HAIRPIN FORMATION IN D-AAGCTTAAGCTT UNDER HIGH-SALT CONDITIONS SHOWS UNUSUAL PROPERTIES

The hairpin-duplex equillibria of the dodecamer d-AAGCTTAAGCTT and int eraction of the duplex form with a pentapeptide, KGWGK, has been studi ed. UV thermal transitions are monophasic at low salt but biphasic at higher salt concentrations. At 10(-5) M or less oligomer concentration biphasic melting curves persist till 900 mM NaCl. The d(Tm)/d log(Na) for the duplex form is 12 degrees C and for the hairpin is 18 degree s C. The Delta H and Delta S values for duplex formation are low(-25 K cal/mole and -59 Cal/mole respectively). KGWGK binds to the duplex for m with a binding constant K = 3.4 X 10(5)M(-1) measured from fluoresce nce quenching of tryptophan. These unusual results are markedly differ ent from that reported for d-AGATCTAGATCT (Biochemistry 31, 6241-6245) and are discussed in terms of sequence dependence of loop folding and cruciform extrusion pathway of hairpin formation.