scholarly journals DNA and RNA oligomer thermodynamics: The effect of mismatched bases on double-helix stability

Biopolymers ◽  
1981 ◽  
Vol 20 (12) ◽  
pp. 2509-2531 ◽  
Author(s):  
Jeffrey W. Nelson ◽  
Francis H. Martin ◽  
Ignacio Tinoco
Keyword(s):  
Double Helix ◽  
Dna And Rna ◽  
Helix Stability

Carrier mobility in double-helix DNA and RNA: A quantum chemistry study with Marcus-Hush theory

2016 ◽  
Vol 145 (23) ◽  
pp. 235101 ◽  
Author(s):  
Tao Wu ◽  
Lei Sun ◽  
Qi Shi ◽  
Kaiming Deng ◽  
Weiqiao Deng ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Carrier Mobility ◽  
Double Helix ◽  
Dna And Rna

Na2CO3Influence on DNA Double Helix Stability: Strong Anion Destabilizing Effect

2003 ◽  
Vol 20 (6) ◽  
pp. 801-809 ◽  
Author(s):  
Elena N. Galyuk ◽  
Dmitri Y. Lando ◽  
Valentina P. Egorova ◽  
Hwa Dai ◽  
Yury M. Dosin
Keyword(s):  
Double Helix ◽  
Helix Stability ◽  
Dna Double Helix

Taxol interaction with DNA and RNA — Stability and structural features

2004 ◽  
Vol 82 (6) ◽  
pp. 1112-1118 ◽  
Author(s):  
A Ahmed Ouameur ◽  
H Malonga ◽  
J F Neault ◽  
S Diamantoglou ◽  
H A Tajmir-Riahi
Keyword(s):  
Capillary Electrophoresis ◽  
Binding Site ◽  
Binding Constant ◽  
Lung Tumor ◽  
Rna Stability ◽  
Structural Features ◽  
Spectroscopic Studies ◽  
Dna And Rna ◽  
Helix Stability

Taxol (paclitaxel) is an anticancer drug that interacts with microtubule proteins in a manner that catalyzes their formation from tubulin and stabilizes the resulting structures. However, in the human lung tumor cell, the concentration of paclitaxel is highest in the nucleus. Therefore, it was of interest to examine the interaction of taxol with DNA and RNA in aqueous solution at physiological pH. Capillary electrophoresis and Fourier transform infrared (FTIR) difference spectroscopic methods were used to characterize the nature of drug–DNA and drug–RNA interactions and to determine the taxol binding site, the binding constant, the sequence selectivity, the helix stability, and the biopolymer secondary structure in the taxol–polynucleotide complexes in vitro. The FTIR spectroscopic studies were conducted with taxol/polynucleotide (phosphate) ratios of 1/80, 1/40, 1/20, 1/10, 1/4, and 1/2 with a final DNA(P) or RNA(P) concentration of 12.5 mmol/L, and capillary electrophoresis was performed after incubation of taxol with polynucleotides at ratios of 1/200 to 1/12 with a final polynucleotide concentration of 1.25 mmol/L. Taxol was shown to bind to DNA and RNA at G–C, A–T, or A–U bases and the backbone PO2 group. Two types of binding were observed for taxol–DNA with K1 = 1.3 × 104 L mol–1 and K2 = 3.5 × 103 L mol–1, whereas taxol–RNA complexes showed one type of binding with K = 1.3 × 104 L mol–1. The taxol–polynucleotide complexation is associated with a partial helix stabilization and no major alterations of B-DNA or A-RNA structure. Key words: DNA, RNA, taxol, binding site, binding constant, conformation, helix stability, electrophoresis, FTIR spectroscopy.

Theory of the influence of oligonucleotide chain conformation on double helix stability

Biopolymers ◽  
1971 ◽  
Vol 10 (10) ◽  
pp. 1809-1827 ◽  
Author(s):  
C. Delisi ◽  
D. M. Crothers
Keyword(s):  
Double Helix ◽  
Chain Conformation ◽  
Helix Stability

scholarly journals Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples

2020 ◽  
Vol 48 (6) ◽  
pp. 3304-3314 ◽  
Author(s):  
Agnieszka Ruszkowska ◽  
Milosz Ruszkowski ◽  
Jacob P Hulewicz ◽  
Zbigniew Dauter ◽  
Jessica A Brown
Keyword(s):  
Triple Helix ◽  
Double Helix ◽  
Structural Parameters ◽  
Three Dimensional ◽  
Accurate Estimation ◽  
Dna And Rna ◽  
Double Helices ◽  
Starting Point ◽  
Triple Helices ◽  
Rna Triple Helix

