Effect of competing self-structure on triplex formation with purine-rich oligodeoxynucleotides containing GA repeats.
Competition between triplex formation with double-stranded DNA and oligonucleotide self-association was investigated in 23mer GA and GT oligonucleotides containing d(GA)5 or d(GT)5 repeats. Whereas triplex formation with GT oligonucleotides was diminished when temperature increased from 4 to 37 degrees C, triplex formation with GA oligonucleotides was enhanced when temperature increased within the same range due to the presence of competing intermolecular GA oligonucleotide self-structure. This self-structure was determined to be a homoduplex stabilized by the internal GA repeats. UV spectroscopy of these homoduplexes demonstrated a single sharp transition with rapid kinetics (Tm = 38.5-43.5 degrees C over strand concentrations of 0.5-4 microM, respectively, with transition enthalpy, delta H = -89 +/- 7 kcal/mol) in 10 mM MgCl2, 100 mM NaCl, pH 7.0. Homoduplex formation was strongly stabilized by multivalent cations (spermine > Mg2+ = Ca2+) and destabilized by low concentrations of monovalent cations (K+ = Li+ = Na+) in the presence of divalent cations. However, unlike GA or GT oligonucleotide-containing triplexes, the homoduplex formed even in the absence of multivalent cations, stabilized by only moderate concentrations of monovalent cations (Li+ > Na+ > K+). Through the development of multiple equilibrium states and the resulting depletion of free oligonucleotide, it was found that the presence of competing self-structure could decrease triplex formation under a variety of experimental conditions.
Noonberg
S B
SB
Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM Unité 201-CNRS UA 481, Paris, France.
François
J C
JC
Garestier
T
T
Hélène
C
C
D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000737:chemistry*; D011687:Purines / Q000737:chemistry*; D013816:Thermodynamics
D009841:Oligonucleotides; D011687:Purines; D004247:DNA; C030985:purine