Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Understanding the Origin of Structural Diversity of DNA Double Helix

Journal Article · · Computation
 [1];  [2];  [1];  [1];  [1];  [1]; ORCiD logo [3];  [3]
  1. Autonomous Univ. of Puebla (Mexico). Physics and Mathematics Dept.
  2. Argonne National Lab. (ANL), Argonne, IL (United States)
  3. Autonomous Univ. of Puebla (Mexico). Institute of Physics
+ Show Author Affiliations

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
Benemerita Universidad Autonoma de Puebla (BUAP); USDOE
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1819677
Journal Information:
Computation, Journal Name: Computation Journal Issue: 9 Vol. 9; ISSN 2079-3197
Publisher:
MDPICopyright Statement
Country of Publication:
United States
Language:
English

References (23)

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? journal January 2000
The role of molecular structure of sugar-phosphate backbone and nucleic acid bases in the formation of single-stranded and double-stranded DNA structures: Role of Sugar-Phosphate Backbone and Bases in Sequence Dependence of DNA journal March 2014
Chemistry with ADF journal January 2001
Effect of the damping function in dispersion corrected density functional theory journal March 2011
DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates journal January 2010
The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals journal July 2007
Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments journal February 2018
Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA journal November 2015
Effect of Microenvironment on the Geometrical Structure of d(A) 5 d(T) 5 and d(G) 5 d(C) 5 DNA Mini-Helixes and the Dickerson Dodecamer: A Density Functional Theory Study journal September 2020
Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions journal January 2006
Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid journal April 1953
Genetical Implications of the Structure of Deoxyribonucleic Acid journal May 1953
Parmbsc1: a refined force field for DNA simulations journal November 2015
DFT Study of B-like Conformations of Deoxydinucleoside Monophosphates Containing Gua and/or Cyt and their Complexes with Na + Cation journal April 2008
The Protein Data Bank journal January 2000
A unified dinucleotide alphabet describing both RNA and DNA structures journal May 2020
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures journal September 2003
DNA conformations and their sequence preferences journal May 2008
The Nucleic Acid Database: new features and capabilities journal October 2013
Generalized Gradient Approximation Made Simple journal October 1996
A DNA structural alphabet provides new insight into DNA flexibility journal January 2018
Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org journal August 2020
Analysis of the conformational features of Watson–Crick duplex fragments by molecular mechanics and quantum mechanics methods journal March 2016

Similar Records

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
DNA conformations
ab initio computations
density functional theory
deoxydinucleoside monophosphates
molecular mechanics
sequence dependence
sugar-phosphate backbone