Facile characterization of translation initiation via nonsense codon suppression

A new strategy for studying the mechanism of translation initiation in eukaryotes has been developed. The strategy involves the use of an in vitro translation system to incorporate a non-natural fluorescent amino acid into a protein from a suppressor tRNAPheCUA misacylated with that amino acid. It is thereby possible to monitor translation initiation efficiency at an AUG codon in different contexts; this is illustrated for three constructs encoding Escherichia coli dihydrofolate reductase mRNA with different translation initiation regions. Fluorescence measurements after in vitro translation of the mRNAs in rabbit reticulocyte lysate reflected differences in the position and efficiency of translation initiation and, therefore, can be used for characterization of the translation initiation process.

DNA polymerase beta inhibitors from Sandoricum koetjape

Bioassay-guided fractionation of Sandoricum koetjape using an assay sensitive to DNA polymerase beta inhibition led to the isolation of three active compounds (1-3) having IC(50) values from 20 to 36 microM. Derivatives 5-14 were prepared from compounds 1 and 2; derivatives 11, 12, and 13 showed activity against DNA polymerase beta with IC(50) values ranging from 16 to 36 microM.

Effects of release factor 1 on in vitro protein translation and the elaboration of proteins containing unnatural amino acids

An in vitro protein synthesizing system was modified to facilitate the improved, site-specific incorporation of unnatural amino acids into proteins via readthrough of mRNA nonsense (UAG) codons by chemically misacylated suppressor tRNAs. The modified system included an S-30 extract derived from Escherichia coli that expresses a temperature-sensitive variant of E. coli release factor 1 (RF1). Mild heat treatment of the S-30 extract partially deactivated RF1 and improved UAG codon readthrough by as much as 11-fold, as demonstrated by the incorporation of unnatural amino acids into positions 25 and 125 of HIV-1 protease and positions 10 and 22 of E. coli dihydrofolate reductase. The increases in yields were the greatest for those amino acids normally incorporated poorly in the in vitro protein synthesizing system, thus significantly enhancing the repertoire of modified amino acids that can be incorporated into the proteins of interest. The substantial increase in mutant protein yields over those obtained with an S-30 extract derived from an RF1 proficient E. coli strain is proposed to result from a relaxed stringency of termination by RF1 at the stop codon (UAG). When RF1 levels were depleted further, the intrinsic rate of DHFR synthesis increased, consistent with the possibility that RF1 competes not only at stop codons but also at other mRNA codons during peptide elongation. It thus seems possible that in addition to its currently accepted role as a protein factor involved in peptide termination, RF1 is also involved in functions that control the rate at which protein synthesis proceeds.

Harbinatic acid, a novel and potent DNA polymerase beta inhibitor from Hardwickia binata

Bioassay-guided fractionation of an active methyl ethyl ketone extract of Hardwickia binata, using an assay sensitive to DNA polymerase beta inhibition, resulted in the isolation of a potent inhibitor. This proved to be a novel diterpenoid, which has been named harbinatic acid (1). The structure of 1 was established as 3alpha-O-trans-p-coumaroyl-7-labden-15-oic acid from spectroscopic analysis and by comparison with the published data for a structurally related compound. Compound 1 strongly inhibited calf thymus DNA polymerase beta, with an IC(50) value of 2.9 microM.

Role of the 20-hydroxyl group in camptothecin binding by the topoisomerase I-DNA binary complex

Recent findings concerning the structure of the covalent binary complex formed by DNA topisomerase I and its DNA substrate, as well as the nature of interactions with inhibitors that bind reversibly to this binary complex, have led to two proposed models for the binding of the prototype inhibitor camptothecin to the DNA-topisomerase I binary complex. While these models differ in many regards, they both suggest the involvement of the 20-OH group of camptothecin in a donor hydrogen bond with an enzyme side chain functional group. Presently, five analogues of camptothecin that differ only at C-20 have been evaluated for their ability to bind to the topoisomerase I-DNA binary complex and thereby inhibit enzyme function. Both 20-chloro- and 20-bromocamptothecin bound as well to the enzyme-DNA binary complex as 20-aminoCPT despite the absence of a substituent at C-20 capable of contributing a donor hydrogen bond.

bis-5-Alkylresorcinols from Panopsis rubescens that inhibit DNA polymerase beta

Bioassay-guided fractionation of Panopsis rubescens, using an assay to detect DNA polymerase beta inhibition, led to the isolation of two new bis-5-alkylresorcinols (1 and 2), in addition to one known bis-5-alkylresorcinol (3). The structures of 1-3 were established as 1,3-dihydroxy-5-[14'-(3' ',5' '-dihydroxyphenyl)-cis-4'-tetradecenyl]benzene (1), 1, 3-dihydroxy-5-[14'-(3' ',5' '-dihydroxyphenyl)-cis-7'-tetradecenyl]benzene (2), and 1, 3-dihydroxy-5-[14'-(3' ',5' '-dihydroxyphenyl)tetradecenyl]benzene (3), respectively, by spectroscopic and chemical analyses. Compounds 1-3 exhibited potent inhibition of calf thymus DNA polymerase beta, with IC50 values of 7.5, 6.5, and 5.8 microM, respectively.

