Download as pdf or txt
Download as pdf or txt
You are on page 1of 4

Dear

Colleagues:

The provided handouts for the lecture on nucleic acids contain much more material
than I will be able to discuss during 75 minutes. In my talk I will concentrate only on
the most essential topics. There is a number of excellent reviews where many more
details can be found. With Richard tefl we have recently summarized essentials of
RNA structure determination in the chapter of a book edited by I. Bertini, K. S.
Greevy, and G. Parigi, where all the basics are briefly discussed (tefl, R. and Sklen,
V., NMR Studies of RNA, NMR of Biomolecules, Towards Mechanistic Systems
Biology, eds. Bertini, I., McGreevy, K.S., Parigi, G., Wiley-VCH, 1st edition, 2012, 118-
135).

My lecture will elaborate the content of this overview with the extension to
basic structural properties of nucleic acids, as well to assignments and structure
determination of both unlabeled and 13C/15N enriched nucleic acids. The full list of
references to this Chapter is provided bellow for your convenience. Two most
important reviews are marked in bold.

Vladimr Sklen

References:

1. R. Stefl et al., The solution structure of the ADAR2 dsRBM-RNA complex reveals a
sequence-specific readout of the minor groove. Cell 143, 225 (Oct 15, 2010).
2. J. F. Milligan, D. R. Groebe, G. W. Witherell, O. C. Uhlenbeck, Oligoribonucleotide
synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res
15, 8783 (Nov 11, 1987).
3. S. R. Price, N. Ito, C. Oubridge, J. M. Avis, K. Nagai, Crystallization of RNA-protein
complexes. I. Methods for the large-scale preparation of RNA suitable for
crystallographic studies. J Mol Biol 249, 398 (Jun 2, 1995).
4. L. Ponchon, G. Beauvais, S. Nonin-Lecomte, F. Dardel, A generic protocol for the
expression and purification of recombinant RNA in Escherichia coli using a tRNA
scaffold. Nat Protoc 4, 947 (2009).
5. L. Ponchon, F. Dardel, Recombinant RNA technology: the tRNA scaffold. Nat
Methods 4, 571 (Jul, 2007).
6. W. S. Marshall, R. J. Kaiser, Recent advances in the high-speed solid phase synthesis
of RNA. Curr Opin Chem Biol 8, 222 (Jun, 2004).
7. A. G. Tzakos, L. E. Easton, P. J. Lukavsky, Complementary segmental labeling of large
RNAs: economic preparation and simplified NMR spectra for measurement of more
RDCs. J Am Chem Soc 128, 13344 (Oct 18, 2006).
8. A. G. Tzakos, L. E. Easton, P. J. Lukavsky, Preparation of large RNA oligonucleotides
with complementary isotope-labeled segments for NMR structural studies. Nat
Protoc 2, 2139 (2007).
9. E. P. Nikonowicz, A. Pardi, An efficient procedure for assignment of the proton,
carbon and nitrogen resonances in 13C/15N labeled nucleic acids. J Mol Biol 232,
1141 (Aug 20, 1993).
10. S. S. Wijmenga, B. N. M. van Buuren, The use of NMR methods for conformational
studies of nucleic acids. Prog Nucl Mag Res Sp 32, 287 (Jun, 1998).
11. A. J. Dingley, S. Grzesiek, Direct observation of hydrogen bonds in nucleic acid base
pairs by internucleotide (2)J(NN) couplings. J Am Chem Soc 120, 8293 (Aug 26,
1998).
