Conformational flexibility of junctions between contiguous B- and Z-DNAs in supercoiled plasmids.
The junctions between contiguous right- and left-handed helical DNA segments in supercoiled plasmids are shown to exhibit both sequence- and superhelical-dependent conformational flexibility. The nonalternating (purine-pyrimidine) tetranucleotide d(G-A-T-C), which is imbedded within a (dC-dG) tract and exists as a junction at low-density values, may be adopting a left-handed helix under the influence of higher negative supercoiling. The effect of supercoiling on the transition from a right- to a left-handed state for (dC-dG)n inserts, where n = 16, 13, and 5, also was evaluated. Only moderate amounts of superhelicity (-0.03 to -0.075) are required for formation and stabilization of left-handed DNA even for the (dC-dG) region of 10 dC X dG base pairs. Finally, we demonstrate that junction formation within a BamHI restriction site causes a drastic inhibition (greater than 80%) of cleavage by this restriction endonuclease.
D004262:DNA Restriction Enzymes / Q000378:metabolism; D004278:DNA, Superhelical / Q000032:analysis*; D015245:Deoxyribonuclease BamHI; D015246:Deoxyribonuclease EcoRI; D004720:Endonucleases / Q000378:metabolism; D009690:Nucleic Acid Conformation; D010957:Plasmids; D011089:Polydeoxyribonucleotides / Q000032:analysis; D015719:Single-Strand Specific DNA and RNA Endonucleases
D004278:DNA, Superhelical; D011089:Polydeoxyribonucleotides; C019530:poly(dC-dG); D004720:Endonucleases; D004262:DNA Restriction Enzymes; D015245:Deoxyribonuclease BamHI; D015246:Deoxyribonuclease EcoRI; D015719:Single-Strand Specific DNA and RNA Endonucleases