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Trapping DNA Polymerases Using Triplex-Forming Oligodeoxyribonucleotides*

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Trapping DNA Polymerases Using Triplex-Forming Oligodeoxyribonucleotides* Gene, 149 (1994) 1277136 0 1994 Elsevier Science B.V. All rights reserved. 0378-l 119/94/$07.00 127 GENE 08089 Trapping DNA polymerases using triplex-forming oligodeoxyribonucleotides* (DNA polymerization;termination; triplex) George M. Samadashwily and Sergei M. Mirkin Department of Genetics, Unioersitr of I/his at Chicago, Chicago, IL 60612, USA Received by J.W. Larrick: 22 March 1994; Accepted: 25 March 1994; Received at publishers: 16 May 1994 SUMMARY Triplexes (triple helices) formed within DNA templates prior to or during DNA synthesis cause DNA polymerase to terminate [Samadashwily et al., EMBO J. 13 (1993) 4975549831. Here, we show that triplex-forming oligodeoxyribo- nucleotides (oligos) efficiently trap DNA polymerases at target DNA sequences within single-stranded (ss) templates. This was observed for all studied DNA polymerases, including Sequenase and the thermophilic Taq and Vent polymer- ases. The termination rate depends on the fine structure of a triplex, as well as on ambient conditions such as temperature and the concentration of magnesium ions. Inhibition of DNA synthesis was observed not only when triplexes blocked the path of DNA polymerase, but also when a polymerization primer was involved in triplex formation. Escherichia coli ss-binding (SSB) protein helps DNA polymerase overcome the triplex barrier, but with an efficiency dramatically dependent on the triplex configuration. These results describe a novel method for blocking DNA replication at target homopurine-homopyrimidine sequences by means of triplex-forming oligos in direct analogy with similar results during transcription. INTRODUCTION images of chemically similar strands in target DNAs (Mirkin et al., 1987; Beal and Dervan, 1991). Triplex-forming oligos (TFOs) interact specifically Homopyrimidine oligos form stable triplexes under acidic with homopurine-homopyrimidine sequences in genomic pH (Lyamichev et al., 1988) a requirement which may DNA (Le-Doan et al., 1987; Moser and Dervan, 1987; be somewhat overcome by methylation of cytosines or Lyamichev et al., 1988). TFOs are usually homopurine by the presence of polyamines (Maher et al., 1989; or homopyrimidine sequences representing mirror Hampel et al., 1991). Homopurine oligos form triplexes under physiological pH in the presence of bivalent cations Correspondence to: Dr. S.M. Mirkin, Department of Genetics (M/C (Malkov et al., 1993, and references therein). Canonical 669) University of Illinois at Chicago, 808 S. Wood Street, Chicago, components of the pyrimidine/purine/pyrimidine (YR*Y) IL 60612-7309, USA. Tel. (1-312) 996-9610; Fax (1-312) 413-0353: triplexes are CG*C+ and TA*T base triads (Felsenfeld e-mail: ~117 [email protected] et al., 1957; Morgan and Wells, 1968) while orthodox *Presented at the Palo Alto Institute of Molecular Medicine pyrimidine/purine/purine (YR*R) triplexes consist of Symposium on “Pharmaceutical Design: Anti-Sense, Triple Helix, Nucleic Acid-Binding Drugs”, January 31-February 1, 1994; Hyatt CG*G and TA*A triads (Kohwi and Kohwi-Shigematsu, Rickeys, Palo Alto, CA, USA. 1988; Bernues et al., 1989). In the latter case, however, thymines may also be incorporated in the otherwise Abbreviations: bp, base pair(s); dd, dideoxy; kb, kilobase or 1000 bp; homopurine strand of the TFO opposite adenines in the nt, nucleotide(s); oligo. ohgodeoxyribonucleotide; ss, single strand(ed); SSB, ss DNA-binding (protein); TFO, triplex-forming oligo; triplex, target sequence, thus forming TA*T triads (Beal and triple helix. Dervan, 1991). Studies of non-canonical triads showed SSDZ 0378-1119(94)00300-H that mismatches could be somewhat tolerated, though TFOs were chosen because YR*R triplexes are favorable each significantly disfavored triplex formation under polymerization conditions (Baran ct al.. 1991: (Belotserkovskii et al., 1990; Mergny et al.. 1991: Beal Dayn et al.. 1992). Our templates were circular and Dervan, 1992). Mismatch energies were within the pBluescript ss DNAs carrying a 18-nt long homopyrimi- range of 3-6 kcal/mol, i.e., similar to the cost of B-DNA dine (Fig. lA--C) or homopurine (Fig. lD-F) targets. mismatches. As a result, TFOs bind to DNA in a highly Different oligos were added to form short Watson-Crick sequence specific manner recognizing, for example, duplexes (Fig. lA,D), hypothetical Hoogsteen duplexes unique sites in the yeast (Strobel and Dervan, 1990) and (Fig. 1E), orthodox interlno1ecLllar triplexes ( Fig. 1B-F). human (Strobe1 et al., 1991) chromosomes. or H-like triplexes formed by a purine-rich hairpin and The sequence-specificity of TFOs is the basis for the its homopyrimidine target (Fig. 1C). All triplexes were anti-gene strategy