Sequence-specific Recognition of B-DNA by Oligo(N-methylpyrrolecarboxamide)s

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1985 May 1

PMID 2986122

Citations 13

Authors

R S Youngquist

P B Dervan

Affiliations

Soon will be listed here.

Abstract

Four homologous oligopeptide-EDTA molecules, tri-, tetra, penta-, and hexa(N-methylpyrrolecarboxamide)-EDTA, in the presence of Fe(II), O2, and dithiothreitol, cleave 32P-end-labeled restriction fragments from plasmid pBR322 DNA at common locations rich in A X T base pairs that differ in the size of the binding site. From analysis of the cleavage patterns visualized by high-resolution denaturing gel electrophoresis, the oligopeptides with three, four, five, and six N-methylpyrrolecarboxamide units, containing four, five, six, and seven amide NHs, bind sites of A X T-rich DNA consisting of five, six, seven, and eight contiguous base pairs, respectively. The general rule of n amides affording binding site sizes of n + 1 base pairs is consistent with the oligopeptides binding in the minor groove of right-handed DNA, with the amide NH groups forming bridges between the adjacent N-3 and O-2 atoms of adenine or thymine on opposite strands of the DNA helix.

Citing Articles

Non-Covalent Binding of Tripeptides-Containing Tryptophan to Polynucleotides and Photochemical Deamination of Modified Tyrosine to Quinone Methide Leading to Covalent Attachment.

Erben A, Sviben I, Mihaljevic B, Piantanida I, Basaric N Molecules. 2021; 26(14).

PMID: 34299591 PMC: 8306964. DOI: 10.3390/molecules26144315.

Polyamide-scorpion cyclam lexitropsins selectively bind AT-rich DNA independently of the nature of the coordinated metal.

Lo A, Salam N, Hibbs D, Rutledge P, Todd M PLoS One. 2011; 6(5):e17446.

PMID: 21573061 PMC: 3090394. DOI: 10.1371/journal.pone.0017446.

Design, synthesis and biological evaluation of a novel class of anticancer agents: anthracenylisoxazole lexitropsin conjugates.

Han X, Li C, Mosher M, Rider K, Zhou P, Crawford R Bioorg Med Chem. 2009; 17(4):1671-80.

PMID: 19167892 PMC: 2978248. DOI: 10.1016/j.bmc.2008.12.056.

Binding, electrochemical activation, and cleavage of DNA by cobalt(II) tetrakis-N-methylpyridyl porphyrin and its beta-pyrrole brominated derivative.

Yellappa S, Seetharamappa J, Rogers L, Chitta R, Singhal R, DSouza F Bioconjug Chem. 2006; 17(6):1418-25.

PMID: 17105219 PMC: 2597228. DOI: 10.1021/bc060153x.

Toward rules for 1:1 polyamide:DNA recognition.

Urbach A, Dervan P Proc Natl Acad Sci U S A. 2001; 98(8):4343-8.

PMID: 11296283 PMC: 31837. DOI: 10.1073/pnas.081070798.

References

McGhee J . Theoretical calculations of the helix-coil transition of DNA in the presence of large, cooperatively binding ligands. Biopolymers. 1976; 15(7):1345-75. DOI: 10.1002/bip.1976.360150710. View

Luck G, Zimmer C, Reinert K, 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; 4(8):2655-70. PMC: 342599. DOI: 10.1093/nar/4.8.2655. View

Patel D, Canuel L . Netropsin-poly(dA-dT) complex in solution: structure and dynamics of antibiotic-free base pair regions and those centered on bound netropsin. Proc Natl Acad Sci U S A. 1977; 74(12):5207-11. PMC: 431654. DOI: 10.1073/pnas.74.12.5207. View

Krylov A, Grokhovsky S, Zasedatelev A, Zhuze A, Gursky G, Gottikh B . 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; 6(1):289-304. PMC: 327689. DOI: 10.1093/nar/6.1.289. View

Sutcliffe J . 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. View

Van Dyke M, Hertzberg R, Dervan P . 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; 79(18):5470-4. PMC: 346925. DOI: 10.1073/pnas.79.18.5470. View

Marky L, Blumenfeld K, Breslauer K . Calorimetric and spectroscopic investigation of drug-DNA interactions. I. The binding of netropsin to poly d(AT). Nucleic Acids Res. 1983; 11(9):2857-70. PMC: 325928. DOI: 10.1093/nar/11.9.2857. View

Peden K . Revised sequence of the tetracycline-resistance gene of pBR322. Gene. 1983; 22(2-3):277-80. DOI: 10.1016/0378-1119(83)90112-9. View

Zimmer C, Luck G, Birch-Hirschfeld E, Weiss R, ARCAMONE F, GUSCHLBAUER W . Chain length-dependent association of distamycin-type oligopeptides with A X T and G X C pairs in polydeoxynucleotide duplexes. Biochim Biophys Acta. 1983; 741(1):15-22. DOI: 10.1016/0167-4781(83)90004-0. View

10.

Schultz P, Dervan P . Sequence-specific double-strand cleavage of DNA by penta-N-methylpyrrolecarboxamide-EDTA X Fe(II). Proc Natl Acad Sci U S A. 1983; 80(22):6834-7. PMC: 390080. DOI: 10.1073/pnas.80.22.6834. View

11.

Zakrzewska K, Lavery R, PULLMAN B . Theoretical studies of the selective binding to DNA of two non-intercalating ligands: netropsin and SN 18071. Nucleic Acids Res. 1983; 11(24):8825-39. PMC: 326627. DOI: 10.1093/nar/11.24.8825. View

12.

Hertzberg R, Dervan P . Cleavage of DNA with methidiumpropyl-EDTA-iron(II): reaction conditions and product analyses. Biochemistry. 1984; 23(17):3934-45. DOI: 10.1021/bi00312a022. View

13.

Kopka M, Yoon C, Goodsell D, Pjura P, DICKERSON R . The molecular origin of DNA-drug specificity in netropsin and distamycin. Proc Natl Acad Sci U S A. 1985; 82(5):1376-80. PMC: 397264. DOI: 10.1073/pnas.82.5.1376. View

14.

Schultz P, Dervan P . Distamycin and penta-N-methylpyrrolecarboxamide binding sites on native DNA. A comparison of methidiumpropyl-EDTA-Fe(II) footprinting and DNA affinity cleaving. J Biomol Struct Dyn. 1984; 1(5):1133-47. DOI: 10.1080/07391102.1984.10507508. View