SpringerProtocols: Abstract: High-Resolution NMR of DNA and Drug-DNA Interactions

High-Resolution NMR of DNA and Drug-DNA Interactions

By: Jill Barber², Helen F. Cross², John A. Parkinson³

Abstract

Full Text

Download PDF (1455K)

The advantage of NMR over most other spectroscopic techniques lies in the ability to gain structural and dynamic information at atomic resolution. Every nucleus with spin gives rise to a signal that is characterized by a number of parameters (chemical shift, J-couplings, relaxation data, and NOE connectivities) that can be used to obtain quite detailed structural information about the molecule under study. They can also be used to determine kinetic properties, for example, the interconversion rates of different conformations of a molecule and the exchange rate of free with bound ligand on a macromolecule. NMR has been widely used to study both static and dynamic aspects of DNA structure and drug-DNA interactions.

Affiliation(s): (2) Department of Pharmacy, University of Manchester, UK
(3) Department of Chemistry, University of Edinburgh, UK

Book Title: Spectroscopic Methods and Analyses: NMR, Mass Spectrometry, and Metalloprotein Techniques

Series: Methods in Molecular Biology | Volume: 17 | Pub. Date: May-23-1993 | Page Range: 87-113 | DOI: 10.1385/0-89603-215-9:87

Subject: Cell Biology

References

Download References

1.	Dervan, P. B. (1986) Design of sequence-specific DNA-binding molecules Science 232, 464–471.

2.	Goodsall, D and Dickerson, R E (1986) Isohelical analysis of DNA groove-binding drugs. J. Med. Chem. 29, 727–733.

3.	Kissinger, K, Krowicki, K, Dabriowak, J C, and Lown, J W (1987) Molecular recognition between oligopeptides and nucleic acids Monocationic imidazole Lexitropsins that display enhanced GC sequence dependent DNA binding. Biochemistry 26, 5590–5595.

4.	Zakrzewska, K and Pullman, B (1988) Theoretical study of the sequence selectivity of isolexins, isohelical DNA groove binding ligands. Proposals for the GC minor groove specific compounds J. Biomol Struct. Dyn 5, 1043–1058.

5.	Thurston, D. E and Thompson, A. S (1990) The molecular recognition of DNA. Chem Br. 26, 767–772.

6.	van de Ven, F J M and Hilbers, C W (1988) Nucleic acids and nuclear magnetic resonance. Eur. J. Biochem. 178, 1–38.

7.	Wemmer, D. E., Chou, S. H, Hare, D. R., and Reid, B R. (1985) Duplexhairpin transitions in DNA NMR studies on CGCGTATACGCG Nucleic Acids Res. 13, 3755–3772.

8.	Delort, A.-M., Neumann, J M, Molko, D., Hervé, M, Téoule, R, and Tran Dinh, S. (1985) Influence of uracil defect on DNA structure ¹H NMR investigation at 500 MHz Nucleic Acids Res 13, 3343–3354.

9.	Feigon, J., Wang, A. H-J., van der Marel, G A., van Boom, J. H, and Rich, A (1984) A one-and two-dimensional NMR study of the B to Z transition of (m⁵dC-dG)₃ in methanolic solution. Nucleic Acids Res 12, 1243–1263.

10.	Rajagopal, P, Gilbert, D E, van der Marel, G. A, van Boom, J. H, and Feigon, J (1988) Observation of exchangeable proton resonances of DNA in two-dimensional NOE spectra using a presaturation pulse. application to d(CGCGAA-TTCGCG) and d(CGCGAm⁶ATTCGCG) J. Magn Reson. 78, 1243–1263.

11.	Hore, P. J (1983) A new method for water suppression in the proton NMR spectrum of aqueous solutions J. Magn. Reson. 54, 539–542.

12.	Hore, P J (1983) Solvent suppression in Fourier transform NMR. J. Magn Reson. 55, 283–300.

13.	Lefèvre, J.-F, Lane, A. N, and Jardetsky, O. (1987) Solution structure of the trp operator of E. coli determined by NMR Biochemistry 26, 5076–5090.

14.	Byrd, R. A., Summers, M F., and Zon, G. (1986) A new approach for assigning ³¹P NMR signals and correlating adjacent nucleoside deoxyribose moieties via ¹H-detected multiple-quantum NMR Apphcation to the adduct of d(TGGT) with the anticancer agent (ethylenediamine) dichloroplatinum. J. Am. Chem Soc. 108, 504,505.

15.	Shah, D. O., Lai, K, and Gorenstein, D. G (1984) Facile synthesis and ³¹P NMR spectra of a double-labelled oligonucleotide d(Ap¹⁷O)Gp(¹⁸O)Cp(¹⁶O)T) J. Am Chem Soc 106, 4302,4303.

