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