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

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 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

Double-helix PnLin chains: novel potential nonlinear optical materials

2018 ◽  
Vol 20 (18) ◽  
pp. 12618-12623 ◽  
Author(s):  
Yangyang Hu ◽  
Xiaodong Xu ◽  
Yingjie Jiang ◽  
Guiling Zhang ◽  
Weiqi Li ◽  
...  
Keyword(s):  
Circular Dichroism ◽  
Quantum Chemistry ◽  
Optical Materials ◽  
Nonlinear Optical ◽  
Double Helix ◽  
Nonlinear Optical Materials ◽  
Cd Spectra ◽  
Chemistry Method ◽  
Circular Dichroïsm ◽  
Quantum Chemistry Method

The structures, circular dichroism (CD) spectra and nonlinear optical (NLO) responses of a series of inorganic double-helix chains, PnLin (n = 6–12), have been investigated using the quantum chemistry method.

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 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.

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experiment

Biopolymers ◽  
2013 ◽  
pp. n/a-n/a ◽  
Author(s):  
Jiří Šponer ◽  
Judit E. Šponer ◽  
Arnošt Mládek ◽  
Petr Jurečka ◽  
Pavel Banáš ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Molecular Mechanics ◽  
Base Stacking ◽  
Dna And Rna

Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential

2011 ◽  
Vol 76 (11) ◽  
pp. 1347-1360 ◽  
Author(s):  
Irina V. Astakhova ◽  
T. Santhosh Kumar ◽  
Jesper Wengel
Keyword(s):  
Fluorescence Quenching ◽  
Double Helix ◽  
Quantum Yields ◽  
Complementary Dna ◽  
Dna And Rna ◽  
Rna Targets ◽  
Analytical Potential ◽  
Target Binding ◽  
Labeled Probe ◽  
Synthetic Oligonucleotides

Herein, a novel fluorescent nucleotide analogue, perylene-2′-amino-α-L-LNA, has been prepared and studied within synthetic oligonucleotides of different sequences. The phosphoramidite reagent was synthesized in 85% overall yield starting from 2′-amino-α-L-LNA nucleoside. Incorporation efficiency of the resulting perylene-2′-amino-α-L-LNA monomer (T*) into synthetic oligonucleotides was significantly improved by replacement of the typically used 1H-tetrazole activator with pyridine hydrochloride. Generally, oligonucleotides containing monomerT* showed high binding affinity towards complementary DNA and RNA targets, batochromically shifted excitation/emission wavelengths with respect to the often applied polyaromatic hydrocarbon pyrene, high fluorescent quantum yields and very low target detection limits (5–10 nM). Fluorescence of single stranded LNA/DNA mixmer oligonucleotide having two incorporations of monomersT* was quenched (quantum yield ΦF= 0.21) relative to duplexes of this probe with complementary DNA and RNA (ΦF= 0.42 and 0.35, respectively). On the contrary, a strong fluorescence quenching upon target binding was demonstrated by two short oligonucleotides of analogues sequences containing monomersT* at 5′- and 3′-terminal positions. We explain the hybridization-induced light-up effect observed for double-labeled probe by a reduction of fluorescence quenching due to precise positioning of the fluorophores within the double-stranded complexes. Furthermore, we propose that a covalent link between twoT* monomers in the double-labeled probe provides a remarkable degree of rigidity in the double helix which enforces positioning of the bulky perylene moieties in the nonpolar groove resulting in reduced fluorescence quenching.

scholarly journals Interaction of Antimicrobial Peptide Ponericin W1, Thanatin, and Mastatopara-S with Geotrichum citri-aurantii Genomic DNA

Foods ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1919
Author(s):  
Hongyan Zhang ◽  
Sha Liu ◽  
Xindan Li ◽  
Wenjun Wang ◽  
Lili Deng ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Double Helix ◽  
Membrane Integrity ◽  
Citrus Fruit ◽  
Base Pairs ◽  
Spectra Analysis ◽  
Dna And Rna ◽  
Visible Spectra ◽  
Double Helix Structure

Antimicrobial peptides of mastatopara-S (M-S), thanatin, and ponericin W1(P W1) were able to disrupt the membrane integrity and alter the morphology of the hyphae of Geotrichum citri-aurantii and then reduced the sour rot of citrus fruit. In order to understand the mechanisms of thanatin, P W1 and M-S other than membrane disruption, the interaction betwixt the peptides and G. citri-aurantii DNA were investigated in this research. The laser confocal microscopy found that P W1, thanatin, and M-S could penetrate the cell membrane. Gel retardation assay demonstrated that P W1, thanatin, and M-S could bind to the G. citri-aurantii genomic DNA in vitro. UV-visible spectra and fluorescence spectra analysis further confirmed that the peptides can bind to the DNA, and then insert into the base pairs in the DNA helix, followed by wrecking the double-helix structure. In addition, M-S, thanatin, and P W1 can suppress the synthesis of DNA and RNA of G. citri-aurantii.

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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