ◽  
Dna And Rna ◽  
Base Pair Mismatch ◽  
Nonequilibrium Dissociation ◽  
Single Base Pair ◽  
Mismatch Discrimination

ABSTRACT The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.

scholarly journals Seven-base-pair inverted repeats in DNA form stable hairpins in vivo in Saccharomyces cerevisiae.

Genetics ◽  
1991 ◽  
Vol 129 (3) ◽  
pp. 669-673 ◽  
Author(s):  
D K Nag ◽  
T D Petes
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Base Pair ◽  
Inverted Repeat ◽  
Inverted Repeats ◽  
Base Pairing ◽  
Yeast Saccharomyces Cerevisiae ◽  
Genetic Method ◽  
Dna And Rna ◽  
Palindromic Sequences

Abstract Palindromic sequences in single-stranded DNA and RNA have the potential for intrastrand base pairing, resulting in formation of "hairpin" structures. We previously reported a genetic method for detecting such structures in vivo in the yeast Saccharomyces cerevisiae. Below, we describe evidence indicating that a 14-base-pair palindrome (7 bp per inverted repeat) is sufficient for formation of a hairpin in vivo.

scholarly journals Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics

2017 ◽  
Vol 114 (27) ◽  
pp. 7049-7054 ◽  
Author(s):  
Alberto Marin-Gonzalez ◽  
J. G. Vilhena ◽  
Ruben Perez ◽  
Fernando Moreno-Herrero
Keyword(s):  
Molecular Dynamics ◽  
Nucleic Acids ◽  
Elastic Constants ◽  
Base Pair ◽  
Mechanical Response ◽  
Atomic Level ◽  
Biological Processes ◽  
Open Structure ◽  
Dna And Rna ◽  
Double Stranded Dna

Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence. The lower dsRNA stretching resistance is linked to its more open structure, whereas the opposite twist-stretch coupling of both molecules is due to the very different evolution of molecules’ interstrand distance with the stretching force. A reduction of this distance leads to overwinding in dsDNA. In contrast, dsRNA is not able to reduce its interstrand distance and can only elongate by unwinding. Interstrand distance is directly correlated with the slide base-pair parameter and its different behavior in dsDNA and dsRNA traced down to changes in the sugar pucker angle of these NAs.

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