Effects of camptothecin analogues on DNA transformations mediated by calf thymus and human DNA topoisomerases I

Camptothecin (CPT) and 10 structural analogues were studied to characterize their effects on specific rearrangements of DNA structure mediated by human and calf thymus DNA topoisomerases I. A 30 base pair DNA duplex containing a single high-efficiency topoisomerase cleavage site was incubated with each of the enzymes in the presence of the inhibitors. Individual inhibitors stabilized the covalent enzyme-DNA binary complex to different extents, as anticipated. However, for several of the inhibitors, the extent of ternary complex formation differed substantially for the human and calf thymus enzymes. In common with calf thymus topoisomerase I, the human enzyme was shown to mediate the rearrangement of branched, nicked, and gapped DNA substrates that constitute models for illegitimate recombination. However, some of these rearrangements proceeded with different rates and efficiencies in the presence of human topoisomerase I. When inhibition of three of the rearrangements by CPT analogues was studied, most of the analogues exhibited differential effects on a given transformation, depending on the source of the enzyme employed.

Differential effects of camptothecin derivatives on topoisomerase I-mediated DNA structure modification

The effects of eleven camptothecin derivatives on calf thymus topoisomerase I-mediated cleavage of synthetic DNA duplex have revealed that the A ring of camptothecin is very important for its biochemical activity. Depending on the type, number, and location of substituents, highly active or inactive analogues were obtained. The persistence of CPT-induced topoisomerase I-DNA covalent binary complexes was investigated by using as substrates DNA containing several good topoisomerase I cleavage sites, or else a synthetic DNA duplex of defined structure with a single high-efficiency cleavage site. The ligation kinetics at a given topoisomerase I cleavage site were sometimes quite different in the presence of CPT derivatives whose structures were closely related. Even in the presence of a single CPT analogue, topoisomerase I-DNA covalent binary complexes underwent ligation with different kinetics, presumably reflecting a dependence on DNA sequences flanking the individual topoisomerase I cleavage sites. Individual camptothecin derivatives also exhibited a spectrum of inhibitory potentials in blocking the topoisomerase I-mediated rearrangement of branched, nicked, and gapped DNA duplex substrates; in some cases the potencies of inhibition observed in these assays for individual camptothecin analogues were quite different than those determined for stabilization of the unmodified DNA-topoisomerase I binary complex.

DNA duplexes containing 3'-deoxynucleotides as substrates for DNA topoisomerase I cleavage and ligation

The DNA cleavage-ligation reaction of DNA topoisomerase I was investigated employing synthetic DNA substrates containing 3'-deoxyadenosine or 3'-deoxythymidine at specific sites and acceptor oligonucleotides of different lengths. The modified nucleotides were substituted systematically within the putative enzyme-binding domain and also next to the high efficiency cleavage site to determine the effect of single base changes on enzyme function. Depending on the site of substitution, the facility of the cleavage and ligation reactions were altered. The bases at positions -1 and -2 on the noncleaved strand were found to be important for determining the site of cleavage. Inclusion of 3'-deoxythymidine in the scissile strand at position -1 permitted the demonstration that topoisomerase I can cleave and form a 2' --> 5'-phosphodiester linkage. Partial duplexes doubly modified at positions -4 or -6 in the noncleaved strand and at positions +1 or -1 within scissile strand were not good substrates for topoisomerase I, showing that cleavage can depend importantly on binding interactions based on structural alterations at spatially separated sites. Substitution of a 3'-deoxynucleotide on the scissile strand at position -6 enhanced formation of the ligation product resulting from cleavage at site 1 and suppressed cleavage at site 2.

