title: Interstrand cross-link formation in duplex and triplex DNA by modified pyrimidines.
abstract: DNA interstrand cross-links have important biological consequences and are useful biotechnology tools. Phenylselenyl substituted derivatives of thymidine (1) and 5-methyl-2'-deoxycytidine (5) produce interstrand cross-links in duplex DNA when oxidized by NaIO4. The mechanism involves a [2,3]-sigmatropic rearrangement of the respective selenoxides to the corresponding methide type intermediates, which ultimately produce the interstrand cross-links. Determination of the rate constants for the selenoxide rearrangements indicates that the rate-determining step for cross-linking is after methide formation. Cross-linking by the thymidine derivative in duplex DNA shows a modest kinetic preference when flanked by pyrimidines as opposed to purines. In contrast, the rate constant for cross-link formation from 5 opposite dG in duplex DNA is strongly dependent upon the flanking sequence and, in general, is at least an order of magnitude slower than that for 1 in an otherwise identical sequence. Introduction of mispairs at the base pairs flanking 5 or substitution of the opposing dG by dI significantly increases the rate constant and yield for cross-linking, indicating that stronger hydrogen bonding between the methide derived from it and dG compared to dA and the respective electrophile derived from 1 limits reaction by increasing the barrier to rotation into the required syn-conformation. Incorporation of 1 or 5 in triplex forming oligonucleotides (TFOs) that utilize Hoogsteen base pairing also yields interstrand cross-links. The dC derivative produces ICLs approximately 10x faster than the thymidine derivative when incorporated at the 5'-termini of the TFOs and higher yields when incorporated at internal sites. The slower, less efficient ICL formation emanating from 1 is attributed to reaction at N1-dA, which requires local melting of the duplex. In contrast, 5 produces cross-links by reacting with N7-dG. The cross-linking reactions of 1 and 5 illustrate the versatility and utility of these molecules as mechanistic probes and tools for biotechnology.
authors.affiliation: Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Peng
authors.forename: In Seok
authors.initials: IS
authors.lastname: Hong
authors.forename: Hong
authors.initials: H
authors.lastname: Li
authors.forename: Michael M
authors.initials: MM
authors.lastname: Seidman
authors.forename: Marc M
authors.initials: MM
authors.lastname: Greenberg
mesh_terms: D020029:Base Pairing; D003432:Cross-Linking Reagents / Q000737:chemistry*; D003562:Cytidine / Q000031:analogs & derivatives / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D010504:Periodic Acid; D011743:Pyrimidines / Q000737:chemistry*; D013936:Thymidine / Q000031:analogs & derivatives / Q000737:chemistry
chemical_list: D003432:Cross-Linking Reagents; D011743:Pyrimidines; C051802:triplex DNA; D010504:Periodic Acid; D003562:Cytidine; D004247:DNA; C009288:metaperiodate; D013936:Thymidine