12. J. Wohnert et al., Direct identification of NH center dot center dot center dot N
hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy. Nucleic
Acids Res 27, 3104 (Aug 1, 1999).
13. A. J. Dingley, J. E. Masse, J. Feigon, S. Grzesiek, Characterization of the hydrogen
bond network in guanosine quartets by internucleotide (3h)J(NC ') and (2h)J(NN)
scalar couplings. J Biomol Nmr 16, 279 (Apr, 2000).
14. A. Z. Liu et al., NMR detection of N-H center dot center dot center dot O=C hydrogen
bonds in C-13,N-15-labeled nucleic acids. J Am Chem Soc 122, 3206 (Apr 5, 2000).
15. J. P. Simorre, G. R. Zimmermann, L. Mueller, A. Pardi, Correlation of the guanosine
exchangeable and nonexchangeable base protons in C-13-(IN)-N-15-labeled RNA
with an HNC-TOCSY-CH experiment. J Biomol Nmr 7, 153 (Mar, 1996).
16. J. P. Simorre, G. R. Zimmermann, A. Pardi, B. T. Farmer, L. Mueller, Triple resonance
HNCCCH experiments for correlating exchangeable and nonexchangeable cytidine
and uridine base protons in RNA. J Biomol Nmr 6, 427 (Dec, 1995).
17. V. Sklenar, T. Dieckmann, S. E. Butcher, J. Feigon, Through-bond correlation of imino
and aromatic resonances in C-13-,N-15-labeled RNA via heteronuclear TOCSY. J
Biomol Nmr 7, 83 (Jan, 1996).
18. J. P. Marino, J. H. Prestegard, D. M. Crothers, Correlation of Adenine H2/H8
Resonances in Uniformly C-13 Labeled Rnas by 2d Hcch-Tocsy - a New Tool for H-1
Assignment. J Am Chem Soc 116, 2205 (Mar 9, 1994).
19. P. Legault, B. T. Farmer, L. Mueller, A. Pardi, Through-Bond Correlation of Adenine
Protons in a C-13-Labeled Ribozyme. J Am Chem Soc 116, 2203 (Mar 9, 1994).
20. R. Fiala, M. L. Munzarova, V. Sklenar, Experiments for correlating quaternary
carbons in RNA bases. J Biomol Nmr 29, 477 (Aug, 2004).
21. J. P. Simorre, G. R. Zimmermann, L. Mueller, A. Pardi, Triple-resonance experiments
for assignment of adenine base resonances in C-13/N-15-labeled RNA. J Am Chem
Soc 118, 5316 (Jun 5, 1996).
22. J. Wohnert, R. Ramachandran, M. Gorlach, L. R. Brown, Triple-resonance
experiments for correlation of H5 and exchangeable pyrimidine base hydrogens in C-
13, N-15-labeled RNA. J Magn Reson 139, 430 (Aug, 1999).
23. R. Fiala, V. Sklenar, C-13-detected NMR experiments for measuring chemical shifts
and coupling constants in nucleic acid bases. J Biomol Nmr 39, 153 (Oct, 2007).
24. B. T. Farmer, L. Muller, E. P. Nikonowicz, A. Pardi, Unambiguous Resonance
Assignments in C-15,N-15-Labeled Nucleic-Acids by 3d Triple-Resonance Nmr. J Am
Chem Soc 115, 11040 (Nov 17, 1993).
25. B. T. Farmer, L. Muller, E. P. Nikonowicz, A. Pardi, Unambiguous through-Bond
Sugar-to-Base Correlations for Purines in C-13, N-15-Labeled Nucleic-Acids - the
Hscsnb, Hscs(N)(B)C-B, and Hbnbcb Experiments. J Biomol Nmr 4, 129 (Jan, 1994).
26. V. Sklenar, R. D. Peterson, M. R. Rejante, J. Feigon, 2-Dimensional and 3-Dimensional
Hcn Experiments for Correlating Base and Sugar Resonances in N-15,C-13-Labeled
Rna Oligonucleotides. J Biomol Nmr 3, 721 (Nov, 1993).
27. V. Sklenar, R. D. Peterson, M. R. Rejante, E. Wang, J. Feigon, 2-Dimensional Triple-
