A structural basis for S1 nuclease sensitivity of double-stranded DNA.
A protonated form of a cloned simple repeating DNA sequence d(TC)n X d(GA) is detectable in equilibrium with the usual Watson-Crick base-paired form at pHs up to 7. This form is anomalously sensitive to a variety of single-strand-specific endonucleases. The observed pH dependent protection of N-7 of dG residues within the insert suggests that these residues are either Hoogsteen or reverse Hoogsteen base-paired to protonated dC residues of the polypyrimidine strand. A structure in which dA:dT Watson-Crick base pairs alternate with Hoogsteen syndG:dCH+ pairs appears to be the most stereochemically acceptable structure consistent with the chemical properties of this protonated DNA. Protonated d(TC)n X d(GA)n interacts with an anti-Z DNA antibody raised against brominated d(GC)n X d(GC)n.
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Haniford
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Morgan
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D003001:Cloning, Molecular; D004247:DNA / Q000378:metabolism*; D004278:DNA, Superhelical / Q000378:metabolism; D004706:Endodeoxyribonucleases / Q000378:metabolism; D004720:Endonucleases / Q000378:metabolism*; D006863:Hydrogen-Ion Concentration; D008274:Magnesium / Q000494:pharmacology; D009690:Nucleic Acid Conformation; D010957:Plasmids; D011522:Protons; D012091:Repetitive Sequences, Nucleic Acid; D015719:Single-Strand Specific DNA and RNA Endonucleases
D004278:DNA, Superhelical; D011522:Protons; D004247:DNA; D004706:Endodeoxyribonucleases; D004720:Endonucleases; D015719:Single-Strand Specific DNA and RNA Endonucleases; D008274:Magnesium