Creation of RNA molecules that recognize the oxidative lesion 7,8-dihydro-8-hydroxy-2'-deoxyguanosine (8-oxodG) in DNA.

We used in vitro evolution to obtain RNA molecules that specifically recognize and bind with high affinity to the oxidative lesion 7, 8-dihydro-8-hydroxy-2'-deoxyguanosine (8-oxodG) in DNA. A pool of approximately 10(15) RNA molecules containing a random insert of 45 nucleotides in length was subject to 10 successive rounds of chromatographic enrichment using an 8-oxodG affinity matrix, reverse transcription, PCR amplification, and RNA synthesis. Selected RNA molecules bind to 8-oxodG located at the 3' terminus (Kd

Synthesis and biological activity of DNA damaging agents that form decoy binding sites for the estrogen receptor.

It is a goal of cancer chemotherapy to achieve the selective killing of tumor cells while minimizing toxicity to normal tissues. We describe the design of selective toxins forming DNA adducts that attract the estrogen receptor (ER), a transcription factor that is overexpressed in many human breast and ovarian tumors. The compounds consist of 4-(3-aminopropyl)-N,N-(2-chloroethyl)-aniline linked to 2-(4'-hydroxyphenyl)-3-methyl-5-hydroxy-indole. The former moiety is a DNA damaging nitrogen mustard and the latter is a ligand for the ER. The connection between these groups was refined to permit DNA adducts formed by the mustard portion of the molecule to present the ligand domain so that it was able to interact efficiently with the ER. By using 16-mers containing specific DNA adducts, it was determined that monoadducts and putative intrastrand crosslinks were preferred targets for the ER over interstrand crosslinks. A series of structurally related 2-phenylindole mustards was prepared, some of which were selectively toxic to the ER-positive breast cancer cell line MCF-7, as compared with the ER(-) negative line MDA-MB231. The ability both to bind to DNA and to interact significantly with the ER were essential to achieve selective lethality toward ER(+) cells. Compounds forming DNA adducts without the ability to bind receptor showed similar toxicities in the two cell lines. Several models could explain the selective toxicity of the mustard-phenylindole compounds toward ER(+) cells. The favored model suggests that a mustard-DNA adduct is shielded by the ER from DNA repair enzymes and hence cells possessing an abundance of the ER selectively retain the adduct and are killed.

An NMR study of [d(CGCGAATTCGCG)]2 containing an interstrand cross-link derived from a distamycin-pyrrole conjugate.

Minor groove binding compounds related to distamycin A bind DNA with high sequence selectivity, recognizing sites which contain various combinations of A.T and G.C base pairs. These molecules have the potential to deliver cross-linking agents to the minor groove of a target DNA sequence. We have studied the covalent DNA-DNA cross-linked complex of 2,3- bis(hydroxymethyl)pyrrole-distamycin and [d(CGCGAATTCGCG)]2. The alkylating pyrrole design is based on the pharmacophore of mitomycin C and is similar in substructure to another important class of natural products, the oxidatively activated pyrrolizidine alkaloids. Ligand-DNA NOEs confirm that the tri(pyrrole-carboxamide) unit of the ligand is bound in the minor groove of the central A+T tract. Unexpectedly, it is shifted by 1 bp with respect to the distamycin A binding site on this DNA sequence. The cross-link bridges the 2-amino position of two guanine residues, G4 and G22. The C3.G22 and G4.C21 base pairs exhibit Watson-Crick base pairing, with some local distortion, as evidenced by unusual intensities observed for DNA-DNA NOE cross-peaks. The model is compared with a related structure of a cross-linked mitomycin C:DNA complex.

Bending of DNA by the mitomycin C-induced, GpG intrastrand cross-link.

Mitomycin C (MC) forms interstrand and intrastrand cross-link adducts and monoalkylation products (monoadducts) with DNA. Each of the three types of adducts was incorporated site-specifically into both a 15-mer and a 21-mer oligodeoxyribonucleotide duplex. The adduct-containing duplexes were 32P-phosphorylated and ligated to form multimers, which were then analyzed for anomalous electrophoretic mobility by nondenaturing polyacrylamide gel electrophoresis, using the method of Koo and Crothers [(1988) Proc. Natl. Acad. Sci. U.S.A. 85, 1763-1767] in order to detect DNA curvature caused by the adducts. The intrastrand cross-link adduct was found to induce a 14.6 +/- 2.0 degrees DNA bend per lesion (minimum value) while no DNA bending was detected for either the interstrand cross-link or the monoadduct. Molecular mechanics modeling indicated that the possible origin of the bend lies in a considerable deviation from parallel of the normals to the best planes of the intrastrand cross-linked guanines, due to a shorter than normal distance between their N2 atoms forced upon them by the cross-link. The observed bending by the MC intrastrand lesion may be the cause of the increased flexibility of MC-modified DNA, localized to distinct regions, as observed in earlier work by hydrodynamic methods and electron microscopy. The MC adduct-caused DNA bend may serve as a recognition site for certain DNA-binding proteins.

A mechlorethamine-induced DNA interstrand cross-link bends duplex DNA.

The dG-to-dG, DNA-DNA interstrand cross-link at the duplex sequence 5'-d(GNC) formed by the antitumor drug mechlorethamine (bis(2-chloroethyl)methylamine) was studied both theoretically and experimentally. Computer models of cross-linked DNA were energy minimized using molecular mechanics. The energy minimized structures possessed local distortion of the DNA helix, especially propeller twisting and buckling, caused by the tether length being too small to bridge the spacing of N7 atoms of dG at the sequence 5'-d(GNC) in B DNA. Overwinding of 2-6 degrees was present at each of the two dinucleotide steps spanned by the cross-link. The predicted structural changes were compatible with the possibility that this cross-link would introduce a static bend into the DNA double helix axis. An experimental study provided evidence for this induced bending of the helix axis in interstrand cross-linked samples. DNAs containing multiple mechlorethamine-induced interstrand cross-links exhibited anomalously low electrophoretic mobility in polyacrylamide gels when the lesions were separated by one or two turns. From the degree of gel retardation, the cross-linked DNAs were estimated to be bent by 12.4-16.8 degrees per lesion; estimation of the extent to which this bend was induced by the lesion was complicated by a preexisting bend in the non-cross-linked DNAs used. The data did not allow distinction of a static from an anisotropic dynamic bend; "universal" and "hinge" joints were excluded. Anomalous mobility was maximal when the lesion spacing was 21 bp, suggesting a helical repeat of 10.5 bp per turn.