title: Methods to detect replication-dependent and replication-independent DNA structure-induced genetic instability.
abstract: DNA can adopt a variety of alternative secondary (i.e., non-B DNA) conformations that play important roles in cellular metabolism, including genetic instability, disease etiology and evolution. While we still have much to learn, research in this field has expanded dramatically in the past decade. We have summarized in our previous Methods review (Wang et al., Methods, 2009) some commonly used techniques to determine non-B DNA structural conformations and non-B DNA-induced genetic instability in prokaryotes and eukaryotes. Since that time, we and others have further characterized mechanisms involved in DNA structure-induced mutagenesis and have proposed both replication-dependent and replication-independent models. Thus, in this review, we highlight some current methodologies to identify DNA replication-related and replication-independent mutations occurring at non-B DNA regions to allow for a better understanding of the mechanisms underlying DNA structure-induced genetic instability. We also describe a new web-based search engine to identify potential intramolecular triplex (H-DNA) and left-handed Z-DNA-forming motifs in entire genomes or at selected sequences of interest.
authors: Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States.
authors: Guliang
authors: G
authors: Wang
authors: Sally
authors: S
authors: Gaddis
authors: Karen M
authors: KM
authors: Vasquez
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004261:DNA Replication; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D005821:Genetic Techniques; D042822:Genomic Instability; D020407:Internet; D009690:Nucleic Acid Conformation; D057386:Search Engine
keywords: 2-D gel electrophoresis; DNA structure; Genetic instability; Mutation; Replication; Search engine
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