Electronic Interactions in DNA

Working at the Interface of Organic Chemistry and DNA Biophysics

The hydrogen-bonded base pairs which constitute the core of duplex DNA form an extended one-dimensional π-stacked array with an average stacking distance of 3.4 Å. This ordered structure is found nowhere else in nature and thus has a special fascination for both biologists and chemists. The electronic interactions within genomic DNA are far too complex to be unraveled experimentally. Thus we have adopted a bottom-up approach to the study of electronic interactions in small synthetic DNA fragments containing as few as two-base pairs. In our laboratory, small synthetic oligonucleotides are designed, synthesized, and characterized by a variety of spectroscopic methods. The oligonucleotides are then employed in a number of studies including of photoinduced electron transfer, molecular assembly, thymine photodimerization, and excitonic interactions between adjacent bases.

We have employed synthetic DNA dumbbells, hairpins, and capped hairpins in our studies. These constructs possess a base-paired domain consisting of two or more base pairs connected by short linkers or possessing capping groups and are designed for the purposes of specific studies, as described below. These novel structures are characterized spectroscopically and their structures explored by means of molecular dynamics simulations (in collaboration with the Schatz group). The structures of several hairpins have been determined in solution using 1H NMR data with constrained molecular dynamics and in the solid state by means of X-ray crystallography. We have also studied the hydrophobic association of hairpins and dumbbells having large hydrophobic linkers.

The principle objective of our studies is elucidation of the mechanism and dynamics of photoinduced electron transfer in DNA. The possibility that the π-stacked base pairs of DNA might serve as a pathway for charge transport was advanced over 40 years ago. However, only recently have experimental techniques become available of the direct observation of the transport of positive charge (holes) or negative charge (electrons) across base pair domains of variable length and base sequence. Our studies employ organic chromophores located either at the ends or within the interior of a base pair domain. Electronic excitation of the chromophore initiates the electron transfer process. We have recently determined rate constants for base-to-base hole hopping in poly(adenine) and poly(guanine) sequences (in collaboration with the Wasielewski group). Similar experiments for base-to-base electron hopping are in progress. We work closely with theoretical chemists in the interpretation of our experimental results.

A second objective of our studies is developing an understanding of the behavior of electronically excited bases. Photodimerization of thymine is a major cause of DNA mutagenesis upon exposure to ultraviolet light. The product structure and efficiency of TT dimerization has been studied in a variety single strand and duplex structures and the results correlated with distributions of ground state TT geometries (in collaboration with Schatz). Dimerization in isolated TT and TTT steps is found to be strongly dependent upon the identities of the flanking bases and also the rigidity of the DNA backbone. Electronic interactions between stacked bases are being investigated using fluorescent base analogs which can replace a normal, non-fluorescent base within a stable DNA duplex structure. Alkane and polyether hairpin linkers are used in these studies to avoid competitive light absorption by the linker.