TITLE

Unveiled electric profiles within hydrogen bonds suggest DNA base pairs with similar bond strengths

AUTHOR(S)
Ruiz-Blanco, Y. B.; Almeida, Y.; Sotomayor-Torres, C. M.; García, Y.
PUB. DATE
October 2017
SOURCE
PLoS ONE;10/05/2017, Vol. 12 Issue 10, p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Electrical forces are the background of all the interactions occurring in biochemical systems. From here and by using a combination of ab-initio and ad-hoc models, we introduce the first description of electric field profiles with intrabond resolution to support a characterization of single bond forces attending to its electrical origin. This fundamental issue has eluded a physical description so far. Our method is applied to describe hydrogen bonds (HB) in DNA base pairs. Numerical results reveal that base pairs in DNA could be equivalent considering HB strength contributions, which challenges previous interpretations of thermodynamic properties of DNA based on the assumption that Adenine/Thymine pairs are weaker than Guanine/Cytosine pairs due to the sole difference in the number of HB. Thus, our methodology provides solid foundations to support the development of extended models intended to go deeper into the molecular mechanisms of DNA functioning.
ACCESSION #
125495927

 

Related Articles

  • Development of ABEEM σπ polarizable force field for oxidized adenine base pairs: investigation of the interaction and mutagenic mechanism. Liu, Cui; Wang, Yang; Zhao, Dong-xia; Gong, Li-dong; Yang, Zhong-zhi // Theoretical Chemistry Accounts: Theory, Computation, & Modeling;Apr2014, Vol. 133 Issue 4, p1 

    Hydrogen-bonding and stacking interactions play a unique role for structure and replication of DNA. When adenine in DNA is oxidized, it increases the number of hydrogen bond donor and acceptor sites, and may lead to various mutations. 8-oxo-A is the most common oxidative product of adenine....

  • Calculating Distortions of Short DNA Duplexes with Base Pairing Between an Oxidatively Damaged Guanine and a Guanine. Suzuki, Masayo; Kino, Katsuhito; Morikawa, Masayuki; Kobayashi, Takanobu; Miyazawa, Hiroshi // Molecules;Aug2014, Vol. 19 Issue 8, p11030 

    DNA is constantly being oxidized, and oxidized DNA is prone to mutation; moreover, guanine is highly sensitive to several oxidative stressors. Several oxidatively damaged forms of guanine-including 2,2,4-triamino-5(2H)-oxazolone (Oz), iminoallantoin (Ia), and spiroiminodihydantoin (Sp)-can be...

  • MODELING DNA THERMAL DENATURATION AT THE MESOSCOPIC LEVEL. DOLFIN, MARINA; LACHOWICZ, MIROSŁAW // Discrete & Continuous Dynamical Systems - Series B;Oct2014, Vol. 19 Issue 8, p2469 

    In this paper a mesoscopic approach is proposed to describe the process of breaking of hydrogen bonds during the DNA thermal denaturation, also known as DNA melting. A system of integro-differential equations describing the dynamic of the variable which characterizes the opening of the base...

  • Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing. Nakano, Shu-ichi; Sugimoto, Naoki // Molecules;Aug2014, Vol. 19 Issue 8, p11613 

    The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic...

  • DNA terminal base pairs have weaker hydrogen bonds especially for AT under low salt concentration. Ferreira, Izabela; Amarante, Tauanne D.; Weber, Gerald // Journal of Chemical Physics;2015, Vol. 143 Issue 17, p1 

    DNA base pairs are known to open more easily at the helix terminal, a process usually called end fraying, the details of which are still poorly understood. Here, we present a mesoscopic model calculation based on available experimental data where we consider separately the terminal base pairs of...

  • Structure of the N6-adenine DNA methyltransferase M•TaqI in complex with DNA and a cofactor analog. Goedecke, Karsten; Pignot, Marc; Goody, Roger S.; Scheidig, Axel J.; Weinhold, Elmar // Nature Structural Biology;Feb2001, Vol. 8 Issue 2, p121 

    The 2.0 Å crystal structure of the N6-adenine DNA methyltransferase M•TaqI in complex with specific DNA and a nonreactive cofactor analog reveals a previously unrecognized stabilization of the extrahelical target base. To catalyze the transfer of the methyl group from the cofactor...

  • Syntheses and crystal structures of new aurate salts of adenine or guanine nucleobases. Savchenkov, Anton; Demina, Ludmila; Safonov, Alexey; Grigoriev, Mikhail; Solovov, Roman; Abkhalimov, Evgeny // Acta Crystallographica: Section C, Structural Chemistry;Feb2020, Vol. 76 Issue 2, p139 

    Two new gold(III) complexes with adenine or guanine nitrogenous bases as counter‐cations were synthesized. These are 6‐amino‐7H‐purine‐1,9‐diium tetrachloridogold(III) chloride monohydrate, (C5H7N5)[AuCl4]Cl·H2O, 1, and...

  • Expanded or Not? ZHARKOV, Dmitry O. // SCIENCE First Hand;2015, Vol. 40 Issue 1, p14 

    The article focuses on a research conducted by Floyd Romesberg which replicated DNA in E. coli bacteria with a pair of unnatural DNA bases X and Y. Topics discussed include incorporation of unnatural amino acids as alternative base pairs, formation of stable DNA base pairs without hydrogen...

  • Theoretical electrical conductivity of hydrogen-bonded benzamide-derived molecules and single DNA bases. Chen, Xiang // Journal of Biological Physics;Sep2013, Vol. 39 Issue 4, p607 

    A benzamide molecule is used as a 'reader' molecule to form hydrogen bonds with five single DNA bases, i.e., four normal single DNA bases A,T,C,G and one for 5methylC. The whole molecule is then attached to the gold surface so that a meta-molecule junction is formed. We calculate the...

  • The role of a diamondoid as a hydrogen donor or acceptor in probing DNA nucleobases. C. Maier, Frank; Sivaraman, Ganesh; Fyta, Maria // European Physical Journal E -- Soft Matter;Oct2014, Vol. 37 Issue 10, p1 

    Abstract.: It has been shown that diamondoids can interact with DNA by forming relatively strong hydrogen bonds to DNA units, such as nucleobases. For this interaction to occur the diamondoids must be chemically modified in order to provide donor/acceptor groups for the hydrogen bond. We show...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics