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Hairpin Formation In d-AAGCTTAAGCTT Under High Salt Conditions Shows Unusual Properties
Authors:Kunal B Roy  Shrikant Kukreti  V S Chauhan  Moganty R Rajeswari
Institution:1. Centre for Biotechnology;2. International Centre for Genetic Engineering and Biotechnology , New Delhi , 110 067
Abstract:Abstract

The hairpin-duplex equillibria of the dodecamer d-AAGCTTAAGCTT and interaction of the duplex form with a pentapeptide, KGWGK, has been studied. UV thermal transitions are monophasic at low salt but biphasic at higher salt concentrations. At 10?5M or less oligomer concentration biphasic melting curves persist till 900 mM NaCl. The d(Tm)/d log(Na+) for the duplex form is 12 °C and for the hairpin is 18 °C. The ΔH and ΔS values for duplex formation are low(-25 Kcal/mole and—59 Cal/mole respectively). KGWGK binds to the duplex form with a binding constant K = 3.4×105M?1measured from fluorescence quenching of tryptophan. These unusual results are markedly different from that reported for d-AGATCT- AGATCT (Biochemistry 31, 6241–6245) and are discussed in ternis of sequence dependence of loop folding and cruciform extrusion pathway of hairpin formation.
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