Abstract
In the presence of O2 and 5 mM dithiothreitol, penta-N-methylpyrrolecarboxamide-EDTA X Fe(II) [P5E X Fe(II)] at 0.5 microM cleaves pBR322 plasmid DNA (50 microM in base pairs) on opposite strands to afford discrete DNA fragments as analyzed by agarose gel electrophoresis. High-resolution denaturing gel electrophoresis of a 32P-end-labeled 517-base-pair restriction fragment containing a major cleavage site reveals that P5E X Fe(II) cleaves 3-5 base pairs contiguous to a 6-base-pair sequence, 5'-T-T-T-T-T-A-3' (4,323-4,328 base pairs). The major binding orientation of the pentapeptide occurs with the amino terminus at the adenine side of this sequence. In the presence of 5 mM dithiothreitol, 0.01 microM P5E X Fe(II) converts form I pBR322 DNA at 0.22 microM plasmid (1.0 mM in base pairs) to 40% form II, indicating the cleavage reaction is catalytic, turning over a minimum of nine times. This synthetic molecule achieves double-strand cleavage of DNA (pH 7.9, 25 degrees C) at the 6-base-pair recognition level and may provide an approach to the design of "artificial restriction enzymes".
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Selected References
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- Berman H. M., Neidle S., Zimmer C., Thrum H. Netropsin, a DNA-binding oligopeptide structural and binding studies. Biochim Biophys Acta. 1979 Jan 26;561(1):124–131. doi: 10.1016/0005-2787(79)90496-9. [DOI] [PubMed] [Google Scholar]
- Giloni L., Takeshita M., Johnson F., Iden C., Grollman A. P. Bleomycin-induced strand-scission of DNA. Mechanism of deoxyribose cleavage. J Biol Chem. 1981 Aug 25;256(16):8608–8615. [PubMed] [Google Scholar]
- Krylov A. S., Grokhovsky S. L., Zasedatelev A. S., Zhuze A. L., Gursky G. V., Gottikh B. P. Quantitative estimation of the contribution of pyrrolcarboxamide groups of the antibiotic distamycin A into specificity of its binding to DNA AT pairs. Nucleic Acids Res. 1979 Jan;6(1):289–304. doi: 10.1093/nar/6.1.289. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Luck G., Zimmer C., Reinert K. E., Arcamone F. Specific interactions of distamycin A and its analogs with (A-T) rich and (G-C) rich duplex regions of DNA and deoxypolynucleotides. Nucleic Acids Res. 1977 Aug;4(8):2655–2670. doi: 10.1093/nar/4.8.2655. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Marky L. A., Blumenfeld K. S., Breslauer K. J. Calorimetric and spectroscopic investigation of drug-DNA interactions. I. The binding of netropsin to poly d(AT). Nucleic Acids Res. 1983 May 11;11(9):2857–2870. doi: 10.1093/nar/11.9.2857. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
- Modrich P. Studies on sequence recognition by type II restriction and modification enzymes. CRC Crit Rev Biochem. 1982;13(3):287–323. doi: 10.3109/10409238209114231. [DOI] [PubMed] [Google Scholar]
- Nosikov V. V., Sain B. Protection of particular endonuclease R. Hind III cleavage sites by distamycin A, propyl-distamycin and netropsin. Nucleic Acids Res. 1977 Jul;4(7):2263–2273. doi: 10.1093/nar/4.7.2263. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Reinert K. E. Adenosine-thymidine cluster-specific elongation and stiffening of DNA induced by the oligopeptide antibiotic netropsin. J Mol Biol. 1972 Dec 30;72(3):593–607. doi: 10.1016/0022-2836(72)90178-7. [DOI] [PubMed] [Google Scholar]
- Roberts R. J. Restriction and modification enzymes and their recognition sequences. Nucleic Acids Res. 1983 Jan 11;11(1):r135–r167. [PMC free article] [PubMed] [Google Scholar]
- Sanger F., Coulson A. R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol. 1975 May 25;94(3):441–448. doi: 10.1016/0022-2836(75)90213-2. [DOI] [PubMed] [Google Scholar]
- Smith H. O. Nucleotide sequence specificity of restriction endonucleases. Science. 1979 Aug 3;205(4405):455–462. doi: 10.1126/science.377492. [DOI] [PubMed] [Google Scholar]
- Sutcliffe J. G. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):77–90. doi: 10.1101/sqb.1979.043.01.013. [DOI] [PubMed] [Google Scholar]
- Tanaka T., Weisblum B. Construction of a colicin E1-R factor composite plasmid in vitro: means for amplification of deoxyribonucleic acid. J Bacteriol. 1975 Jan;121(1):354–362. doi: 10.1128/jb.121.1.354-362.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Van Dyke M. W., Dervan P. B. Footprinting with MPE.Fe(II). Complementary-strand analyses of distamycin- and actinomycin-binding sites on heterogeneous DNA. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):347–353. doi: 10.1101/sqb.1983.047.01.040. [DOI] [PubMed] [Google Scholar]
- Van Dyke M. W., Hertzberg R. P., Dervan P. B. Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA.Fe(II). Proc Natl Acad Sci U S A. 1982 Sep;79(18):5470–5474. doi: 10.1073/pnas.79.18.5470. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wartell R. M., Larson J. E., Wells R. D. Netropsin. A specific probe for A-T regions of duplex deoxyribonucleic acid. J Biol Chem. 1974 Nov 10;249(21):6719–6731. [PubMed] [Google Scholar]
- Zimmer C. Effects of the antibiotics netropsin and distamycin A on the structure and function of nucleic acids. Prog Nucleic Acid Res Mol Biol. 1975;15(0):285–318. doi: 10.1016/s0079-6603(08)60122-1. [DOI] [PubMed] [Google Scholar]
- Zimmer C., Luck G., Thrum H., Pitra C. Binding of analogues of the antibiotics distamycin A and netropsin to native DNA. Effect of chomophore systems and basic residues of the oligopeptides on thermal stability, conformation and template activity of the DNA complexes. Eur J Biochem. 1972 Mar 15;26(1):81–89. doi: 10.1111/j.1432-1033.1972.tb01742.x. [DOI] [PubMed] [Google Scholar]