Abstract Three-dimensional structures have been solved for several naturally occurring RNA triple helices, although all are limited to six or fewer consecutive base triples, hindering accurate estimation of global and local structural parameters. We present an X-ray crystal structure of a right-handed, U•A-U-rich RNA triple helix with 11 continuous base triples. Due to helical unwinding, the RNA triple helix spans an average of 12 base triples per turn. The double helix portion of the RNA triple helix is more similar to both the helical and base step structural parameters of A′-RNA rather than A-RNA. Its most striking features are its wide and deep major groove, a smaller inclination angle and all three strands favoring a C3′-endo sugar pucker. Despite the presence of a third strand, the diameter of an RNA triple helix remains nearly identical to those of DNA and RNA double helices. Contrary to our previous modeling predictions, this structure demonstrates that an RNA triple helix is not limited in length to six consecutive base triples and that longer RNA triple helices may exist in nature. Our structure provides a starting point to establish structural parameters of the so-called ‘ideal’ RNA triple helix, analogous to A-RNA and B-DNA double helices.

scholarly journals Mendelian Disease caused by variants affecting recognition of Z-DNA and Z-RNA by the Zα domain of the double-stranded RNA Editing Enzyme ADAR

2019 ◽  
Author(s):  
Alan Herbert
Keyword(s):  
Double Helix ◽  
Protein Isoforms ◽  
Mendelian Disease ◽  
Loss Of Function ◽  
Double Stranded Rna ◽  
Parental Chromosome ◽  
Dna And Rna ◽  
Left Handed ◽  
Z Dna ◽  
Editing Enzyme

Variants in the human double-stranded RNA (dsRNA) editing enzyme ADAR produce three well-characterized rare Mendelian Diseases: Dyschromatosis Symmetrica Hereditaria (DSH)(OMIM: 127400), Aicardi-Goutières syndrome (AGS)(OMIM: 615010) and Bilateral Striatal Necrosis/Dystonia (BSD). ADAR encodes p150 and p110 protein isoforms. p150 incorporates the Zα domain that binds left-handed Z-DNA and Z-RNA with high affinity through contact of highly conserved residues with the DNA and RNA double-helix. In certain individuals, frameshift variants on one parental chromosome in the second exon of ADAR produce haploinsufficiency of p150 while maintaining normal expression of p110. In other individuals, loss of p150 expression from one chromosome allows mapping of Zα p150 variants from the other parental chromosome directly to phenotype. The analysis reveals that loss of function Zα variants cause dysregulation of innate interferon responses to dsRNA. This approach confirms a biological role for the left-handed conformation in human disease, further validating the power of Mendelian genetics to provide unambiguous answers. The findings reveal that the human genome encodes genetic information using both shape and sequence.

scholarly journals Double-stranded DNA fragment shows a significant decrease in double-helix stability after binding of monofunctional platinum amine compounds

1989 ◽  
Vol 111 (11) ◽  
pp. 4123-4125 ◽  
Author(s):  
Carla J. Van Garderen ◽  
Leo P. A. Van Houte ◽  
Hans Van den Elst ◽  
Jacques H. Van Boom ◽  
Jan Reedijk
Keyword(s):  
Double Helix ◽  
Double Stranded Dna ◽  
Helix Stability ◽  
Dna Fragment ◽  
Amine Compounds

scholarly journals Hachimoji DNA and RNA: A genetic system with eight building blocks

Science ◽  
2019 ◽  
Vol 363 (6429) ◽  
pp. 884-887 ◽  
Author(s):  
Shuichi Hoshika ◽  
Nicole A. Leal ◽  
Myong-Jung Kim ◽  
Myong-Sang Kim ◽  
Nilesh B. Karalkar ◽  
...  
Keyword(s):  
Double Helix ◽  
Building Blocks ◽  
Genetic System ◽  
Molecular Structures ◽  
Darwinian Evolution ◽  
Structural Requirements ◽  
Dna And Rna ◽  
The Stability ◽  
Dna Double Helix ◽  
Orthogonal Pairs

We report DNA- and RNA-like systems built from eight nucleotide “letters” (hence the name “hachimoji”) that form four orthogonal pairs. These synthetic systems meet the structural requirements needed to support Darwinian evolution, including a polyelectrolyte backbone, predictable thermodynamic stability, and stereoregular building blocks that fit a Schrödinger aperiodic crystal. Measured thermodynamic parameters predict the stability of hachimoji duplexes, allowing hachimoji DNA to increase the information density of natural terran DNA. Three crystal structures show that the synthetic building blocks do not perturb the aperiodic crystal seen in the DNA double helix. Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. These results expand the scope of molecular structures that might support life, including life throughout the cosmos.

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