Specific recognition of napthyridine-based ligands toward guanine-containing bulges in RNA duplexes and RNA-DNA heteroduplexes.
Mismatched bulges in nucleic acid constructs are important in the recognition event between biological molecules. Herein, it is observed that napthyridine dimer 2 is able to specifically bind G-G mismatches in all nucleic acid constructs comprising of RNA-RNA, RNA-DNA and DNA-DNA duplexes. However, the binding affinity of 2 is strongest toward DNA duplex, followed by RNA-DNA heteroduplex and RNA duplex being the weakest binding partner. Nonetheless, this binding behavior suggests that the binding process primarily occurs between the guanine base pairs and the napthyridine moiety, and is independent of the tertiary structure of the nucleic acid duplexes.
Tok
Jeffrey B-H
JB
Department of Chemistry, York College and Graduate Center, The City University of New York, 94-20 Guy R. Brewer Blvd., Jamaica, NY 11451, USA. tok2@llnl.gov
Bi
Lanrong
L
Saenz
Max
M
D019380:Anti-HIV Agents / Q000138:chemical synthesis; D020137:Base Pair Mismatch; D001665:Binding Sites; D015752:Genes, env; D006147:Guanine; D006801:Humans; D008024:Ligands; D009287:Naphthyridines / Q000737:chemistry*; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009691:Nucleic Acid Denaturation / Q000187:drug effects; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry; D013329:Structure-Activity Relationship; D013696:Temperature
D019380:Anti-HIV Agents; D008024:Ligands; D009287:Naphthyridines; D009692:Nucleic Acid Heteroduplexes; D012367:RNA, Viral; D006147:Guanine