16.	James, T L., Bendel, P., James, J.L., Keepers, J W., Kollman, P. A., Lapidot, A., Murphy-Boesch, J., and Taylor, J. E. (1983) Conformational flexibility of nucleic acids Jerusalem Symp Quantum Chem Biochem 16, 155–167.

17.	Kessler, H., Gehrke, M., and Griesinger, C (1988) Two-dimensional NMR spectroscopy—background and overview of the experiments Angew Chem Int Ed. Engl. 27, 490–536.

18.	Wuthrich, K. (1986) NMR of Proteins and Nucleic Acids Wiley, New York.

19.	Hare, D. R, Wemmer, D. E, Chou, S-H, Drobny, G, and Reid, B R. (1983) Assignment of the non-exchangeable proton resonances of d(CGCGAATTCGCG) using two dimensional nuclear magnetic resonance methods. J Mel Biol 171, 319–336.

20.	Parkinson, J. A (1989) NMR Studies on the Met J Operator from Escherichia coli. Ph D Thesis University of Leeds, UK.

21.	Orbons, L. P. M, van der Marel, G A., van Boom, J. H, and Altona, C (1986) The B and Z forms of the d(m⁵C-G)₃ and d(br⁵C-G)₃ hexamers in solution a 300 MHz and 500 MHz two-dimensional NMR study. Eur J. Biochem 160, 131–139.

22.	Haasnoot, C A G., Westerink, H. P, van der Marel, G A, and van Boom, J. H. (1984) Discrimination between A-type and B-type conformations of double helical nucleic acid fragments in solution by means of two dimensional nuclear Overhauser experiments. J Biomol Struct Dyn 2, 345–360.

23.	Nerdal, W, Hare, D R, and Reid, B R. (1988) Three-dimensional structure of the wild-type lac Pribnow promoter DNA in solution J Mel Biol 201, 717–739.

24.	Clore, G M, Oschkinat, H, McLaughlin, L W, Benseler, F, Happ, C. S, Happ, E, and Gronenborn, A M (1988) Refinement of the structure of the DNA dodecamer 5-d(CGCGPATTCGCG)₂ containing a stable purine-thymine base pair combined use of nuclear magnetic resonance and restrained molecular dynamics Biochemistry 27, 4185–4197.

25.	Metzler, W. J., Wang, C., Kitchen, D. B, Levy, R M., and Pardi, A (1990) Determining local conformational variation in DNA. J. Mol Biol 214, 711–736.

26.	Quignard, E, Fazakerley, G V, van der Marel, G A., van Boom, J. H., and Guschlbauer, W (1987) Comparison of the conformation of an oligonucleotide containing a central G-T base pair with non-mismatch sequence by proton NMR Nucleic Acids Res.. 15, 3397–3409.

27.	Patel, D J., Kozlowski, S. A, Marky, L. A., Rice, J. A, Broka, C, Dallas, J, Itakura, K., and Breslauer, K. J. (1982) Structure, dynamics, and energetics of deoxy guanosine-thymidine wobble base pair formation in the self complementary d(CGTGAATTCGCG) duplex in solution Biochemistry 21, 437–444.

28.	Joshua-Tor, L., Rabinovich, D., Hope, H., Frowlow, F., Appella, E., and Sussman, J. L (1988) The three-dimensional structure of a DNA duplex containing looped-out bases. Nature 334, 82–84.

29.	Patel, D.J., Kozlowski, S A., Marky, L. A., Rice, J A., Broka, C., Itakura, K, and Breslauer, K J. (1982) Extra adenosine stacks into the self complementary d(CGCAGAATTCGCG) duplex in solution. Biochemistry 21, 445–451.

30.	Morden, K M, Chu, Y. G., Martin, F. H., and Tinoco, I (1983) Unpaired cytosine in the deoxyoligonucleotide duplex dCA₃Ca₃G • dCT₆G is outside of the helix. Biochemistry 22, 5557–5563.

31.	Patel, D J. and Shapiro, L (1985) Molecular recognition in noncovalent antitumour agent-DNA complexes NMR studies of the base and sequence dependent recognition of the DNA minor groove by netropsin Biochimie 67, 887–915.

32.	Parkinson, J A, Barber, J, Douglas, K. T., Sharples, D, and Rosamond, J (1990) Minor-groove recognition of the self-complementary duplex d(CGCGAATTCGCG)₂ by Hoechst 33258 a high-field NMR study Biochemistry 29, 10,181–10,190.

33.	Patel, D J. (1982) Antibiotic-DNA interactions intermolecular nuclear Overhauser effects in the netropsin-d(CGCGAATTCGCG) complex in solution. Proc. Natl. Acad Sci USA 79, 6424–6428.

