U. Dornberger et al., HAIRPIN-DIMER EQUILIBRIUM OF A PARALLEL-STRANDED DNA HAIRPIN - FORMATION OF A 4-STRANDED COMPLEX, Nucleic acids research, 25(4), 1997, pp. 822-829
The 24mer deoxyoligonucleotide 3'-d(T)(10)-5'-5'-d(C)(4)-d(A)(10)-3' (
psC4) with an uncommon 5'-p-5' phosphodiester linkage was designed to
enable the formation of a hairpin structure with unusual parallel-stra
nded stem, As reference hairpin structure with an antiparallel-strande
d stem, the 24mer 5'-d(T)(10)-d(C)(4)-d(A)(10)-3' (apsC4) was chosen,
The behaviour of these oligonucleotides at different temperatures, DNA
and salt concentrations was characterised by a combination of UV melt
ing, CD, CD melting, infrared and Raman spectroscopy, infrared melting
and analytical ultracentrifugation. The parallel-stranded hairpin str
ucture was found to be formed by psC4 only under conditions of low DNA
concentration and low salt concentration, Increase of the NaCl concen
tration beyond the physiological level or high DNA concentration suppo
rts the formation of intermolecular multi-stranded structures, The exp
erimental data are in agreement with a four-stranded complex formed by
two molecules of psC4. The base pairing model of this asymmetric four
-stranded complex is based on the pyrimidine motif of a triple helix w
ith two bifurcated hydrogen bonds at the O4 of the thymine each direct
ed towards one of the amino protons of both adenines, In contrast, the
reference oligonucleotide apsC4 forms only an antiparallel-stranded h
airpin under all experimental conditions.