Effect of linker length on DNA duplexes containing a mismatched O6-2'-deoxyguanosine-alkyl interstrand cross-link.
DNA duplexes containing a directly opposed O(6)- alkyl-2'-deoxyguanosine interstrand cross-link were synthesized to serve as structural mimics of lesions formed by the bifunctional chemotherapeutic alkylating agents busulfan and hepsulfam. One of the key steps to prepare the necessary bis-phosphoramidites involved the Mitsunobu reaction between a diol linking two protected 2'-deoxyguanosine nucleosides at the O(6) position. These bis-phosphoramidites were incorporated into 11-bp DNA duplexes by solid phase synthesis to produce cross-linked DNA probes in high yields. UV thermal denaturation studies revealed that these interstrand cross-linked containing oligonucleotides were stabilized compared to a DNA duplex containing a central 2'-deoxyguanosine mismatch. The duplex containing the four carbon cross-link was stabilized by 10 degrees C relative to the seven carbon linker. Molecular models of these duplexes that were geometry optimized by the AMBER force field suggest that the seven carbon cross-link was less efficiently accommodated in the major groove of the duplex relative to the four carbon linker, accounting for the observed destabilization.
Booth
Jason D
JD
Department of Chemistry & Biochemistry, Concordia University, 7141 Sherbooke St. West, Montreal, Canada.
Murphy
Sebastian P
SP
Noronha
Anne M
AM
Wilds
Christopher J
CJ
D018906:Antineoplastic Agents, Alkylating / Q000633:toxicity*; D020137:Base Pair Mismatch; D004247:DNA / Q000737:chemistry*; D004249:DNA Damage; D003849:Deoxyguanosine / Q000737:chemistry*; D009691:Nucleic Acid Denaturation
D018906:Antineoplastic Agents, Alkylating; D004247:DNA; D003849:Deoxyguanosine