STRUCTURAL CHARACTERIZATION OF D(CAACCCGTTG) AND D(CAACGGGTTG) MINI-HAIRPIN LOOPS BY HETERONUCLEAR NMR - THE EFFECTS OF PURINES VERSUS PYRIMIDINES IN DNA HAIRPINS

The DNA decamers, d(CAACCCGTTG) and d(CAAC-GGGTTG) were studied in sol ution by proton and heteronuclear NMR, Under appropriate conditions of pH, temperature, salt concentration and DNA concentration, both decam ers form hairpin conformations with similar stabilities [Avizonis and Kearns (1995) Biopolymers, 35, 187-200], Both decamers adopt mini-hair pin loops, where the first and last four nucleotides are involved in W atson-Crick hydrogen bonding and the central two nucleotides, CC or GG respectively, form the loop, Through the use of proton-proton, proton -phosphorus and natural abundance proton-carbon NMR experiments, backb one torsion angles (beta, gamma and epsilon), sugar puckers and interp roton distances were measured, The nucleotides forming the loops of th ese decamers were found to stack upon one another in an L1 type of loo p conformation, Both show gamma(tr) and unusual beta torsion angles in the loop-closing nucleotide G(7), as expected for mini-hairpin loop f ormation, Our results indicate that the beta and epsilon torsion angle s of the fifth and sixth nucleotides that form the loop and the loop-c losing nucleotide G(7) are not in the standard trans conformation as f ound in B-DNA, Although the loop structures calculated from NMR-derive d constraints are not well defined, the stacking of the bases in the t wo different hairpins is different, This difference in the base stacki ng of the loop may provide an explanation as to why the cytosine-conta ining hairpin is thermodynamically more stable than the guanine-contai ning hairpin.