scholarly journals The base-pairing ability of the base pair-mimic nucleosides

2007 ◽  
Vol 51 (1) ◽  
pp. 71-72
Author(s):  
S.-i. Nakano ◽  
K. Uenishi ◽  
M. Fujii ◽  
N. Sugimoto
Keyword(s):  
Base Pair ◽  
Base Pairing

scholarly journals Supercoiling and looping promote DNA base accessibility and coordination among distant sites

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonathan M. Fogg ◽  
Allison K. Judge ◽  
Erik Stricker ◽  
Hilda L. Chan ◽  
Lynn Zechiedrich
Keyword(s):  
Mechanical Stress ◽  
Genomic Instability ◽  
Base Pair ◽  
Base Pairing ◽  
Complex Interplay ◽  
Site Specific ◽  
Torsional Strain ◽  
Dna Base ◽  
Dna Backbone ◽  
Negative Supercoiling

AbstractDNA in cells is supercoiled and constrained into loops and this supercoiling and looping influence every aspect of DNA activity. We show here that negative supercoiling transmits mechanical stress along the DNA backbone to disrupt base pairing at specific distant sites. Cooperativity among distant sites localizes certain sequences to superhelical apices. Base pair disruption allows sharp bending at superhelical apices, which facilitates DNA writhing to relieve torsional strain. The coupling of these processes may help prevent extensive denaturation associated with genomic instability. Our results provide a model for how DNA can form short loops, which are required for many essential processes, and how cells may use DNA loops to position nicks to facilitate repair. Furthermore, our results reveal a complex interplay between site-specific disruptions to base pairing and the 3-D conformation of DNA, which influences how genomes are stored, replicated, transcribed, repaired, and many other aspects of DNA activity.

Four cocrystals of thymine with phenolic coformers: influence of the coformer on hydrogen bonding

2015 ◽  
Vol 71 (7) ◽  
pp. 602-609 ◽  
Author(s):  
Balasubramanian Sridhar ◽  
Jagadeesh Babu Nanubolu ◽  
Krishnan Ravikumar
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Base Pair ◽  
Chemical Species ◽  
Molecular Solids ◽  
Base Pairing ◽  
One Dimensional ◽  
Twofold Axis ◽  
Dimeric Unit ◽  
Donor And Acceptor

Cocrystals are molecular solids composed of at least two types of neutral chemical species held together by noncovalent forces. Crystallization of thymine [systematic name: 5-methylpyrimidine-2,4(1H,3H)-dione] with four phenolic coformers resulted in cocrystal formation,viz.catechol (benzene-1,2-diol) giving thymine–catechol (1/1), C5H6N2O2·C6H6O2, (I), resorcinol (benzene-1,3-diol) giving thymine–resorcinol (2/1), 2C5H6N2O2·C6H6O2, (II), hydroquinone (benzene-1,4-diol) giving thymine–hydroquinone (2/1), 2C5H6N2O2·C6H6O2, (III), and pyrogallol (benzene-1,2,3-triol) giving thymine–pyrogallol (1/2), C5H6N2O2·2C6H6O3, (IV). The resorcinol molecule in (II) occupies a twofold axis, while the hydroquinone molecule in (III) is situated on a centre of inversion. Thymine–thymine base pairing is common across all four structures, albeit with different patterns. In (I)–(III), the base pair is propagated into an infinite one-dimensional ribbon, whereas it exists as a discrete dimeric unit in (IV). In (I)–(III), the two donor N atoms and one carbonyl acceptor O atom of thymine are involved in thymine–thymine base pairing and the remaining carbonyl O atom is hydrogen bonded to the coformer. In contrast, in (IV), just one donor N atom and one acceptor O atom are involved in base pairing, and the remaining donor N atom and acceptor O atom of thymine form hydrogen bonds to the coformer molecules. Thus, the utilization of the donor and acceptor atoms of thymine in the hydrogen bonding is influenced by the coformers.

scholarly journals Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Anustup Poddar ◽  
Muhammad S. Azam ◽  
Tunc Kayikcioglu ◽  
Maksym Bobrovskyy ◽  
Jichuan Zhang ◽  
...  
Keyword(s):  
Small Rna ◽  
Base Pair ◽  
High Throughput Sequencing ◽  
Base Pairing ◽  
Target Search ◽  
Single Base ◽  
Base Pair Mismatch ◽  
Single Base Pair ◽  
Bacterial Small Rna

AbstractBase-pairing interactions mediate many intermolecular target recognition events. Even a single base-pair mismatch can cause a substantial difference in activity but how such changes influence the target search kinetics in vivo is unknown. Here, we use high-throughput sequencing and quantitative super-resolution imaging to probe the mutants of bacterial small RNA, SgrS, and their regulation of ptsG mRNA target. Mutations that disrupt binding of a chaperone protein, Hfq, and are distal to the mRNA annealing region still decrease the rate of target association, kon, and increase the dissociation rate, koff, showing that Hfq directly facilitates sRNA–mRNA annealing in vivo. Single base-pair mismatches in the annealing region reduce kon by 24–31% and increase koff by 14–25%, extending the time it takes to find and destroy the target by about a third. The effects of disrupting contiguous base-pairing are much more modest than that expected from thermodynamics, suggesting that Hfq buffers base-pair disruptions.

