Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study

The Journal of Physical Chemistry. B
U Deva Priyakumar, Alexander D Mackerell

Abstract

DNA.RNA hybrid duplexes are biologically important molecules and are shown to have potential therapeutic properties. To investigate the relationship between structures, energetics, solvation and RNase H activity of hybrid duplexes in comparison with pure DNA and RNA duplexes, a molecular dynamics study using the CHARMM27 force field was undertaken. The structural properties of all four nucleic acids considered are in very good agreement with the experimental data. The backbone dihedral angles and the puckering of the (deoxy)ribose indicate that the purine rich strands retain their A-/B-like properties but the pyrimidine rich DNA strand undergoes A-B conformational transitions. The minor groove widths of the hybrid structures are narrower than those in the RNA duplex, a requirement for RNase H binding. In addition, sampling of noncanonical phosphodiester backbone dihedrals by the DNA strands, differential solvation properties and helical properties, most notably rise, are suggested to contribute to hybrids being RNase H substrates. Differential RNase H activity toward hybrids containing purine versus pyrimidine rich RNA strands is suggested to be due to sampling of values of the phosphodiester backbone dihedrals in the DNA stran...Continue Reading

References

Aug 1, 1988·Journal of Biomolecular Structure & Dynamics·R Lavery, H Sklenar
Feb 1, 1989·Journal of Biomolecular Structure & Dynamics·R Lavery, H Sklenar
Apr 25, 1994·Nucleic Acids Research·S R Sanghani, R Lavery
Mar 1, 1994·Biopolymers·E Stofer, R Lavery
Oct 5, 1993·Journal of Molecular Biology· Fedoroff OYuB R Reid
Apr 18, 1998·Nature Structural Biology·M BachelinH Kessler
Mar 1, 1985·Physical Review A: General Physics·W G Hoover
Apr 27, 1999·Journal of Biomolecular Structure & Dynamics·T E CheathamP A Kollman
Jun 22, 2000·Journal of Molecular Biology·C SudarsanakumarM Sundaralingam
Feb 15, 2001·Acta Crystallographica. Section D, Biological Crystallography·G W Han
Apr 20, 2001·International Journal of Biological Macromolecules·E HantzT Huynh Dinh
Jun 1, 2001·Journal of Biochemical and Biophysical Methods·E ZamaratskiJ Chattopadhyaya
Jul 27, 2001·Biochemistry·K Snoussi, J L Leroy
May 23, 2002·Journal of the American Chemical Society·Michael PetersenJens Peter Jacobsen
Oct 31, 2002·Journal of the American Chemical Society·Melanie A O'Neill, Jacqueline K Barton
Jun 6, 2003·Journal of the American Chemical Society·Brent M ZnoskoDouglas H Turner
Jul 23, 2003·Proceedings of the National Academy of Sciences of the United States of America·Gye Won HanRichard E Dickerson
Jan 30, 2004·Annual Review of Medicine·Stanley T Crooke
Nov 25, 2004·Nucleic Acids Research·Alberto PérezModesto Orozco
Mar 31, 2005·Journal of the American Chemical Society·Agnes NoyModesto Orozco
Apr 21, 2005·Journal of the American Chemical Society·Mafalda NinaSebastian Wendeborn
Sep 24, 2005·Current Medicinal Chemistry·T Aboul-Fadl
Mar 21, 2006·The Journal of Biological Chemistry·Alexander Rich

❮ Previous
Next ❯

Citations

Aug 10, 2015·Journal of Molecular Graphics & Modelling·Gorle Suresh, U Deva Priyakumar
Feb 7, 2014·Journal of the American Chemical Society·Li Li, Jack W Szostak
May 3, 2012·Journal of Computational Chemistry·Tomasz BereźniakPetra Imhof
Oct 16, 2012·Wiley Interdisciplinary Reviews. Computational Molecular Science·Xiao ZhuAlexander D Mackerell
Apr 7, 2011·Journal of Computational Chemistry·Elizabeth J DenningAlexander D Mackerell
Sep 23, 2010·Biophysical Journal·Ignacio FaustinoModesto Orozco
Oct 14, 2011·The Journal of Physical Chemistry. B·Smritimoy PramanikNaoki Sugimoto
Mar 21, 2018·The Journal of Biological Chemistry·Andrey G BaranovskiyTahir H Tahirov

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Methods : a Companion to Methods in Enzymology
Yaser Hashem, Pascal Auffinger
Journal of Computational Chemistry
B R BrooksM Karplus
© 2021 Meta ULC. All rights reserved