DNA is a relatively simple polymer composed of repeating nucleotide units. Each nucleotide contains a phosphate group, a sugar, and a pyridine or purine base. A simple schematic of a DNA strand and the 4 common bases are shown at right.
    Hydrogen bonding between complimentary bases on two DNA strands (A·T and C·G) leads to duplex formation and the famous double-helix structure described by Watson and Crick. Additional studies, however, have shown that DNA actually forms a variety of helical structures and can even form triplexes and quadruplexes. These various helical structures are the result of variations in the structures of the nucleotides (in particular, the conformation of the sugar and the relative positions of the bases with respect to the sugars) [Sinden, R.R. DNA Structure and Function; Academic Press: San Diego, 1994]. The transition from a right-handed "B" helix is accompanied by a change in the sugar pucker and a rotation of a base. A change in sugar pucker also accompanies the transition of a "B" helix into a more compact "A" helix. Protonation of adenine (A) leads to the formation of A+·C and A+·G base pairs, instead of the "normal" A·T pairs. Protonation of cytosine (C) is essential for the stabilization of triplexes.
    Most structural studies of DNA are performed in the condensed phase using X-ray crystallography or multidimensional NMR analysis. However, recent advances in ionization sources (such as MALDI and ESI) have led to an increase in the number of gas-phase studies on DNA using mass spectrometry. There has also been an increase in the number of studies involving the theoretical modeling of DNA structures. Gas-phase experiments are ideal for direct comparison with these theoretical investigations.
    We have used mass spectrometry and ion mobility methods to investigate the conformational and energetic properties of a series of mono-, di-, and trinucleotides. Questions concerning structural differences between protonated and deprotonated nucleotides, base-base interactions, and zwitterion formation are addressed.

  • Mononucleotide Structures
  • Hydration of Mononucleotides
  • Dinucleotides
  • Trinucleotides
  • Duplex Structures
  • Quadruplex Structures

Bowers group members who have worked on these projects include