Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases
Language English Country United States Media print
Document type Journal Article, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S., Research Support, U.S. Gov't, P.H.S., Review
Grant support
RCMI G1 2RR13459-21
CCR NIH HHS - United States
PubMed
11891626
DOI
10.1002/1097-0282(2001)61:1<3::aid-bip10048>3.0.co;2-4
PII: 10.1002/1097-0282(2001)61:1<3::AID-BIP10048>3.0.CO;2-4
Knihovny.cz E-resources
- MeSH
- DNA chemistry metabolism MeSH
- Electrons * MeSH
- Cations metabolism MeSH
- Nucleic Acid Conformation * MeSH
- Models, Molecular MeSH
- RNA chemistry metabolism MeSH
- Static Electricity MeSH
- Hydrogen Bonding MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
- Research Support, U.S. Gov't, P.H.S. MeSH
- Names of Substances
- DNA MeSH
- Cations MeSH
- RNA MeSH
This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years. We first explain advantages and limitations of modern QM calculations of nucleobases and provide a brief history of this still rather new field. Then we provide an overview of key electronic properties of standard and selected modified nucleobases, such as their charge distributions, dipole moments, polarizabilities, proton affinities, tautomeric equilibria, and amino group hybridization. Then we continue with hydrogen bonding of nucleobases, by analyzing energetics of standard base pairs, mismatched base pairs, thio-base pairs, and others. After this, the nature of aromatic stacking interactions is explained. Also, nonclassical interactions in nucleic acids such as interstrand bifurcated hydrogen bonds, interstrand close amino group contacts, C [bond] H...O interbase contacts, sugar-base stacking, intrinsically nonplanar base pairs, out-of-plane hydrogen bonds, and amino-acceptor interactions are commented on. Finally, we overview recent calculations on interactions between nucleic acid bases and metal cations. These studies deal with effects of cation binding on the strength of base pairs, analysis of specific differences among cations, such as the difference between zinc and magnesium, the influence of metalation on protonation and tautomeric equlibria of bases, and cation-pi interactions involving nucleobases. In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed.
References provided by Crossref.org
Hydrogen-Bonding Interactions of 8-Substituted Purine Derivatives
The accuracy of quantum chemical methods for large noncovalent complexes
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM
Molecular dynamics simulations and their application to four-stranded DNA
Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E