reviewed by H&!ne ( 199 1) where selec- built from CG*G and TA*T base triads (Samadashwily tive binding of a TFO to a target gene prevents its normal et al., 1993). This triad composition was chosen because functioning. Most such studies concerned the inhibition such triplexes appear to be more stable than orthodox of trallscription. This is due to the existence of function- YR*R triplexes that consist of CG*G and TA*A triads ally important homopurine-homopyrimidine stretches in (Beal and Dervan, 1991). To prevent these oligos from many eukaryotic promoters which are appropriate serving as primers for DNA polymerization, their 3’-ends targets for TFOs (reviewed in Mirkin and Frank- were blocked by a 3’ amino group (Nelson ct al., 1989). Kamenetskii, 1994). The inhibitory effects of TFOs on A standard ‘reverse’ primer was annealed to all these the transcription of the c-tnyc (Cooney et al., 198X), meth- templates and the pattern of DNA polymerization was allothionein (Maher et al., 1989; 1992) and interleukin-2 analyzed by DNA sequencing or primer extension. receptor (Grigoriev et al., 1992) genes were observed in vitro. The likely mechanism of transcriptional inhibition (b) DNA triplexes block elongation of different DNA in these cases is competition between the TFO and the polymerases transcriptional activators for a target promoter sequence. We have previously found that T7 DNA polymerase TFOs also arrest initiation and elongation of transcrip- tion in vitro (Young et al., 1991; Duval-Valentin et al., (Sequenase) was completely blocked by short triplexes 1992). Recently it was found that TFOs inhibit transcrip- within ss templates (Samadashwily et al., 1993). In that tion from the c-mq’c and interleukin-2 receptor genes in study we used the DNA templates presented in cell cultures (Postel et al., 1991; Grigoriev et al., 1993). Fig. lA-C. No apparent differences were observed be- The influence of TFOs on DNA replication is less tween intermolecular and H-like triplexes. Since only ho- studied. An octathymidilate bound with an acridine de- mopyrimidine sequences served as templates for the rivative recognizes a d(A), stretch in SV40 DNA adjacent polymerase in those cases, it was not clear if termination to the T-antigen binding site. In vivo it inhibits SV40 would be the same for homopyrimidinc templates. replication presumably by interfering with the DNA- Neither is it clear that the purine-rich TFO alone causes binding or unwinding activities of the T-antigen (Birg termination of DNA synthesis by forming either a hypo- et al., 1990). We have recently shown the inhibitory effect thetical Hoogsteen-type duplex, or complex quadruple of TFOs on the elongation of DNA synthesis in vitro structures (reviewed in Williamson, 1994) with the tem- (Samadashwily et al., 1993). TFOs completely blocked plate. To address these questions, we studied DNA poly- purified T7 DNA polymerase at a target site within a ss merization on the templates presented in Fig. lD-F template. where the homopurine-strand is replicated. The results Here we describe that the same is true for different presented in Fig. 2 show that neither short Watson-Crick DNA polymerases including such highly processive en- duplexes, nor the G-rich strand alone cause prominent zymes as Taq and Vent polymerases. E. coli SSB protein termination of polymerization, but triplex formation un- partially ameliorate the termination of polymerization conditionally blocks Sequenase at the triplex border. caused by TFOs, but some triplexes escape the action of Taken together with our previous work, these results SSB. Finally, we found that TFOs may also prevent the show that triplexes prevent Sequenase elongation regard- initiation of DNA polymerization. These results raise less the chemical nature of the template DNA. hopes that TFOs could be further used for impeding To see if the TFO-caused termination of polymeriza- DNA replication in vivo. tion was general to other polymerases, we repeated our experiments on the DNA templates presented in RESULTS AND DISCUSSION Fig. lA-C but with Tttq poiymerase. The results of DNA (a) General strategy sequencing are shown in Fig. 3. Similarly to Sequenase, We studied the influence of purine-rich TFOs on the short duplex does not block Toq polymerase. Triplexes activity of several different DNA polymerases. These do lead to the premature termination of polymerization 129 5’-ACCGGAGGGAGGAGGGAA-3’# TCCCCTCCCTCCTCCCTT X3’-TGGGGTGGGTGGTGGGTT-5’ ****************** 5 ’ -AGGGGAGGGAGGAGGGAA-3’ # TCCCCTCCCTCCTCCCTT ATGGGGTGGGTGGTGGGTT-5’ T •~~ir~~*~~~~~~*~~~~ T AGGGGAGGGAGGAGGGAA-3’ # TCCCCTCCCTCCTCCCTT 5’-TTCCCTCCTCCCTCCCCT-3’# AACGGAGGAGGGAGGGGA 5’-TTCCCTCCTCCCTCCCCT-3’X AAGGGACGAGGGAGGGGA ****************** F 5’-TTCGGTCGTGGGTGGGGT-3’# Fig. 1. DNA templates containing short double- and triple-helical stretches. Hoogsteen pairs are shown by
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