DNA topoisomerase I-mediated formation of structurally modified DNA duplexes. Effects of metal ions and topoisomerase I inhibitors

The ability of DNA topoisomerase I to mediate the formation of structurally modified DNA duplexes was studied utilizing suicide substrates containing high-efficiency cleavage sites and acceptor oligonucleotides in which the 5'-terminal nucleotides were varied. When the substrates were nicked duplexes, the divalent cations Mg2+ and Ca2+ were found to facilitate the topoisomerase I-mediated formation of ligation products containing 3-nucleotide deletions on the scissile strand, but to suppress the formation of 1-nucleotide deletions. The presence of a complementary nucleotide at the 5'-end of the acceptor strand was not required for the ligation reaction to proceed, but duplex formation to produce duplexes containing a mismatch proceeded more slowly than formation of the fully complementary duplex. Topoisomerase I-mediated mismatch formation in the ligation reaction was inhibited more readily by camptothecin than the corresponding ligation reaction to form a fully complementary duplex; the extent of inhibition was comparable for all three mismatches studied. In comparison, the topoisomerase I inhibitors nitidine and coralyne exhibited quite different effects on the same ligation reactions.

Structurally altered substrates for DNA topoisomerase I. Effects of inclusion of a single 3'-deoxynucleotide within the scissile strand

A partial DNA duplex containing a high efficiency topoisomerase I cleavage site was substituted singly at each of three sites with 3'-deoxyadenosine. Depending on the site of substitution, the facility of the topoisomerase I-mediated cleavage or ligation reactions was altered. Inclusion of the modified nucleoside at the 5'-end of the acceptor oligonucleotide diminished the rate of religation following substrate cleavage by the enzyme.

In vitro suppression as a tool for the investigation of translation initiation

An in vitro protein synthesizing system that employs rabbit reticulocyte lysates has been employed for protein production from mRNAs containing nonsense (UAG) codons in the presence of misacylated suppressor tRNAs.The system includes a misacylated Escherichia coli tRNAAlaCUA that functions at least as efficiently as any suppressor tRNA transcript reported to date and which has been shown not to be a substrate for (re)activation by alanyl-tRNA synthetase. Application of the optimized system for preparation of dihydrofolate analogs has also permitted analysis of competing mechanisms that control the sites(s) of translation initiation.

On the chemistry of RNA degradation by Fe.bleomycin

The chemistry of RNA degradation by Fe.bleomycin was studied using two RNA substrates that are modified efficiently at a small number of sites by the antitumor antibiotic. Cleavage of tRNAHis precursor transcript by Fe(II).BLM A2 was shown to require O2; cleavage was also observed when the same substrate was treated with Fe(III).BLM A2 + H2O2. Consistent with earlier observations made for DNA, the extent of tRNAHis precursor cleavage was greater for Fe(II).BLM A5 than for Fe(II).BLM A2; the least cleavage was obtained using Fe(II).BLM demethyl A2. By the use of 32P end labeled tRNAHis precursor transcript that was also 3H labeled within the uracil moieties, it was shown that release of uracil was nearly stoichiometric with tRNA strand scission by Fe(II).BLM A2. Nonetheless, treatment of the tRNAHis with hydrazine following BLM-mediated cleavage indicated formation of a new product that must have derived from a BLM-induced lesion. Also employed for characterization of BLM cleavage of RNA were the octanucleotides CGCTAGCG, C3-ribo-CGCTAGCG and C3-ara-CGCTAGCG. Analysis of the products of cleavage indicates that Fe.BLM is capable of mediating cleavage by abstraction of a H atom either from C-4' H or c-1' H of the chimeric oligonucleotides.

Fe.bleomycin as a probe of RNA conformation

Two crystallographically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage by Fe.bleomycin to facilitate definition at high resolution of the structural elements in RNAs conducive to bleomycin binding and cleavage. Yeast tRNAAsp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52 and A66. Only two of these six sites involved oxidative cleavage of a 5'-G.Pyr-3' sequence, but three sites were at the junction between single- and double-stranded regions of the RNA, consistent with a binding model in which the bithiazole + C-terminal substituent of bleomycin bind to minor groove structures on the RNA. Also studied were four tRNA transcripts believed on the basis of biochemical and chemical mapping experiments to share structural elements in common with the mature tRNAs. Cleavage of these tRNAs by Fe.bleomycin gave patterns of cleavage very different from each other and than those of the mature tRNAs. This observation suggests strongly that Fe.bleomycin cannot be used for chemical mapping in the same fashion as more classical reagents, such as Pb2+ or dimethyl sulfate. However, the great sensitivity of Fe.bleomycin to changes in nucleic acid structure argues that those species which do show similar patterns of cleavage must be very close in structure.

