Solution structure of the aminoacyl-capped oligodeoxyribonucleotide duplex(W-TGCGCAC)(2)

Reported here is the solution structure of the aminoacyl-DNA duplex (W-TGCG CAC)(2). This duplex forms a continuously pi-stacked helix consisting of bo th nucleobases and amino acid side chains. According to NMR and UV analyses , the duplex melts in a cooperative transition and with 1.3-1.8% greater hy perchromicity than the control duplex (TGCGCAC)(2). A van't Hoff analysis o f UV melting points at different concentrations shows that the two tryptoph an residues contribute 4.8 kcal/mol to the Delta H degrees of complex forma tion at 10 mM salt concentration and less than 1 kcal/mol at 150 mM I salt. The entropic cost for duplex association in the presence of the amino acid residues is 13 cal/molK greater than that for the control at 10 mM salt co ncentration, and 3 cal/molK lower than that of the control at 0.15 ionic st rength. The conformation of W-TGCGCAC in duplex form, determined via restra ined torsion angle molecular dynamics, shows an undisturbed B-form DNA dupl ex with dangling 3'-termini. The tryptophanyl residue at the 5'-terminus pa cks tightly against T2 and the proximal part of adenine, without engaging i n hydrogen bonding. While not providing strong enthalpic net stabilization of the duplex, the tryptophan "cap" on the duplex does seem to reduce the f raying at the termini, indicating a subtle balance of entropic and enthalpi c factors contributing to the molecular dynamics. The structure also shows that, at least in the present sequence context, stacking on the terminal ba se pair is more favorable than intercalation, probably because the enthalpi c cost associated with breaking up the stacking between DNA base pairs cann ot be paid for by favorable pi-stacking interactions with the indole ring o f tryptophan. These results are of importance for understanding stacking in teractions in protein-DNA complexes, particularly those in enzyme-substrate complexes involving exposed nucleobases.