NMR_10_mwgLecture2

NMR_10_mwgLecture2 - Nucleic Acid NMR Part II O3 and pose...

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Nucleic Acid NMR Part II
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! " # $ % & O5’ O3’ ( 3 ( 0 ( 1 ( 2 ( 4 O4’ nucleotide unit α and ζ pose problems Determinants of 31 P chem shift. ε and ζ correlate. ζ = -317-1.23 ε Ranges χ α β γ δ ε ζ B-DNA -119 -61 180 57 122 -187 -91 Bf-DNA -102 -41 136 38 139 -133 -157 Af-DNA -154 -90 -149 47 83 -175 -45 Sanger, Principles of nucleic acid Springer 1984
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Backbone Experiments: CT-NOESY, CT-COSY Bax, A., Tjandra, N., Zhengrong, W., ( 2001). Measurements of 1 H- 31 P dipolar couplings in a DNA oligonucleotide by constant time NOESY difference spectroscopy, J. Mol. Biol., 19, 367-270. ε Attenuated Scan
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Σ Backbone Experiments • Z. Wu, N. Tjandra, and A. Bax, Measurement of H3’- 31 P dipolar couplings in a DNA oligonucleotide by constant-time NOESY difference spectroscopy, J. Biomol. NMR 19, 367-370 (2001). • A. Bax, N. Tjandra, W. Zhengrong. Measurements of 1 H- 31 P dipolar couplings in a DNA oligonucleotide by constant time NOESY difference spectroscopy, J. Mol. Biol., 19, 367-270, 91 ( 2001). • G. M. Clore, E. C. Murphy, A. M. Gronenborn, and A. Bax, Determination of three-bond H3’- 31 P couplings in nucleic acids and protein-nucleic acid complexes by quantitative J correlation spectroscopy, J. Mag. Reson. 134, 164-167 (1998). • H. Schwalbe, W. Samstag, J. W. Engels, W. Bermel, & C. Griesinger, "Determination of 3 J(C,P) and 3 J(H,P) Coupling Constants in Nucleotide Oligomers", J. Biomol. NMR 3, 479-486 (1993). • BioNMR in Drug Research 2003 Edito: O. Zerbe Methods for the Measurement of Angle Restraints from Scalar, Dipolar Couplings and from Cross- Correlated Relaxation: Application to BiomacromoleculesChapter Author: Christian Griesinger: J-Resolved Constant Time Experiment for the Determination of the Phosphodiester Backbone Angles α and ζ .
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Resonance Assignment DNA/RNA (Homonuclear) A) Non Exchangeable Protons •Aromatic Spin Systems NOESY, DQFCOSY, TOCSY •Sugar Spin Systems DQFCOSY, TOCSY •Sequential Assignment NOESY, 31 P- 1 H HETCOR B) Exchangeable Protons 1D, NOESY (11, WG, etc) C) Correlation of Exchangeable NOESY (excitation sculpting) and Non Exchangeable Protons
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NH N O O N N NH 2 O C U A)Assignment of Non Exchangeable Protons Base and Sugar COSY/TOCSY C: H5-H6 U: H5-H6 TOCSY A: H8-H2 (H2 are generally difficult to assign) COSY/TOCSY H1’ -H2’ (H2’’) etc N N N N H 2 N H H A J Zhang, A Spring, M W Germann J. Am. Chem. Soc. 131 5
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Resonance Assignment DNA/RNA (Homonuclear) Sequential Assignment
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7.4 α C8 A5 ppm 5.4 5.6 5.8 6.0 6.2 ppm 7.6 8.0 T6 C10 T7 C2 G1 G9 G3 A4 8.2 7.8 7.2 NOESY Connectivity (e.g. α C Decamer) G1-H1 G1- H8
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7.4 α C8 A5 ppm 5.4 5.6 5.8 6.0 6.2 ppm 7.6 8.0 T6 C10 T7 C2 G1 G9 G3 A4 8.2 7.8 7.2
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7.4 α C8 A5 ppm 5.4 5.6 5.8 6.0 6.2 ppm 7.6 8.0 T6 C10 T7 C2 G1 G9 G3 A4 8.2 7.8 7.2
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7.4 α C8 A5 ppm 5.4 5.6 5.8 6.0 6.2 ppm 7.6 8.0 T6 C10 T7 C2 G1 G9 G3 A4 8.2 7.8 7.2 2'2'' 2'2'' 2'2'' G α C T 3'-3 5'-5' H H H C G T T A A G C G-5’ 5’-G C G A A T T G C α C α C alphaC
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5’- CATGCATG GTACGTAC – 5’ DNA Miniduplex Excercise
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31 P NMR
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NMR_10_mwgLecture2 - Nucleic Acid NMR Part II O3 and pose...

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