Inhibition of topoisomerase I function by coralyne and 5,6-dihydrocoralyne

The antitumor agent coralyne and a number of structural analogues were found to be inhibitors of DNA topoisomerase I and were characterized biochemically. Several of these analogues stabilized the covalent binary complex formed between calf thymus topoisomerase I and pSP64 plasmid DNA; coralyne and 5,6-dihydrocoralyne had the greatest potency as inhibitors in this assay. In common with camptothecin, the effects of coralyne and 5,6-dihydrocoralyne were reversed in the presence of increasing salt concentration or temperature, consistent with the interpretation that both functioned mechanistically in a fashion analogous to camptothecin. The sequence specificity of DNA cleavage by coralyne and 5,6-dihydrocoralyne was also studied in comparison with camptothecin using a 471-bp DNA duplex as a substrate for topoisomerase I. Seven sites of cleavage were apparent, four of which were shared in common by coralyne, 5,6-dihydrocoralyne and camptothecin. Coralyne and 5,6-dihydrocoralyne produced cleavage at one sequence, 5'-TCTC decreases GTAA=3', that was not apparent in the presence of camptothecin; correspondingly, two cleavage bands appeared only when camptothecin was present. Coralyne and 5,6-dihydrocoralyne also inhibited topoisomerase I-mediated relaxation of supercoiled plasmid DNA. Coralyne was the most potent inhibitor of DNA relaxation; the effects of camptothecin and 5,6-dihydrocoralyne were roughly equal. At high concentrations, coralyne completely suppressed the formation of the topoisomerase I-DNA covalent binary complex.

Specific cleavage of a DNA triple helix by FeII.bleomycin

The specific cleavage of a DNA triple helix by FeII.bleomycin (BLM) is demonstrated. Triplex-specific cleavage was observed on both strands of the 32-base pair (bp) duplex at the duplex-triplex junctions. Strand scission products and alkali labile lesions were both formed. The strongest BLM cleavage site was located at the 5'-duplex-triplex junction, which is also the preferred triplex binding site of intercalating agents [Collier, D. A., Mergny, J.-L., Thuong, N. T., & Hélène, C. (1991) Nucleic Acids Res. 19, 4219-4224]. The preference of BLM for the 5'-junction does not appear to derive from selective intercalative binding at this site. This is supported by the observation that phleomycin, which contains a thiazolinylthiazole moiety rather than a planar bithiazole ring system, exhibited the same selectivity of triplex cleavage as BLM. Cleavage of the triple helix by FeII.BLM was unaffected by concentrations of Mg2+ up to 5 mM, suggesting possible therapeutic applications of this novel DNA target. Molecular-modeling calculations of the triplex region suggested that dramatic variations in minor groove width and depth occur at the duplex-triplex junctions, particularly at the 5'-junction. Moreover, the minor groove at these sites was calculated to be somewhat shallower and wider than the minor groove of B-DNA. These results suggest that the preference of BLM for the duplex-triplex junctions derives from selective recognition of minor groove shape at these sites and thus reflects conformation-selective, rather than sequence-selective, DNA recognition by FeII.BLM.

Phosphoryl migration during the chemical synthesis of RNA

By the use of high sensitivity assay systems, we have measured the occurrence of strand scission and phosphoryl migration that accompany the deblocking of chemically synthesized oligoribonucleotides. Substantial phosphoryl migration was observed for both enzymatically derived poly(uridylic acid) and synthetic uridine oligoribonucleotides 2'-O-protected with the 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp) group, when these species were subjected to the acidic conditions suggested for Fpmp deprotection. Strand scission occurred in parallel and could be demonstrated readily by 5'-32P end labeling, but not by 3'-32P end labeling, of the acid-treated oligoribonucleotides. Increasing the pH of the deprotection solution and decreasing the temperature at which the deprotection was accomplished diminished both phosphoryl migration and strand scission. A mechanism that can rationalize these results is discussed.

Sequence-specific hydrolysis of yeast tRNA(Phe) mediated by metal-free bleomycin

Bleomycin A2 (BLM) was found to mediate sequence specific hydrolysis of tRNA(Phe) in the absence of added metal ions. BLM A2 promoted phosphodiester bond hydrolysis 3' to the pyrimidine residue at all resolved Py-Pu sites not involving modified bases, as demonstrated by high-resolution electrophoretic analysis of 5'- and 3'-32P-end-labeled substrates. The reaction proceeded with surprising facility, approaching efficiency that of oxidative strand scission mediated by the FeII.BLM A2 complex. By the use of a number of BLM congeners, as well as a study of the time, temperature, and salt dependence of the hydrolysis, it was shown that in many respects the hydrolytic reaction parallels the oxidative degradation of RNA and DNA mediated by metallobleomycins. Thus, in contrast to the well-characterized oxidative degradation of DNA and RNA by bleomycin studied for two decades, the present report documents the ability of certain metal-free bleomycins to mediate RNA hydrolysis.

