Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases

Abstract

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—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–π 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. © 2002 Wiley Periodicals, Inc. Biopoly (Nucleic Acid Sci) 61: 3–31, 2002; DOI 10.1002/bip.10048

(G–H) • –C and G–(C–H) • radicals derived from the guanine·cytosine base pair cause DNA subunit lesions

“…Our predicted G⅐C dissociation energy (30). These authors estimate the Hartree-Fock limit to be 24.6 kcal͞mol, the basis set limit for MP2 to be 25.8 kcal͞mol, and the final estimated D e to be 26.3 kcal͞mol.…”

“…Complexation energies upon base pair formation have also been computed for both of the DNA base pairs (26)(27)(28)(29)(30)(31), and electron affinities of the single bases (32) and base pairs have been evaluated (27,33).…”

Infrared Absorption Detection of Metal Ion-Deoxyguanosine Monophosphate Binding: Experimental and Theoretical Study

“…[1][2][3][4][5][6] A vast number of experimental and theoretical studies have been dedicated to metal interactions with nucleic acids and their components. [5][6][7][8][9][10] In the present work we systematically investigate interactions of some common metal ions with deoxyguanosine monophosphate (dGMP) as a model system, in order to better explain previously observed changes in infrared absorption (IR) spectra of nucleic acids upon the interaction with the metals.…”

“…[32][33][34] Because of the computational limits, the modeling is often restricted to simplified nucleic acid components. This approach was proven to be very successful, although the preceding studies mostly concentrated on the geometry and energetics, 10,[32][33][34][35][36][37][38][39][40] whereas the vibrational analysis can be encountered less frequently. 36 Particularly for the nucleotide-metal ion complexes, we are not aware of any direct comparison of the computed and experimental IR data pursued in the present study.…”

“…1-6 A vast number of experimental and theoretical studies have been dedicated to metal interactions with nucleic acids and their components. [5][6][7][8][9][10] In the present work we systematically investigate interactions of some common metal ions with deoxyguanosine monophosphate (dGMP) as a model system, in order to better explain previously observed changes in infrared absorption (IR) spectra of nucleic acids upon the interaction with the metals.Being relatively simple and widely available, infrared spectroscopy provided precious information about the interaction of metal ions with nucleic acids (e.g., see refs 11-23). Detailed structural information could be obtained from the IR spectra when observed bands were assigned to particular bonds or DNA functional groups.…”