Residual Conformational Entropies on the Sugar–Phosphate Backbone of Nucleic Acids: An Analysis of the Nucleosome Core DNA and the Ribosome

2015 ◽  
Vol 119 (33) ◽  
pp. 10434-10447 ◽  
Author(s):  
Chi H. Mak ◽  
Levana L. Sani ◽  
Amber N. Villa
Keyword(s):  
Nucleic Acids ◽  
Sugar Phosphate ◽  
Nucleosome Core ◽  
Phosphate Backbone

scholarly journals Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

2008 ◽  
Vol 112 (27) ◽  
pp. 8188-8197 ◽  
Author(s):  
Daniel Svozil ◽  
Judit E. Šponer ◽  
Ivan Marchan ◽  
Alberto Pérez ◽  
Thomas E. Cheatham ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Nucleic Acids ◽  
Sugar Phosphate ◽  
Phosphate Backbone

scholarly journals Dioxaphosphorinane-Constrained Nucleic Acid Dinucleotides as Tools for Structural Tuning of Nucleic Acids

2012 ◽  
Vol 2012 ◽  
pp. 1-17 ◽  
Author(s):  
Dan-Andrei Catana ◽  
Brice-Loïc Renard ◽  
Marie Maturano ◽  
Corinne Payrastre ◽  
Nathalie Tarrat ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Secondary Structure ◽  
Nucleic Acids ◽  
Polymer Structure ◽  
Rational Approach ◽  
Sugar Phosphate ◽  
Torsion Angles ◽  
Sugar Moiety ◽  
Phosphate Backbone ◽  
Structure Stabilization

We describe a rational approach devoted to modulate the sugar-phosphate backbone geometry of nucleic acids. Constraints were generated by connecting one oxygen of the phosphate group to a carbon of the sugar moiety. The so-called dioxaphosphorinane rings were introduced at key positions along the sugar-phosphate backbone allowing the control of the six-torsion anglesαtoζdefining the polymer structure. The syntheses of all the members of the D-CNA family are described, and we emphasize the effect on secondary structure stabilization of a couple of diastereoisomers ofα,β-D-CNA exhibiting wether B-type canonical values or not.

The interaction of the 2′-OH group with the vicinal phosphate in ribonucleoside 3′-ethylphosphate drives the sugar-phosphate backbone into unique (S,ω−) conformational state

Tetrahedron ◽  
1995 ◽  
Vol 51 (43) ◽  
pp. 11775-11792 ◽  
Author(s):  
J. Plavec ◽  
C. Thibaudeau ◽  
G. Viswanadham ◽  
C. Sund ◽  
A. Sandström ◽  
...  
Keyword(s):  
Conformational State ◽  
Sugar Phosphate ◽  
Phosphate Backbone

scholarly journals Theoretical modelling of epigenetically modified DNA sequences

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 52 ◽  
Author(s):  
Alexandra Teresa Pires Carvalho ◽  
Maria Leonor Gouveia ◽  
Charan Raju Kanna ◽  
Sebastian K. T. S. Wärmländer ◽  
Jamie Platts ◽  
...  
Keyword(s):  
Molecular Mechanics ◽  
Dna Sequences ◽  
Base Pair ◽  
Density Functional ◽  
Epigenetic Modifications ◽  
Theoretical Modelling ◽  
Sugar Phosphate ◽  
Base Pairs ◽  
Phosphate Backbone ◽  
Modified Dna

We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts.

scholarly journals De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as Bio-Information Storage Molecules

Life ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 346
Author(s):  
Kevin G Devine ◽  
Sohan Jheeta
Keyword(s):  
Nucleic Acids ◽  
Genetic Information ◽  
De Novo ◽  
Chemical Properties ◽  
Amino Acid Sequences ◽  
Information Storage ◽  
Heterocyclic Base ◽  
Dna And Rna ◽  
Phosphate Backbone ◽  
Physical And Chemical