A model for topoisomerase I-mediated insertions and deletions with duplex DNA substrates containing branches, nicks, and gaps

The ability of DNA topoisomerase I to promote insertions and deletions in vitro has been studied at nucleotide resolution for structurally diverse DNA substrates that uncouple the cleavage and ligation reactions of the enzyme. Topoisomerase I-mediated ligations afforded DNA duplexes having deletions and insertions with "branched" substrates and deletions up to 18 nucleotides in length with substrates containing nicks or gaps. In addition, a number of the acceptor substrates altered the preferred site of DNA cleavage, thereby increasing the diversity of accessible ligation products. Also demonstrated by the production of two "recombinant" duplexes from a single set of reactants was the potential for amplification of such alterations. These findings illustrate plausible mechanisms by which topoisomerase I-mediated illegitimate recombination may obtain at a molecular level.

Iron(II) bleomycin-mediated degradation of a DNA-RNA heteroduplex

The effect of iron(II) bleomycin on a DNA-RNA heteroduplex was investigated using a substrate formed by reverse transcription of Escherichia coli 5S ribosomal RNA. Both strands of the heteroduplex were cleaved by FeII.BLM A2 at comparable concentrations; complete digestion of both strands was observed using 5 microM FeII.BLM A2. The DNA strand of the heteroduplex was cleaved predominantly at 5'-G-pyr-3' sites; the sites of cleavage of the DNA strand were a subset of those observed for the corresponding DNA strand of a DNA duplex of identical sequence. The sites of cleavage of the RNA strand of the heteroduplex involved both purines and pyrimidines and were found to be different than the sites of cleavage of the 5S rRNA alone, demonstrating that cleavage of the former must actually have involved heteroduplex recognition by FeII.BLM A2. Both the DNA and RNA strands of the heteroduplex were cleaved by FeII.BLM A2 in the presence of physiological concentrations of Mg2+, consistent with the possibility that DNA-RNA heteroduplexes may be therapeutically relevant targets for bleomycin.

On the role of the bithiazole moiety in sequence-selective DNA cleavage by Fe.bleomycin

A recent study of Fe(II).bleomycin-mediated DNA strand scission suggested that the metal binding domain of the drug is also the primary determinant of the observed sequence selectivity of strand scission (Carter, B. J., Murty, V. S., Reddy, K. S., Wang, S.-N., and Hecht, S. M. (1990) J. Biol. Chem. 265, 4193-4196). Although it is well established that the bithiazole moiety+C-terminal substituent of bleomycin are required for DNA binding, the role of the bithiazole in sequence-selective DNA recognition remains unclear. To determine whether the bithiazole moiety exhibits an intrinsic DNA binding selectivity, three synthetic EDTA-conjugated bithiazole derivatives were used to mediate DNA cleavage in the presence of Fe2+ and dithiothreitol. Incubation of these Fe(II).EDTA-bithiazoles in the presence of a 5'-32P end-labeled DNA duplex resulted in strand scission at every position to essentially the same extent. The relative cleavage efficiencies among the bithiazoles were a strong function of their ionic state. These findings imply that the bithiazoles can bind to many sites on the DNA; they support a model of bleomycin-DNA interaction in which the bithiazole moiety+C-terminal substituent are required only for DNA binding, whereas the metal binding domain is responsible for metal ion coordination and oxygen activation as well as being the primary determinant of sequence-selective DNA cleavage.

Fe.bleomycin cleaves a transfer RNA precursor and its "transfer DNA" analog at the same major site

Previously, Fe.bleomycin (BLM) has been shown to mediate RNA cleavage in a fashion more highly selective than that of DNA. Because RNAs often assume secondary and tertiary structures not commonly encountered with DNAs, it was not clear whether the greater selectivity of RNA cleavage was a consequence of differences in the mononucleotide constituents of RNA and DNA, or of the three-dimensional structures of the individual substrates. Accordingly, we prepared a "tDNA" identical in sequence with Bacillus subtilis tRNA(His) precursor, the latter of which is known to be a good substrate for Fe(II).BLM A2 and which undergoes oxidative cleavage predominantly at U35. Remarkably, the tDNA underwent cleavage predominantly at T35. At higher concentrations of Fe(II).BLM A2, the tDNA was extensively degraded, while the tRNA(His) precursor was not. Competition experiments suggested that this was not due to more efficient binding of Fe.BLM to the tDNA; in fact the tRNA precursor appeared to be bound more efficiently. The lesser cleavage of the tRNA(His) may be due to limitations in the facility of chemical transformation following Fe.BLM binding, or else to the formation of RNA lesions that do not lead directly to RNA strand scission.