Factors influencing the extent and regiospecificity of cross-link formation between single-stranded DNA and reactive complementary oligodeoxynucleotides

• Published in: Biochemistry (Easton) Vol. 33; no. 1; pp. 375 - 383
• Main Authors: Tabone, John C, Stamm, Michael R, Gamper, Howard B, Meyer, Rich B
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 11.01.1994
• Subjects: Antineoplastic agents; Base Sequence; Binding Sites; Biological and medical sciences; Cross-Linking Reagents; Deoxyuridine - analogs & derivatives; Deoxyuridine - chemical synthesis; DNA, Single-Stranded - chemistry; General aspects; Indicators and Reagents; Medical sciences; Models, Molecular; Nucleic Acid Conformation; Oligodeoxyribonucleotides - chemistry; Pharmacology. Drug treatments; Structure-Activity Relationship; Antineoplastic agent; Alkylating agent; Antiviral; Crosslinking; Single stranded DNA; Antisense DNA; Mechanism of action; Oligodeoxyribonucleotide; In vitro; Regiospecificity
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi00167a048

Cross-link formation, within the duplex, by oligodeoxynucleotides containing a 5-[omega-(omega-haloacylamido)alkyl]-2'-deoxyuridine to a complementary oligodeoxynucleotide was investigated under conditions approximating the physiologic environment. The site and extent of crosslinking to the target strand were determined for several electrophilic haloacylamidoalkyl structures. The regiospecificity of alkylation was primarily determined by the length of the electrophilic haloacylamidoalkyl group, while the extent of reaction was dependent upon both the structure of the acylamidoalkyl group and the reactivity of the electrophile. Cross-linking was additionally modulated by the sequence of the duplex in the vicinity of the alkylation site. The exact placement of the electrophile adjacent to the targeted nucleophile, an N-7 group on a specific guanine base in the target strand, was the most important factor in determining the rate of reaction. With the optimal haloacylamidoalkyl structure and duplex sequence, the most rapid rate obtained was t1/2 = 1.3 h at 37 degrees C.