DNA Electrochemistry through the Base Pairs Not the Sugar−Phosphate Backbone

2005 ◽  
Vol 127 (29) ◽  
pp. 10160-10161 ◽  
Author(s):  
Tao Liu ◽  
Jacqueline K. Barton
Keyword(s):  
Sugar Phosphate ◽  
Base Pairs ◽  
Phosphate Backbone ◽  
Dna Electrochemistry

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.

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

1-(2′-Deoxy-β-D-xylofuranosyl)cytosine: Base pairing of oligonucleotides with a configurationally altered sugar-phosphate backbone

1994 ◽  
Vol 77 (4) ◽  
pp. 883-896 ◽  
Author(s):  
Frank Seela ◽  
Karlheinz Wörner ◽  
Helmut Rosemeyer
Keyword(s):  
Sugar Phosphate ◽  
Base Pairing ◽  
Phosphate Backbone

DNA triplex formation of oligonucleotide analogs consisting of linker groups and octamer segments that have opposite sugar-phosphate backbone polarities

Biochemistry ◽  
1991 ◽  
Vol 30 (41) ◽  
pp. 9914-9921 ◽  
Author(s):  
Akira Ono ◽  
Ching Nien Chen ◽  
Lou Sing Kan
Keyword(s):  
Sugar Phosphate ◽  
Triplex Formation ◽  
Phosphate Backbone ◽  
Dna Triplex

NMR study of the effect of sugar-phosphate backbone ethylation on the stability and conformation of DNA double helix

Biochemistry ◽  
1987 ◽  
Vol 26 (13) ◽  
pp. 3807-3812 ◽  
Author(s):  
Pradip Pramanik ◽  
Lou Sing Kan
Keyword(s):  
Double Helix ◽  
Sugar Phosphate ◽  
Nmr Study ◽  
Phosphate Backbone ◽  
The Stability ◽  
Dna Double Helix

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 RNA structural motifs that entail hydrogen bonds involving sugar–phosphate backbone atoms of RNA

2010 ◽  
Vol 34 (5) ◽  
pp. 910 ◽  
Author(s):  
Nikolai B. Ulyanov ◽  
Thomas L. James
Keyword(s):  
Hydrogen Bonds ◽  
Sugar Phosphate ◽  
Structural Motifs ◽  
Phosphate Backbone ◽  
Rna Structural Motifs ◽  
Backbone Atoms
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