Triple-helix formation is compatible with an adjacent DNA protein complex

• Published in: Biochemistry (Easton) 1992-02, Vol.31 (4), p.993-998
• Main Authors: Huang, Chiao Chain, Nguyen Dat, Martinez, Ricardo, Edwards, Cynthia A
• Format: Article
• Language: English
• Subjects: Analytical, structural and metabolic biochemistry; Animals; Base Sequence; Binding and carrier proteins; Binding Sites; Binding, Competitive; Biological and medical sciences; DNA, Viral - chemistry; DNA-Binding Proteins - chemistry; Fundamental and applied biological sciences. Psychology; Kinetics; Molecular Sequence Data; Nucleic Acid Conformation; Proteins; Pyrimidine Nucleotides - chemistry; Pyrimidines - chemistry; Simplexvirus - chemistry; Simplexvirus - genetics; Viral Proteins - chemistry
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi00119a007

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.