Hairpin formation in d-AAGCTTAAGCTT under high salt conditions shows unusual properties.
The hairpin-duplex equilibria 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(-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 degrees 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 form with a binding constant K = 3.4 x 10(5)M-1 measured from fluorescence quenching of tryptophan. These unusual results are markedly different 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.
Roy
K B
KB
Centre for Biotechnology, Jawaharlal Nehru University, New Delhi.
Kukreti
S
S
Chauhan
V S
VS
Rajeswari
M R
MR
D000595:Amino Acid Sequence; D001483:Base Sequence; D002021:Buffers; D006358:Hot Temperature; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D010710:Phosphates / Q000737:chemistry; D013056:Spectrophotometry, Ultraviolet
D002021:Buffers; D009838:Oligodeoxyribonucleotides; D010710:Phosphates