In vitro expansion of DNA triplet repeats with bulge binders and different DNA polymerases

• Published in: The FEBS journal Vol. 275; no. 18; pp. 4510 - 4521
• Main Authors: Ouyang, Di, Yi, Long, Liu, Liangliang, Mu, Hong-Tao, Xi, Zhen
• Format: Journal Article
• Language: English
• Published: Oxford, UK Oxford, UK : Blackwell Publishing Ltd 01.09.2008; Blackwell Publishing Ltd
• Subjects: Binding sites; Biochemistry; bulge binder; DNA - biosynthesis; DNA - chemistry; DNA - drug effects; DNA polymerase; DNA Replication; DNA slippage; DNA-Directed DNA Polymerase - metabolism; drug–DNA interaction; Glucosamine - chemistry; Glucosamine - pharmacology; Kinetics; Molecular biology; Molecular structure; Nucleic Acid Conformation; repeat sequences; Spiro Compounds - chemistry; Spiro Compounds - pharmacology; Templates, Genetic; Trinucleotide Repeat Expansion - drug effects
• ISSN: 1742-464X; 1742-4658
• DOI: 10.1111/j.1742-4658.2008.06593.x

The expansion of DNA repeat sequences is associated with many genetic diseases in humans. Simple bulge DNA structures have been implicated as intermediates in DNA slippage within the DNA repeat regions. To probe the possible role of bulged structures in DNA slippage, we designed and synthesized a pair of simple chiral spirocyclic compounds [Xi Z, Ouyang D & Mu HT (2006) Bioorg Med Che m Lett16, 1180-1184], DDI-1A and DDI-1B, which mimic the molecular architecture of the enediyne antitumor antibiotic neocarzinostatin chromophore. Both compounds strongly stimulated slippage in various DNA repeats in vitro. Enhanced slippage synthesis was found to be synchronous for primer and template. CD spectra and UV thermal stability studies supported the idea that DDI-1A and DDI-1B exhibited selective binding to the DNA bulge and induced a significant conformational change in bulge DNA. The proposed mechanism for the observed in vitro expansion of long DNA is discussed.