34.	Lee, M., Hartley, J. A., Pon, R T., Krowicki, K, and Lown, J. W. (1988) Sequence specific molecular recognition by a monocationic lexitropsin of the decadeoxyribonucleotide d(CATGGCATG)₂, structural and dynamic aspects deduced from the high field ¹H NMR studies Nucleic Acids Res 16, 665–684.

35.	Pelton, J G and Wemmer, D. E. (1989) Structural characterisation of a 2·1 distamycin A d(CGCAAATTGGC) complex by two-dimensional NMR. Proc. Natl Acad. Sci USA 86, 5723–5727.

36.	Klevit, R. E., Wemmer, D E., and Reid, B. R (1986) ¹H NMR studies of the interaction between distamycin A and a symmetrical DNA dodecamer Biochemistry 25, 3296–3303.

37.	Wilson, W. D. and Jones, R. L (1982) Interaction of actinomycin D, ethidium, quinacrine, daunorubicin, and tetra-lysine with DNA: ³¹P NMR chemical shift and relaxation investigation. Nucleic Acids Res. 10, 1399–1410.

38.	Chandrasekaran, S, Kusuma, S., Boykin, D. W., and Wilson, W. D. (1986) A new approach utilising high-resolution proton NMR in structural analysis on intercalation complexes of natural DNA Magn. Reson. Chem 24, 630–637.

39.	Shafer, R H., Brown, S. C., Delbarre, A., and Wade, D (1984) Binding of ethidium and bis(methidium) spermine to Z DNA by intercalation. Nucleic Acids Res. 12, 4679–4690.

40.	Mirau, P A, Shafer, R H., James, T L, and Bolton, P. H (1982) Fluoroquinacrine binding to nucleic acids: investigation of the ¹⁹F NMR, optical, and fluorescence properties in the presence of DNA, poly(A) and tRNA Biopolymers 21, 909–921.

41.	Wilson, W. D, Jones, R. L, Zon, G, Banville, D. L, and Marzilli, L G. (1986) Specificity in DNA interactions: an NMR investigation of the interaction of propidium with oligodeoxynucleotides containing normal and G-T base pairs Biopolymers 25, 1991–2015.

42.	Mariam, Y H and Wilson, W D (1983) Effect of intercalating drugs and temperature on the association of sodium ions with DNA ²³Na NMR studies J Am Chem Soc. 105, 627,628.

43.	Gao X and Patel, D J (1989)Antitumour drug-DNA interactions. NMR studies of echinomycin and chromomycin complexes Q Rev Biophys 22, 93–138.

44.	Wilson, W D., Jones, R L., Scott, E V., Zon, G, and Marzilli, L. G. (1986) Actinomycin D binding to oligonucleotides with 5′d(GCGC)3′ sequences Definitive ¹H and ³¹P NMR evidence for two distinct d(GC) 1 1 adducts and for adjacent sate binding in a unique 2·1 adduct J Am Chem Soc 108, 7113,7114.

45.	Jones. R L., Scott, E V, Zon, G., Marzilli, L. G, and Wilson, W D (1988) An NMR investigation of the binding of the anticancer drug actinomycin D to oligodeoxyribonucleosides with isolated 5′d(GC)3′ binding sites. Biochemistry 27, 6021–6026.

46.	Scott, E V, Jones, R L., Banville, D L, Zon, G, Marzilli, L G, and Wilson, W. D. (1986) ¹H and ³¹P NMR investigations of actinomycin D binding selectivity with deoxyribonucleosides containing multiple adjacent d(GC) sites Biochemistry 27, 915–923.

47.	Banville, D. L., Keniry, M. A, Kam, M, and Shafer, R H (1990) NMR studies of the interaction of chromomycin A₃ with small DNA duplexes. Binding to GC-containing sequences Biochemistry 29, 6521–6534.

48.	den Hartog, J H J., Altona, C, Chottard, J-C, Girault, J-P., Lallemand, Y, de Leeuw, F. A A. M, Marcelis, A T. M., and Reedjik, J (1982) Conformational analysis of the adduct cis-[Pt(NH₃)₂ d(GpG)]⁺ in aqueous solution A high field (500–300 MHz) NMR study Nucleic Acids Res 10, 4715–3730.

49.	den Hartog, J H J., Altona, C, van der Marel, G A, and Reedjik, J (1984) A ¹H and ³¹P NMR study of cis-Pt(NH₃)₂ [d(CpGpG)-N7(2), N7(3)] Eur J Biochem 147, 371–379.

50.	Harris, T M., Stone, M P., and Harris, C M. (1988) Application of NMR spectroscopy to studies of reactive intermediates and their interactions with nucleic acids Chem Res Toxiccol 1, 79–97.

Comments (Loading...)

Post comment/View all comments