Studies of DNA dumbbells VII: Evaluation of the next nearest-neighbor sequence-dependent interactions in duplex DNA

Melting experiments were conducted oil 22 DNA dumbbells as a function of so lvent ionic strength from 25-115 mM Na+. The dumbbell molecules have short duplex regions comprised of 16-20 base pairs linked on both ends by T-4 sin gle-strand leaps. Only the 4-8 central base pairs of the dumbbell stems dif fer for different molecules, and the six base pairs on both sides of the ce ntral sequence and adjoining loops oil both ends are the same in every mole cule, Results of melting analysis on rite 22 new DNA dumbbells are combined with our previous results on 17 other DNA dumbbells, with stein lengths co ntaining from 14-18 base pairs, reported in the first article of this serie s (Doktycz, Goldstein, Paner; Gallo, and Benight, Biopoly 32, 1992, 849-864 ). The combination of results comprises a database of optical melting param eters for 39 DNA dumbbells in ionic strengths from 25-115 mM Na+. This data base is employed to evaluate the thermodynamics of singlet, doublet, and tr ipler sequence-dependent interactions in duplex DNA. Analysis of the 25 mM Na+ data reveals the existence of significant sequence-dependent triplet or next-nearest-neighbor inter-actions, The enthalpy of these interactions is evaluated for all possible triplets. Some of the tripler enthalpy values a re less than the uncertainty in their evaluation, indicating no measurable interaction for that particular sequence. This finding suggests that the th ermodynamic stability of duplex DNA depends on solvent ionic strength in a sequence-dependent manner. As a parr of the analysis, the nearest-neighbor (base pair doublet) interactions in 55, 85 and 115 mM Na+ are also reevalua ted from the larger database. (C) 2000 John Wiley & Sons, Inc.