title: Nuclease S1-sensitive sites on superhelical DNA molecules carrying the LTR region of Moloney murine leukemia virus.
abstract: The long terminal repeat (LTR) from proviral DNA of Moloney murine leukemia virus (Mo-MLV) was cloned on a derivative of pBR322, and after introducing superhelical torsions into the resulting recombinant, the sites of conformational transition were investigated by the nuclease S1-digestion method. With an increase in the negative linking differences, fourteen dominant cutting sites were identified, of which two were mapped inside the LTR and one at the 3' end of the LTR. By searching the sequence data, all these sites were localized in the regions having either palindromic sequences or AT-rich sequences. Free energy calculation for the local secondary structure on one strand indicated that nuclease S1 attacked the palindromic sequence regions which could form relatively stable hairpin structures. Under the conditions used, no correlation was found between the S1-sensitive sites and the potential Z-DNA-forming regions, including those within the enhancer sequence.
mesh_terms: D001483:Base Sequence; D003201:Computers; D004262:DNA Restriction Enzymes; D004274:DNA, Recombinant; D004278:DNA, Superhelical / Q000378:metabolism*; D004279:DNA, Viral / Q000378:metabolism*; D004720:Endonucleases / Q000378:metabolism*; D008979:Moloney murine leukemia virus / Q000235:genetics*; D009690:Nucleic Acid Conformation; D010957:Plasmids; D012091:Repetitive Sequences, Nucleic Acid; D015719:Single-Strand Specific DNA and RNA Endonucleases
chemical_list: D004274:DNA, Recombinant; D004278:DNA, Superhelical; D004279:DNA, Viral; D004720:Endonucleases; D004262:DNA Restriction Enzymes; D015719:Single-Strand Specific DNA and RNA Endonucleases