Contacts between 5 S DNA and Xenopus TFIIIA identified using 5-azido-2'-deoxyuridine-substituted DNA

Highly efficient and facile synthesis of 5-azido-2'-deoxyuridine

Previously reported syntheses of the photoaffinity label 5-azido-2'-deoxyuridine are rather inefficient and involve the tedious preparation of a 5-nitro intermediate. To overcome these inconveniences, we have developed a new approach from the commercially available 5-bromo-2'-deoxyuridine nucleoside. Our synthetic route makes use of a benzylamination reduction sequence. Using this strategy, the 5-azido-2'-deoxyuridine photolabel is prepared in three steps and quantitative yields.

Unraveling the photochemistry of the 5-azido-2'-deoxyuridine photoaffinity label

UV irradiation of 5-azido-2'-deoxyuridine in water provides up to seven products. All likely result from a pivotal azirene, formed by the intramolecular rearrangement of the initially formed nitrene, that undergoes nucleophilic addition at its C5 position. This study strongly suggests that only nucleophilic amino acid residues in close proximity are cross-linkable in photolabeling experiments by using the 5-azidouracil photophore.

Ultraviolet crosslinking of DNA protein complexes via 8-azidoadenine

The synthesis of 8-azido-2'-deoxyadenosine-5'-triphosphate is described. The photoreactive dATP analog was characterized by thin layer chromatography and UV spectroscopy. Its photoreactivity upon UV irradiation was studied. After incorporation of this dATP analog by nick translation into DNA containing the tet operator sequence the investigation of the interactions between tet operator DNA and Tet repressor becomes possible. Photocrosslinking of protein to DNA was demonstrated by the reduced migration of the DNA protein crosslinks in SDS polyacrylamide gel electrophoresis.

Synthesis and evaluation of oligodeoxyribonucleotides containing an aryl(trifluoromethyl)diazirine moiety as the cross-linking probe: photoaffinity labeling of mammalian DNA polymerase beta

Photolabile 2'-deoxy- E -5-[4-(3-trifluoromethyl-3 H-diazirin-3-yl)styryl]uridine and its protected phosphoramidite derivatives have been synthesized and introduced into DNA oligomers through solid-phase DNA synthesis. The (trifluoromethyldiazirinyl)stylyl moiety of this nucleoside was found to be sufficiently stable for automated DNA synthesis. In addition, this moiety was found to be stable at 60 degrees C in aqueous solution under the annealing conditions for duplex formation with complementary strands, since >95% of the photolabile nucleoside remained after heating for 1 h. The oligo(dT) 15mer analog bearing the photolabile residue was activated/decomposed by near-UV irradiation. In photoaffinity cross-linking experiments with recombinant rat DNA polymerasebeta, constituted from a 40 kDa polypeptide, using oligo(dT) 15mer analogs bearing the photolabile residue near the 3'-terminus, a covalently bound complex of 45 kDa was obtained in the presence of complementary templates. Thus it was demonstrated that our method for synthesis of photolabile oligodeoxyribonucleotides may be useful for studies of DNA-related enzymes and DNA binding proteins.

Photocross-linking of nucleic acids to associated proteins

Photocross-linking is a useful technique for the partial definition of the nucleic acid-protein interface of nucleoprotein complexes. It can be accomplished by one or two photon excitations of wild-type nucleoprotein complexes or by one photon excitation of nucleoprotein complexes bearing one or more substitutions with photoreactive chromophores. Chromophores that have been incorporated into nucleic acids for this purpose include aryl azides, 5-azidouracil, 8-azidoadenine, 8-azidoguanine, 4-thiouracil, 5-bromouracil, 5-iodouracil, and 5-iodocytosine. The various techniques and chromophores are described and compared, with attention to the photochemical mechanism.

Contribution of individual base pairs to the interaction of TFIIIA with the Xenopus 5S RNA gene

The effects of a series of point mutations within the Xenopus borealis somatic-type 5S RNA gene on transcription factor IIIA (TFIIIA) binding affinity were quantified. These data define a critical sequence-dependent contact region within the classical box C promoter element from base pair 80 to 91. Substitution of GC base pairs at positions 81, 85, 86, 89, and 91 significantly reduce TFIIIA binding affinity. Base pairs located at other positions within the box C contact region provide a moderate contribution to TFIIIA-5S gene interaction. In contrast to the extensive set of sequence contacts within the box C element, TFIIIA interaction is localized primarily to two GC base pairs at positions 70 and 71 within the intermediate promoter element. A selected amplification and binding assay (SAAB) was performed with a synthetic internal control region (ICR) randomized from base pair 78 to 95 to identify box C promoter sequences bound with high affinity by TFIIIA. The wild-type 5S RNA gene sequence from 79 to 92 is strongly selected. These results are consistent with the critical role of the box C element in sequence-dependent promoter recognition by TFIIIA.

Transcription factor IIIA (TFIIIA): an update

Xenopus transcription factor, termed TFIIIA, is the first eukaryotic transcription factor purified to homogeneity and one of the most extensively characterized polymerase III gene factors at the levels both of the protein and its gene. It is an abundant protein in oocytes and is specifically required for the 5S RNA gene transcription. It promotes the formation of a stable transcription complex by first binding to the internal control region of the 5S RNA gene through its zinc finger motifs. It contains two structural domains and associates with 5S RNA to form 7S ribonucleoprotein particles in oocytes. Its expression is developmentally controlled at the level of transcription and translation. It participates in the assembly of active chromatin templates and, at least in part, is responsible for the differential expression of two kinds of 5S RNA genes in Xenopus.

Specific interaction of the first three zinc fingers of TFIIIA with the internal control region of the Xenopus 5 S RNA gene

A DNA plasmid encoding the first 101 amino acid residues of the Xenopus 5 S RNA gene-specific transcription factor IIIA (TFIIIA) was derived by polymerase chain reaction amplification of this region from the cDNA for TFIIIA. This polypeptide includes the first three zinc fingers of the TFIIIA DNA binding domain. The polypeptide was expressed in Escherichia coli and purified to greater than 95% homogeneity. The three finger polypeptide binds the internal control region of the 5 S RNA gene with sequence specificity and high affinity. Binding is metal-dependent and treatment of the polypeptide with EDTA abolishes binding. Polypeptide-DNA complexes exhibit a dissociation constant of 5.6(+/- 0.9) nM, while that for full-length Xenopus TFIIIA is 2.2(+/- 0.4) nM, measured under the same conditions. This suggests that the majority of the free energy of TFIIIA binding resides in these amino-terminal zinc fingers. The polypeptide protects 21 base-pairs of the internal control region from attack by DNase I, with protection from nucleotides +75 to +95 of the 120 base-pair gene. This region includes the C-block promoter element and several guanine residues that are essential for TFIIIA binding. Methylation interference experiments suggest that the mode of binding of the polypeptide and TFIIIA are similar. The minimal DNA sequences required for polypeptide binding were determined using a series of synthetic double-stranded deoxyribo-oligonucleotides. A 13 base-pair oligonucleotide spanning nucleotides +80 to +92 of the 5 S RNA gene retained specific and high-affinity binding, although the latter was reduced sixfold relative to longer DNA fragments. Polypeptides containing fingers 1 and 2, or fingers 2, 3 and 4 of TFIIIA do not exhibit sequence-specific DNA binding. Overall, these studies provide strong support for a model in which the first three zinc fingers of TFIIIA bind with high affinity between nucleotides +80 and +92 of the internal control region of the 5 S RNA gene.