Assignments of phosphorus-31 NMR resonances in oligodeoxyribonucleotides: origin of sequence-specific variations in the deoxyribose phosphate backbone conformation and the phosphorus-31 chemical shifts of double-helical nucleic acids

Biochemistry ◽  
1988 ◽  
Vol 27 (19) ◽  
pp. 7223-7237 ◽  
Author(s):  
David G. Gorenstein ◽  
Stephen A. Schroeder ◽  
Josepha M. Fu ◽  
James T. Metz ◽  
Vikram Roongta ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Chemical Shifts ◽  
Phosphate Backbone ◽  
Backbone Conformation

scholarly journals Classification of RNA backbone conformation into rotamers using 13C′ chemical shifts: How far we can go?

2019 ◽  
Author(s):  
A. A. Icazatti ◽  
J.M. Loyola ◽  
I. Szleifer ◽  
J.A. Vila ◽  
O. A. Martin
Keyword(s):  
Chemical Shifts ◽  
Conformational Space ◽  
Phosphate Backbone ◽  
Ribose Phosphate ◽  
Conformational Preferences ◽  
Backbone Conformation ◽  
Rna Backbone ◽  
Rna Backbone Conformation ◽  
Torsional Angles

ABSTRACTThe conformational space of the ribose–phosphate backbone is very complex as is defined in terms of six torsional angles. To help delimit the RNA backbone conformational preferences 46 rotamers have been defined in terms of the these torsional angles. In the present work, we use the ribose experimental and theoretical 13C′ chemical shifts data and machine learning methods to classify RNA backbone conformations into rotamers and families of rotamers. We show to what extent the use of experimental 13C′ chemical shifts can be used to identify rotamers and discuss some problem with the theoretical computations of 13C′ chemical shifts.

Temperature dependence of the phosphorus-31 chemical shifts of nucleic acids. A probe of phosphate ester torsional conformations

Biochemistry ◽  
1976 ◽  
Vol 15 (17) ◽  
pp. 3796-3803 ◽  
Author(s):  
David G. Gorenstein ◽  
John B. Findlay ◽  
Robert K. Momii ◽  
Bruce A. Luxon ◽  
Debojyoti Kar
Keyword(s):  
Nucleic Acids ◽  
Temperature Dependence ◽  
Chemical Shifts ◽  
Phosphate Ester

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.

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

Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations

2013 ◽  
Vol 9 (3) ◽  
pp. 1641-1656 ◽  
Author(s):  
Jana Přecechtělová ◽  
Markéta L. Munzarová ◽  
Juha Vaara ◽  
Jan Novotný ◽  
Martin Dračínský ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Dft Calculations ◽  
Chemical Shifts

Separation of Nucleic Acids Using Single- and Multimodal Chromatography

2018 ◽  
Vol 20 (1) ◽  
pp. 49-55 ◽  
Author(s):  
Tiago Matos ◽  
Leif Bülow
Keyword(s):  
Nucleic Acids ◽  
Chemical Properties ◽  
Single Mode ◽  
Major Groove ◽  
Base Pairs ◽  
Chromatographic Separations ◽  
Multimodal Chromatography ◽  
Phosphate Backbone ◽  
Target Molecules ◽  
Polymerase Chain

The needs for purified nucleic acids for preparative and analytical applications have increased constantly, demanding for the development of new and more efficient methods for their recovery and isolation. DNA molecules harbour some intrinsic chemical properties that render them suitable for chromatographic separations. These include a negatively charged phosphate backbone as well as a hydrophobic character originating mainly from the major groove of DNA which exposes the base pairs on the surface of the molecule. In addition, single stranded DNA often allows for a free exposure of the hydrophobic aromatic bases. In this review, multimodal chromatography (MMC) has been evaluated as an alternative tool for complex separations of nucleic acids. MMC embraces more than one kind of interaction between the chromatographic ligand and the target molecules. These resins have often proved superior to conventional single-mode chromatographic materials for DNA isolation, including, e.g., the purification of plasmid DNA from crude cell lysates and for the preparation of DNA fragments before or after a polymerase chain reaction (PCR).

Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment

2012 ◽  
Vol 18 (39) ◽  
pp. 12372-12387 ◽  
Author(s):  
Judith M. Fonville ◽  
Marcel Swart ◽  
Zuzana Vokáčová ◽  
Vladimír Sychrovský ◽  
Judit E. Šponer ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Nucleic Acids ◽  
Density Functional ◽  
Chemical Shifts ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Comparison With Experiment
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