Nucleic Acids Research, Vol 24, Issue 24 5004-5012, Copyright © 1996 by Oxford University Press
MC Shiber, EH Braswell, H Klump and JR Fresco
d(A-G)10 forms two helical structures at neutrality, at low ionic strength
a single-hairpin duplex, and at higher ionic strength a double- hairpin
tetraplex. An ionic strength-dependent equilibrium between these forms is
indicated by native PAGE, which also reveals additional single-stranded
species below 0.3 M Na+, probably corresponding to partially denatured
states. The equilibrium also depends upon oligomer concentration: at very
low concentrations, d(A-G)10 migrates faster than the random coil d(C-T)10,
probably because it is a more compact single hairpin; at high
concentrations, it co-migrates with the linear duplex d(A-G)10 x d(C-T)10,
probably because it is a two-hairpin tetraplex. Molecular weights measured
by equilibrium sedimentation in 0.1 M Na+, pH 7, reveal a mixture of
monomer and dimer species at 1 degree C, but only a monomer at 40 degrees
C; in 0.6 M Na+, pH 7, only a dimer species is observed at 4 degrees C.
That the single- and double- stranded species are hairpin helices, is
indicated by preferential S1 nuclease cleavage at the center of the
oligomer(s), i.e., the loop of the hairpin(s). The UV melting transition
below 0.3 M Na+ or K+, exhibits a dTm/dlog[Na+/K+] of 33 or 36 degrees C,
respectively, consistent with conversion of a two-hairpin tetraplex to a
single- hairpin duplex with extrahelical residues. When [Na+/K+] > or =
0.3 M, dTm/dlog [Na+/K+] is 19 or 17 degrees C, respectively, consistent
with conversion of a two-hairpin tetraplex directly to single strands. A
two- hairpin structure stabilized by G-tetrads is indicated by differential
scanning calorimetry in 0.15 M Na+/5 mM Mg2+, with deltaH of formation per
mole of the two-hairpin tetraplex of -116.9 kcal or -29.2 kcal/mol of
G-tetrad.
ARTICLES
Duplex-tetraplex equilibrium between a hairpin and two interacting hairpins of d(A-G)10 at neutral pH
Department of Molecular Biology, Princeton University, NJ 08544-1014, USA.
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