RNA versus DNA G-Quadruplex: The Origin of Increased Stability

Chemistry : a European Journal
Francesco Zaccaria, Célia Fonseca Guerra

Abstract

DNA quadruplexes have been the subject of investigation because of their biological relevance and because of their potential application in supramolecular chemistry. Similarly, RNA quadruplexes are now gaining increasing attention. Although DNA and RNA quadruplexes are structurally very similar, the latter show higher stability. In this study we report dispersion-corrected density functional theory (DFT-D) quantum chemical calculations that were undertaken to understand the difference in stabilities of RNA and DNA quadruplexes. The smallest meaningful model of a stack of quartets, interacting with alkali metal cations, was simulated in an aqueous environment. The energy decomposition analysis allows for in-depth examination of the interaction energies, emphasising the role of noncovalent interactions and better electrostatics in determining RNA-GQs higher stabilities, particularly pinpointing the role of the extra 2'-OH groups. Furthermore, our computations present new insights on why the cation is required for self-assembly: unexpectedly the cation is not necessary to relieve the repulsion between the oxygen atoms in the central cavity, but it is needed to overcome the entropic penalty.

References

Mar 16, 2006·Journal of the American Chemical Society·Manuel RuedaModesto Orozco
Sep 7, 2006·Journal of Computational Chemistry·Stefan Grimme
Feb 27, 2007·Nature Chemical Biology·Sunita KumariShankar Balasubramanian
Dec 25, 2007·Nature Cell Biology·Stefan Schoeftner, Maria A Blasco
Feb 26, 2008·Journal of the American Chemical Society·Ramsey Ida, Gang Wu
Sep 5, 2008·The Journal of Physical Chemistry. B·Bruno PaganoFranca Fraternali
Feb 7, 2009·The Journal of Physical Chemistry. B·Chris M Olsen, Luis A Marky
Apr 2, 2009·Angewandte Chemie·Tushar van der WijstBernhard Lippert
Jul 4, 2009·The Journal of Physical Chemistry. B·Amit Arora, Souvik Maiti
Sep 9, 2009·Bioorganic & Medicinal Chemistry·Astrid JoachimiJörg S Hartig
Apr 24, 2010·Nucleic Acids Research·Gavin W CollieGary N Parkinson
Jun 24, 2010·Nucleic Acids Research·Dennis GomezPatrick Calsou
Aug 4, 2010·Proceedings of the National Academy of Sciences of the United States of America·Yan XuMakoto Komiyama
Mar 4, 2011·Journal of Computational Chemistry·Stefan GrimmeLars Goerigk
Oct 15, 2011·Chemistry : a European Journal·Célia Fonseca GuerraF Matthias Bickelhaupt
Oct 26, 2012·Journal of Nucleic Acids·Takashi Kawakami, Hiroshi Murakami
Mar 26, 2013·Chemistry & Biology·Kentaro TakahamaTakanori Oyoshi
Dec 2, 2014·Physical Chemistry Chemical Physics : PCCP·Lando P WoltersCélia Fonseca Guerra
May 18, 2016·Physical Chemistry Chemical Physics : PCCP·F ZaccariaC Fonseca Guerra
May 13, 2017·Physical Chemistry Chemical Physics : PCCP·Trevor A HamlinF Matthias Bickelhaupt

❮ Previous
Next ❯

Citations

Jan 12, 2020·Nature Protocols·Pascal VermeerenTrevor A Hamlin
Jul 10, 2020·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Olga A StasyukHalina Szatylowicz
Jun 18, 2020·International Journal of Molecular Sciences·Chiara Reina, Vincenzo Cavalieri
Sep 22, 2020·Physical Chemistry Chemical Physics : PCCP·C NieuwlandC Fonseca Guerra
Aug 14, 2020·Chemistry : a European Journal·Zheng WangQianming Chen
Dec 3, 2020·Nucleic Acids Research·Prakash KharelPavel Ivanov
Feb 18, 2021·Cell Chemical Biology·Pauline LejaultDavid Monchaud
Apr 4, 2021·International Journal of Molecular Sciences·Georgina BezziPablo Armas
Feb 10, 2021·Annual Review of Biophysics·Iker Ortiz de LuzuriagaAdrià Gil
Aug 27, 2021·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Francesco ZaccariaCélia Fonseca Guerra

❮ Previous
Next ❯

Software Mentioned

NOSYM
COSMO
ADF
Amsterdam Density Functional ( ADF )

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

Physical Chemistry Chemical Physics : PCCP
Francesco ZaccariaCélia Fonseca Guerra
Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry
Tushar van der WijstF Matthias Bickelhaupt
© 2022 Meta ULC. All rights reserved