Triple-helix formation is compatible with an adjacent DNA-protein complex.
The effect of oligonucleotide-directed triple-helix formation on the binding of a protein to an immediately adjacent sequence has been examined. A double-stranded oligonucleotide was designed with a target site for the binding of a pyrimidine oligonucleotide located immediately adjacent to the recognition sequence for the herpes simplex virus type 1 (HSV-1) origin of replication binding protein, which is encoded by the UL9 gene of HSV-1. Since the optimal conditions for the binding of the UL9 protein and the pyrimidine oligonucleotide to the duplex DNA are markedly different, a pyrimidine oligonucleotide was designed to optimize binding affinity and specificity for the target duplex oligonucleotide. Consideration was given to length and sequence composition in an effort to maximize triple-strand formation under conditions amenable to the formation of the UL9-DNA complex. Using gel mobility shift assays, a trimolecular complex composed of duplex DNA bound to both a third oligonucleotide strand and the UL9 protein was detected, indicating that the UL9-DNA complex is compatible with the presence of a triple helix in the immediately adjacent sequences.
Huang
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CC
Drug Discovery Systems Research Group, Genelabs Incorporated, Redwood City, California 94063.
Nguyen
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D
Martinez
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R
Edwards
C A
CA
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D004279:DNA, Viral / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011742:Pyrimidine Nucleotides / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry; D018139:Simplexvirus / Q000737:chemistry / Q000235:genetics*; D014764:Viral Proteins / Q000737:chemistry*
D004279:DNA, Viral; D004268:DNA-Binding Proteins; D011742:Pyrimidine Nucleotides; D011743:Pyrimidines; D014764:Viral Proteins; C064565:UL9 protein, Human herpesvirus 1