Non-Watson−Crick Base Pairing in RNA. Quantum Chemical Analysis of the cis Watson−Crick/Sugar Edge Base Pair Family

2005 ◽  
Vol 109 (10) ◽  
pp. 2292-2301 ◽  
Author(s):  
Judit E. Šponer ◽  
Nad'a Špačková ◽  
Petr Kulhánek ◽  
Jerzy Leszczynski ◽  
Jiří Šponer
Keyword(s):  
Chemical Analysis ◽  
Base Pair ◽  
Quantum Chemical ◽  
Base Pairing ◽  
Quantum Chemical Analysis

scholarly journals Base pairing and mutagenesis: observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR.

1986 ◽  
Vol 83 (15) ◽  
pp. 5434-5438 ◽  
Author(s):  
L. C. Sowers ◽  
G. V. Fazakerley ◽  
R. Eritja ◽  
B. E. Kaplan ◽  
M. F. Goodman
Keyword(s):  
Base Pair ◽  
Proton Nmr ◽  
Base Pairing

Model Calculations on Base-Pair Interactions in DNA

1979 ◽  
Vol 32 (8) ◽  
pp. 1635 ◽  
Author(s):  
RGAR Maclagan
Keyword(s):  
Interaction Energy ◽  
Base Pair ◽  
Double Helix ◽  
Pair Interaction ◽  
Dna Bases ◽  
Base Pairing ◽  
Adjacent Pair ◽  
Model Calculations ◽  
Pair Interaction Energy ◽  
Phosphate Backbone

Calculations are reported using the potential field of Momany, Carruthers, McGuire and Scheraga of the intra-pair interaction energy for all 29 base-pairing schemes proposed by Donohue. Optimized relative orientations and separations of the DNA bases are given. The observed base pairing would appear to be determined principally by the base positions and orientations imposed by the fairly rigid sugar-phosphate backbone. The inter-pair interaction energies for the various possible combinations of the DNA bases in the double-helix models for the A and B forms of DNA are reported. In the model for the B form, the inter-pair interaction energy was found to be almost independent of the base-pair combination. The importance of base overlap in determining the extent to which one base pair is rotated with respect to an adjacent pair was also investigated in a preliminary manner.

Base Pairing and Base Pair Substitution

2001 ◽  
pp. 193-197
Author(s):  
L.C. Sowers ◽  
M.F. Goodman
Keyword(s):  
Base Pair ◽  
Base Pairing ◽  
Base Pair Substitution

scholarly journals RNA Sequence and Base Pairing Effects on Insertion Editing in Trypanosoma brucei

2002 ◽  
Vol 22 (5) ◽  
pp. 1567-1576 ◽  
Author(s):  
Robert P. Igo ◽  
Sobomabo D. Lawson ◽  
Kenneth Stuart
Keyword(s):  
Trypanosoma Brucei ◽  
Rna Editing ◽  
Base Pair ◽  
Editing Site ◽  
Base Pairing ◽  
Editing Efficiency ◽  
Rna Sequence ◽  
Guide Rnas

ABSTRACT RNA editing inserts and deletes uridylates (U's) in kinetoplastid mitochondrial pre-mRNAs by a series of enzymatic steps. Small guide RNAs (gRNAs) specify the edited sequence. Editing, though sometimes extensive, is precise. The effects of mutating pre-mRNA and gRNA sequences in, around, and upstream of the editing site on the specificity and efficiency of in vitro insertion editing were examined. U's could be added opposite guiding pyrimidines, but guiding purines, particularly A's, were required for efficient ligation. A base pair between mRNA and gRNA immediately upstream of the editing site was not required for insertion editing, although it greatly enhanced its efficiency and accuracy. In addition, a gRNA/mRNA duplex upstream of the editing site enhanced insertion editing when it was close to the editing site, but prevented cleavage, and hence editing, when immediately adjacent to the editing site. Thus, several aspects of mRNA-gRNA interaction, as well as gRNA base pairing with added U's, optimize editing efficiency, although they are not required for insertion editing.

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