Modern terran life uses several essential biopolymers like nucleic acids, proteins and polysaccharides. The nucleic acids, DNA and RNA are arguably life’s most important, acting as the stores and translators of genetic information contained in their base sequences, which ultimately manifest themselves in the amino acid sequences of proteins. But just what is it about their structures; an aromatic heterocyclic base appended to a (five-atom ring) sugar-phosphate backbone that enables them to carry out these functions with such high fidelity? In the past three decades, leading chemists have created in their laboratories synthetic analogues of nucleic acids which differ from their natural counterparts in three key areas as follows: (a) replacement of the phosphate moiety with an uncharged analogue, (b) replacement of the pentose sugars ribose and deoxyribose with alternative acyclic, pentose and hexose derivatives and, finally, (c) replacement of the two heterocyclic base pairs adenine/thymine and guanine/cytosine with non-standard analogues that obey the Watson–Crick pairing rules. This manuscript will examine in detail the physical and chemical properties of these synthetic nucleic acid analogues, in particular on their abilities to serve as conveyors of genetic information. If life exists elsewhere in the universe, will it also use DNA and RNA?

scholarly journals Making Molecules with Clay: Layered Double Hydroxides, Pentopyranose Nucleic Acids and the Origin of Life

Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 19 ◽  
Author(s):  
Harold Bernhardt
Keyword(s):  
Nucleic Acids ◽  
Lipid Bilayers ◽  
Information Transfer ◽  
Prebiotic Synthesis ◽  
Base Pairing ◽  
Phosphate Backbone ◽  
The Origin Of Life ◽  
Double Hydroxide ◽  
Double Hydroxides ◽  
Purine Pyrimidine

A mixture of sugar diphosphates is produced in reactions between small aldehyde phosphates catalysed by layered double hydroxide (LDH) clays under plausibly prebiotic conditions. A subset of these, pentose diphosphates, constitute the backbone subunits of nucleic acids capable of base pairing, which is not the case for the other products of these LDH-catalysed reactions. Not only that, but to date no other polymer found capable of base pairing—and therefore information transfer—has a backbone for which its monomer subunits have a plausible prebiotic synthesis, including the ribose-5-phosphate backbone subunit of RNA. Pentose diphosphates comprise the backbone monomers of pentopyranose nucleic acids, some of the strongest base pairing systems so far discovered. We have previously proposed that the first base pairing interactions were between purine nucleobase precursors, and that these were weaker and less specific than standard purine-pyrimidine interactions. We now propose that the inherently stronger pairing of pentopyranose nucleic acids would have compensated for these weaker interactions, and produced an informational polymer capable of undergoing nonenzymatic replication. LDH clays might also have catalysed the synthesis of the purine nucleobase precursors, and the polymerization of pentopyranose nucleotide monomers into oligonucleotides, as well as the formation of the first lipid bilayers.

scholarly journals Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides

Molecules ◽  
2020 ◽  
Vol 25 (20) ◽  
pp. 4659 ◽  
Author(s):  
Steven Ochoa ◽  
Valeria T. Milam
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Chemical Structure ◽  
Chemical Diversity ◽  
Physiochemical Properties ◽  
Phosphate Backbone ◽  
Modified Nucleic Acids ◽  
Recent Developments ◽  
Diagnostic Applications

In the last three decades, oligonucleotides have been extensively investigated as probes, molecular ligands and even catalysts within therapeutic and diagnostic applications. The narrow chemical repertoire of natural nucleic acids, however, imposes restrictions on the functional scope of oligonucleotides. Initial efforts to overcome this deficiency in chemical diversity included conservative modifications to the sugar-phosphate backbone or the pendant base groups and resulted in enhanced in vivo performance. More importantly, later work involving other modifications led to the realization of new functional characteristics beyond initial intended therapeutic and diagnostic prospects. These results have inspired the exploration of increasingly exotic chemistries highly divergent from the canonical nucleic acid chemical structure that possess unnatural physiochemical properties. In this review, the authors highlight recent developments in modified oligonucleotides and the thrust towards designing novel nucleic acid-based ligands and catalysts with specifically engineered functions inaccessible to natural oligonucleotides.

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