Resonance Hcnch Experiment for Direct Correlation of Ribose H1' and Base H8, H6
Protons in C-13, N-15 Labeled Rna Oligonucleotides. J Am Chem Soc 115, 12181 (Dec
15, 1993).
28. S. Tate, A. Ono, M. Kainosho, An Alternative Triple-Resonance Method for the
through-Bond Correlation of Intranucleotide H1' and H8 Nmr Signals of Purine
Nucleotides - Application to a DNA Dodecamer with Fully C-13/N-15-Labeled
Deoxyadenosine Residues. J Am Chem Soc 116, 5977 (Jun 29, 1994).
29. R. Fiala, J. Czernek, V. Sklenar, Transverse relaxation optimized triple-resonance
NMR experiments for nucleic acids. J Biomol Nmr 16, 291 (Apr, 2000).
30. B. Brutscher, J. P. Simorre, Transverse relaxation optimized HCN experiment for
nucleic acids: Combining the advantages of TROSY and MQ spin evolution. J Biomol
Nmr 21, 367 (Dec, 2001).
31. H. Schwalbe, J. P. Marino, S. J. Glaser, C. Griesinger, Measurement of H,H-Coupling
Constants Associated with Nu-1, Nu-2, and Nu-3 in Uniformly C-13-Labeled Rna by
Hcc-Tocsy-Cch-E.Cosy. J Am Chem Soc 117, 7251 (Jul 12, 1995).
32. H. A. Heus, S. S. Wijmenga, F. J. M. Vandeven, C. W. Hilbers, Sequential Backbone
Assignment in C-13-Labeled Rna Via through-Bond Coherence Transfer Using 3-
Dimensional Triple-Resonance Spectroscopy (H-1, C-13, P-31) and 2-Dimensional
Hetero Tocsy. J Am Chem Soc 116, 4983 (Jun 1, 1994).
33. J. P. Marino et al., A 3-Dimensional Triple-Resonance H-1,C-13,P-31 Experiment -
Sequential through-Bond Correlation of Ribose Protons and Intervening Phosphorus
Along the Rna Oligonucleotide Backbone. J Am Chem Soc 116, 6472 (Jul 13, 1994).
34. J. P. Marino et al., Sequential Correlation of Anomeric Ribose Protons and
Intervening Phosphorus in Rna Oligonucleotides by a H-1,C-13,P-31 Triple-
Resonance Experiment - Hcp-Cch-Tocsy. J Biomol Nmr 5, 87 (Jan, 1995).
35. R. Ramachandran, C. Sich, M. Grune, V. Soskic, L. R. Brown, Sequential assignments
in uniformly C-13- and N-15-labelled RNAs: The HC(N,P) and HC(N,P)-CCH-TOCSY
experiments. J Biomol Nmr 7, 251 (May, 1996).
36. M. Ebrahimi, P. Rossi, C. Rogers, G. S. Harbison, Dependence of 13C NMR chemical
shifts on conformations of rna nucleosides and nucleotides. J Magn Reson 150, 1
(May, 2001).
37. L. Trantirek, R. Stefl, J. E. Masse, J. Feigon, V. Sklenar, Determination of the
glycosidic torsion angles in uniformly C-13-labeled nucleic acids from vicinal coupling
constants (3)J(C2/4-H1 ') and (3)J(C6/8-H1 '). J Biomol Nmr 23, 1 (May, 2002).
38. E. Duchardt et al., Determination of the glycosidic bond angle chi in RNA from cross-
correlated relaxation of CH dipolar coupling and N chemical shift anisotropy. J Am
Chem Soc 126, 1962 (Feb 25, 2004).
39. B. Furtig, C. Richter, J. Wohnert, H. Schwalbe, NMR spectroscopy of RNA.
Chembiochem 4, 936 (Oct 6, 2003).
40. S. Nozinovic et al., Quantitative 2D and 3D Gamma-HCP Experiments for the
Determination of the Angles alpha and zeta in the Phosphodiester Backbone of
Oligonucleotides. J Am Chem Soc 132, 10318 (Aug 4, 2010).
41. L. Zidek, H. H. Wu, J. Feigon, V. Sklenar, Measurement of small scalar and dipolar
