SLOW CONFORMATIONAL EXCHANGE IN DNA MINIHAIRPIN LOOPS - A CONFORMATIONAL STUDY OF THE CIRCULAR DUMBBELL D[PCGC-TT-GCG-TT]

In recent years various examples of highly stable two-residue hairpin loops (miniloops) in DNA have been encountered. As the derailed struct ure and stability of miniloops appear to be determined not only by the nature and sequence of the two bases in the loop, but also by the clo sing base pair, it is desirable to carry out in-depth studies of espec ially designed small model DNA compounds. Therefore, a circular DNA du mbbell-like molecule is tailored to consist of a stem of three Watson- Crick base pairs, flanked on each side by a minihairpin loop. The resu lting circular DNA decamer 5'-d[pCGC-TT-GCG-TT]-3'(I) is studied in so lution by means of nmr spectroscopy. At a temperature of 269 K the mol ecule occurs in a 50/50 mixture of two dumbbell structures (denoted L2 L2 and L2L4). L2L2 contains three Watson-Crick C-G base pairs and two two-residue loops (H2-family type) in opposite parts of the molecule. On raising the temperature from 269 to 314 K, the L2L4 conformer becom es increasingly dominant (95% at 314 K). This conformer has a partiall y disrupted closing G-C base pair in the 5'-GTTC-3' loop with only one remaining solvent-accessible hydrogen bond between NHalpha, of the C( 1) and O6 of the guanine G(8), whereas the opposite 5'-CTTG-3' loop re mains stable. The disruption of the C(1)-G(8) basepair in the L2L4 for m is correlated with the presence of a syn orientation for the C(1) ba se at the 5'-3' loop-stem junction in the 5'-GTTC-3' loop. The two con formers, L2L2 and L2L4, occur in slow equilibrium (2-20 s(-1)). Modera te line broadening of specific H-1, C-13, and P-31 resonances of resid ues C(1), G(8), T(9), and T(10) at low temperatures, due to chemical e xchange between L2L2 and L2L4, show that the interconversion from an a nti to syn conformer in residue C(1) has a small local effect on the s tructure of the dumbbell. T-1 relaxation measurements, chemical-shift considerations, and complete bandshape calculations of the exchange pr ocess of the G(8) imino proton reveal a possibility for the existence of multiconformational states in the anti-syn equilibrium. (C) 1995 Jo hn Wiley & Sons, Inc.