Effect of thymine tract length on the structure and stability of model telomeric sequences.
DNA from the telomeres at the ends of eukaryotic chromosomes contains a stretch of simple tandemly repeated sequences in which clusters of G residues alternate with clusters of T/A sequences along one DNA strand. Model telomeric G-clusters form four-stranded structures in Na+ or K+, stabilized by Hoogsteen pairing between G bases. DNA containing a single copy of the G-cluster can self-associate to form tetramers, with a parallel-stranded, right-handed helical structure. Two copies of the 3'-terminal G strand form a folded-back hairpin that dimerizes to create an antiparallel quadruplex structure. We show here that the tetrameric structure is strongly influenced by the T residue flanking either side of the G-cluster. The parallel tetraplex formed by single copies of the sequences dTnG4 is most stable for n = 1 and least stable for n = 8, the longest tract we have studied. At least two thymine residues are required to allow formation of antiparallel folded-back hairpin dimers from two-copy oligomers of sequence d(TnG4)2 in Na+; additional T's destabilize this structure. In K+, the predominant structure formed is the four-stranded parallel tetramer in all cases. Kinetic analysis indicates that the quadruplex structure formed by Oxytricha telomeric DNA overhangs in the presence of Na+ arises by dimerization of two Hoogsteen base-paired hairpins, with a relatively low energy barrier.
Guo
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Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.
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Kallenbach
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D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D004355:Drug Stability; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D046911:Macromolecular Substances; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011188:Potassium / Q000494:pharmacology; D012964:Sodium / Q000494:pharmacology; D016615:Telomere / Q000737:chemistry*; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry*
D046911:Macromolecular Substances; D009838:Oligodeoxyribonucleotides; D004247:DNA; D012964:Sodium; D013941:Thymine; D011188:Potassium