couplings in purine and pyrimidine bases. J Biomol Nmr 21, 153 (2001).
42. B. S. Tolbert et al., Major groove width variations in RNA structures determined by
NMR and impact of C-13 residual chemical shift anisotropy and H-1-C-13 residual
dipolar coupling on refinement. J Biomol Nmr 47, 205 (Jul, 2010).
43. B. Simon, T. Madl, C. D. Mackereth, M. Nilges, M. Sattler, An efficient protocol for
NMR-spectroscopy-based structure determination of protein complexes in solution.
Angew Chem Int Ed Engl 49, 1967 (Mar 8, 2010).
44. P. Guntert, Automated structure determination from NMR spectra. Eur Biophys J 38,
129 (Feb, 2009).
45. E. Suzuki, N. Pattabiraman, G. Zon, T. L. James, Solution structure of [d(A-T)5]2 via
complete relaxation matrix analysis of two-dimensional nuclear Overhauser effect
spectra and molecular mechanics calculations: evidence for a hydration tunnel.
Biochemistry-Us 25, 6854 (Nov 4, 1986).
46. R. S. Lipsitz, N. Tjandra, Residual dipolar couplings in NMR structure analysis. Annu
Rev Bioph Biom 33, 387 (2004).
47. B. S. Tolbert et al., Major groove width variations in RNA structures determined by
NMR and impact of 13C residual chemical shift anisotropy and 1H-13C residual
dipolar coupling on refinement. J Biomol Nmr 47, 205 (Jul, 2010).
48. R. W. W. Hooft, C. Sander, G. Vriend, Objectively judging the quality of a protein
structure from a Ramachandran plot. Computer Applications in the Biosciences 13,
425 (Aug, 1997).
49. C. A. E. M. Spronk, S. B. Nabuurs, E. Krieger, G. Vriend, G. W. Vuister, Validation of
protein structures derived by NMR spectroscopy. Prog Nucl Mag Res Sp 45, 315 (Dec
17, 2004).
50. G. Vriend, WHAT IF: a molecular modeling and drug design program. J Mol Graph 8,
52 (Mar, 1990).
51. M. S. Babcock, E. P. Pednault, W. K. Olson, Nucleic acid structure analysis.
Mathematics for local Cartesian and helical structure parameters that are truly
comparable between structures. J Mol Biol 237, 125 (Mar 18, 1994).
52. I. W. Davis et al., MolProbity: all-atom contacts and structure validation for proteins
and nucleic acids. Nucleic Acids Res 35, W375 (Jul, 2007).
53. S. S. Wijmenga, M. Kruithof, C. W. Hilbers, Analysis of (1)H chemical shifts in DNA:
Assessment of the reliability of (1)H chemical shift calculations for use in structure
refinement. J Biomol Nmr 10, 337 (Dec, 1997).
54. P. Davanloo, A. H. Rosenberg, J. J. Dunn, F. W. Studier, Cloning and expression of the
gene for bacteriophage T7 RNA polymerase. Proc Natl Acad Sci U S A 81, 2035 (Apr,
1984).
55. G. A. Diaz, M. Rong, W. T. McAllister, R. K. Durbin, The stability of abortively cycling
T7 RNA polymerase complexes depends upon template conformation. Biochemistry-
Us 35, 10837 (Aug 20, 1996).
56. L. E. Easton, Y. Shibata, P. J. Lukavsky, Rapid, nondenaturing RNA purification using
weak anion-exchange fast performance liquid chromatography. RNA 16, 647 (Mar,
2010).
57. I. E. Ichetovkin, N. V. Symbatyan, G. Bagherzaden, G. A. Korshunova, Synthesis of
peptide analogue of oligoribonucleotide. Vestn Mosk U Khim+ 38, 120 (Mar-Apr,
1997).

You might also like