Dinucleotides - Introduction

    One of the most important interactions that influence the structure of DNA is that which occurs between the nucleobases. The bases are involved in two primary types of interactions: hydrogen bonding and base stacking. In duplexes, bases on one strand can hydrogen bond to a base on another strand. The bases also stack on top of each other within their own strands.
    In this section, the gas-phase conformations of 16 deprotonated dinucleotide ions are presented. The conformations were determined by measuring collision cross sections of each ion using a MALDI-Sector instrument and comparing them to cross sections obtained for theoretical structures calculated by molecular mechanics.
Shown at right is a simple schematic of the deprotonated dinucleotides. Of particular importance is the interaction between two bases on a single strand, without the influence of base pairing from a second strand.

More detailed information can be found in:

"Gas-Phase Conformational and Energetic Properties of Deprotonated Dinucleotides" J. Gidden and M. T. Bowers Eur. Phys. J. D 2002, 20, 409-419

"Gas-Phase Conformations and Folding Energetics of Oligonucleotides: dTG- and dGT-" Jennifer Gidden, John E. Bushnell, and Michael T. Bowers J. Am. Chem. Soc. 2001, 123, 5610-5611