Paranemic structures of DNA and their role in DNA unwinding.
A DNA structure is defined as paranemic if the participating strands can be separated without mutual rotation of the opposite strands. The experimental methods employed to detect paranemic, unwound, DNA regions is described, including probing by single-strand specific nucleases (SNN), conformation-specific chemical probes, topoisomer analysis, NMR, and other physical methods. The available evidence for the following paranemic structures is surveyed: single-stranded DNA, slippage structures, cruciforms, alternating B-Z regions, triplexes (H-DNA), paranemic duplexes and RNA, protein-stabilized paranemic DNA. The problem of DNA unwinding during gene copying processes is analyzed; the possibility that extended paranemic DNA regions are transiently formed during replication, transcription, and recombination is considered, and the evidence supporting the participation of paranemic DNA forms in genes committed to or undergoing copying processes is summarized.
Yagil
G
G
Department of Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
D000818:Animals; D001483:Base Sequence; D002875:Chromosomes / Q000648:ultrastructure; D004247:DNA / Q000187:drug effects / Q000378:metabolism / Q000648:ultrastructure*; D004265:DNA Helicases / Q000378:metabolism; D004261:DNA Replication; D004264:DNA Topoisomerases, Type I / Q000378:metabolism; D004250:DNA Topoisomerases, Type II / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000187:drug effects / Q000378:metabolism / Q000648:ultrastructure; D004278:DNA, Superhelical / Q000187:drug effects / Q000378:metabolism / Q000648:ultrastructure; D004268:DNA-Binding Proteins / Q000378:metabolism; D004720:Endonucleases / Q000378:metabolism; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009691:Nucleic Acid Denaturation; D010957:Plasmids; D014158:Transcription, Genetic
D004277:DNA, Single-Stranded; D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; D004247:DNA; D004720:Endonucleases; D004265:DNA Helicases; D004264:DNA Topoisomerases, Type I; D004250:DNA Topoisomerases, Type II