A Host-guest Approach for Determining Drug-DNA Interactions: an Example Using Netropsin

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2005 Jul 29

PMID 16049022

Citations 19

Authors

Kristie D Goodwin

Eric C Long

Millie M Georgiadis

Affiliations

Soon will be listed here.

Abstract

Netropsin is a well-characterized DNA minor groove binding compound that serves as a model for the study of drug-DNA interactions. Our laboratory has developed a novel host-guest approach to study drug-DNA interactions in which the host, the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) is co-crystallized with a DNA oligonucleotide guest in the presence and absence of drug. We have co-crystallized netropsin with the RT fragment bound to the symmetric 16mer d(CTTAATTCGAATTAAG)2 and determined the structure of the complex at 1.85 A. In contrast to previously reported netropsin-DNA structures, our oligonucleotide contains two AATT sites that bind netropsin with flanking 5' and 3' sequences that are not symmetric. The asymmetric unit of the RT fragment-DNA-netropsin crystals contains one protein molecule and one-half of the 16mer with one netropsin molecule bound. The guanidinium moiety of netropsin binds in a narrow part of the minor groove, while the amidinium is bound in the widest region within the site. We compare this structure to other Class I netropsin-DNA structures and find that the asymmetry of minor groove widths in the AATT site contributes to the orientation of netropsin within the groove while hydrogen bonding patterns vary in the different structures.

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References

Cote M, Yohannan S, Georgiadis M . Use of an N-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs. Acta Crystallogr D Biol Crystallogr. 2000; 56(Pt 9):1120-31. DOI: 10.1107/s0907444900008246. View

Lu X, Olson W . 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 2003; 31(17):5108-21. PMC: 212791. DOI: 10.1093/nar/gkg680. View

Otwinowski Z, Minor W . Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997; 276:307-26. DOI: 10.1016/S0076-6879(97)76066-X. View

Sun D, Jessen S, Liu C, Liu X, Najmudin S, Georgiadis M . Cloning, expression, and purification of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase: crystallization of nucleic acid complexes. Protein Sci. 1998; 7(7):1575-82. PMC: 2144058. DOI: 10.1002/pro.5560070711. View

Sriram M, van der Marel G, Roelen H, VAN Boom J, Wang A . Structural consequences of a carcinogenic alkylation lesion on DNA: effect of O6-ethylguanine on the molecular structure of the d(CGC[e6G]AATTCGCG)-netropsin complex. Biochemistry. 1992; 31(47):11823-34. DOI: 10.1021/bi00162a022. View

Cote M, Georgiadis M . Structure of a pseudo-16-mer DNA with stacked guanines and two G-A mispairs complexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase. Acta Crystallogr D Biol Crystallogr. 2001; 57(Pt 9):1238-50. DOI: 10.1107/s090744490100943x. View

Potterton E, Briggs P, Turkenburg M, Dodson E . A graphical user interface to the CCP4 program suite. Acta Crystallogr D Biol Crystallogr. 2003; 59(Pt 7):1131-7. DOI: 10.1107/s0907444903008126. View

Goodsell D, Kopka M, DICKERSON R . Refinement of netropsin bound to DNA: bias and feedback in electron density map interpretation. Biochemistry. 1995; 34(15):4983-93. DOI: 10.1021/bi00015a009. View

Gavathiotis E, Sharman G, Searle M . Sequence-dependent variation in DNA minor groove width dictates orientational preference of Hoechst 33258 in A-tract recognition: solution NMR structure of the 2:1 complex with d(CTTTTGCAAAAG)(2). Nucleic Acids Res. 2000; 28(3):728-35. PMC: 102559. DOI: 10.1093/nar/28.3.728. View

10.

Merritt E, Murphy M . Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D Biol Crystallogr. 1994; 50(Pt 6):869-73. DOI: 10.1107/S0907444994006396. View

11.

Balendiran K, Rao S, Sekharudu C, Zon G, Sundaralingam M . X-ray structures of the B-DNA dodecamer d(CGCGTTAACGCG) with an inverted central tetranucleotide and its netropsin complex. Acta Crystallogr D Biol Crystallogr. 1995; 51(Pt 2):190-8. DOI: 10.1107/S0907444994010759. View

12.

Abrescia N, Malinina L, Subirana J . Stacking interaction of guanine with netropsin in the minor groove of d(CGTATATACG)2. J Mol Biol. 1999; 294(3):657-66. DOI: 10.1006/jmbi.1999.3280. View

13.

Harris S, Laughton C, Searle M . Induced fit DNA recognition by a minor groove binding analogue of Hoechst 33258: fluctuations in DNA A tract structure investigated by NMR and molecular dynamics simulations. Nucleic Acids Res. 2001; 29(3):693-702. PMC: 30379. DOI: 10.1093/nar/29.3.693. View

14.

Chen X, Mitra S, Rao S, Sekar K, Sundaralingam M . A novel end-to-end binding of two netropsins to the DNA decamers d(CCCCCIIIII)2, d(CCCBr5CCIIIII)2and d(CBr5CCCCIIIII)2. Nucleic Acids Res. 1998; 26(23):5464-71. PMC: 148001. DOI: 10.1093/nar/26.23.5464. View

15.

Nunn C, Garman E, Neidle S . Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin. Biochemistry. 1997; 36(16):4792-9. DOI: 10.1021/bi9628228. View

16.

Najmudin S, Cote M, Sun D, Yohannan S, Montano S, Gu J . Crystal structures of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain. J Mol Biol. 2000; 296(2):613-32. DOI: 10.1006/jmbi.1999.3477. View

17.

Tabernero L, Verdaguer N, Coll M, Fita I, van der Marel G, VAN Boom J . Molecular structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor groove binding drug netropsin. Biochemistry. 1993; 32(33):8403-10. DOI: 10.1021/bi00084a004. View

18.

Brunger A, Adams P, Clore G, DeLano W, Gros P, Grosse-Kunstleve R . Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 5):905-21. DOI: 10.1107/s0907444998003254. View

19.

Fratini A, Kopka M, Drew H, DICKERSON R . Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J Biol Chem. 1982; 257(24):14686-707. View

20.

Brown P, Fox K . DNA sequence preferences of several AT-selective minor groove binding ligands. Nucleic Acids Res. 1995; 23(17):3385-92. PMC: 307215. DOI: 10.1093/nar/23.17.3385. View