Solution Structures of 5-Fluorouracil-Substituted DNA and RNA Decamer Duplexes

Abstract

The structures in solution of eight oligonucleotide duplexes each containing either zero, one, or two 5-fluorodeoxyuridine (FdUrd) or 5-fluorouridine (FUrd) nucleosides were determined by the combined use of NMR spectroscopy, restrained molecular dynamics, and full relaxation matrix refinement to determine how FdUrd and FUrd substitution affects the structure of duplex DNA and RNA and to establish whether structural differences due to FdUrd and FUrd substitution in nucleic acids may be responsible, in part, for the biological effects of the anticancer drug 5-fluorouracil (FUra). The nucleic acid directed effects of FUra include induction of single-strand breaks in duplex DNA and altered processing of pre-mRNA and rRNA. Four self-complementary oligodeoxyribonucleotide sequences were prepared and studied as duplexes in aqueous solution: (5' dGCGAAUUCGC)2, (5' dGCGAAUFCGC)2, (5' dGCGAAFUCGC)2, and (5' dGCGAAFFCGC)2. The corresponding oligoribonucleotide sequences (5' rGCGAAUUCGC)2, (5' rGCGAAUFCGC)2, (5' rGCGAAFUCGC)2, and (5' rGCGAAFFCGC)2 were also prepared and studied. The helical parameters for the structures of these eight duplexes were analyzed to determine how substitution of FdUrd and FUrd affects the three-dimensional structures of duplex DNA and RNA. FdUrd substitution affects the base roll angle at the site of FdUrd substitution, causing the helical axis of FdUrd-substituted DNA duplexes to be bent compared to the nonsubstituted duplex. A-FUrd base pairs show substantial RMS deviations from A-Urd base pairs in all three of the RNA duplexes substituted with FUrd. Bending of the helical axis due to FdUrd substitution may contribute to the occurrence of single-strand breaks in duplex DNA while the altered structures of A-FUrd base pairs may affect RNA-RNA and RNA-protein recognition.

High Mobility Group Protein B1 Is an Activator of Apoptotic Response to Antimetabolite Drugs

“…Therefore, changes in chromatin architecture or gene regulation patterns could be important determinants of antimetabolite therapy. Structural analysis of synthetic DNA showed that incorporation of nucleoside analogs into DNA does not introduce gross changes in DNA geometry (Sahasrabudhe et al, 1996;Somerville et al, 2003). Instead, drastic shifts in DNA dynamics occur; for example, incorporation of deoxythioguanosine makes DNA more flexible (Somerville et al, 2003).…”

“…Several antimetabolite agents do not disrupt integrity of DNA and lead only to minute alterations in DNA geometry (Sahasrabudhe et al, 1996;Somerville et al, 2003). Instead, incorporation of these chemical moieties into DNA increases local flexibility of the double helix in the area surrounding the modification, and changes the DNA-protein interactions (Krynetskaia et al, 2000;Somerville et al, 2003;Seibert et al, 2005).…”

A Novel Polypyrimidine Antitumor Agent FdUMP[10] Induces Thymineless Death with Topoisomerase I-DNA Complexes

“…At the DNA level, FdU substitution has been reported to enhance base pair opening (43) and to form stable ionized and wobble base pairs with dG in duplex DNA (44). The nuclear magnetic resonance structure of an FdU-substituted DNA duplex shows alteration in base roll at the site of FdU substitution (45). The structural distortions resulting from FdU:dG base pairs probably account for the enhancement of Top1-mediated DNA cleavage.…”

Raltitrexed increases tumorigenesis as a single agent yet exhibits anti-tumor synergy with 5-fluorouracil in ApcMin/+ Mice1

“…Spectroscopic studies have shown that the solution structure of FUra-substituted DNA duplexes is quite different from that of Ura-substituted duplexes. 42 In addition, thymine-DNA glycosylase, an enzyme involved in base excision repair, has been shown to remove FUra from DNA more efficiently than it removes Ura. [43][44][45][46] Therefore, FUra and Ura may have very different downstream consequences when incorporated into DNA, a scenario that may help explain tumor induction by RTX, and tumor inhibition by FUra or RTX/FUra.…”