NMR_10_mwgLecture1 - Nucleic Acids NMR Spectroscopy Markus...

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Nucleic Acids NMR Spectroscopy Markus W. Germann Departments of Chemistry and Biology Georgia State University
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NMR of Nucleic Acids 1 1) NMR Spectroscopy for Structural Studies 2) Primary Structure of DNA and RNA 3) Resonance Assignment of DNA/RNA by Homonuclear NMR A) 1 H Chemical shifts B) Assignment of exchangeable C) Assignment of non-exchangeable proton D) Typical NOEs in helical structures E) Correlation between non-exchangeable and exchangeable protons
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http://www.rcsb.org/pdb NMR Spectroscopy is an Important Method for Structural Studies o Nucleic Acids: Technique Molecule X-ray Diffraction NMR Other 1) total PDB Holding, March 2, 2010 Proteins Nucleic Acids Protein/Nucleic Acid Complexes Other 1) EM, Hybrid, other 51 485 7 219 322 59 026 1 193 894 23 2 109 2 372 153 78 2 603 17 7 14 38 55 067 8 273 436 63 776
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Numbering 1 2 3 4 5 6 Sugar Sugar Sugar
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Numbering 9 7 8 3 2 1 6 5 4 Sugar Sugar
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Alternate Bases & Modifications (small selection):
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HETERO BASE PAIRS N N O O H 3 C N N N N N H H H N N N N O N H H H N N O N H H H + Hoogsteen N N O O H 3 C N N N N N H H H N N N N O N H H H N N O N H H Watson-Crick N N O O H 3 C N N N N N H H H N N N N O N H H H N N O N H H Reverse Watson-Crick Germann et al., Methods in Enzymology (1995), 261, 207-225. Nucleic acids: structures, properties, an functions (2000) By Victor A. Bloomfie Donald M. Crothers, Ignacio Tinoco
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N N H O O H 3 C N N H O O CH 3 N N H O O CH 3 N N H O O CH 3 HOMO BASE PAIRS N N O N H H N N O N H H H + CC + TT(I) TT(II) N N N N N H H N N N N N H H AA(I) N N N N O N H H H N N N N O N H H H GG(I) N N N N N H H N N N N N H H AA(II) GG(II) N N N N O H N N N N O H NH 2 NH 2 Germann et al., Methods in Enzymolog (1995), 261, 207-225. Nucleic acids: structures, properties, an functions (2000) By Victor A. Bloomfie Donald M. Crothers, Ignacio Tinoco
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Structure Determination: I) Assignment II) Local Analysis •glycosidic torsion angle, sugar puckering, backbone conformation base pairing III) Global Analysis •sequential, inter strand/cross strand, dipolar coupling Nucleic Acids have few protons…. . •NOE accuracy > account for spin diffusion •Backbone may be difficult to fully characterize > especially α and ζ . •Dipolar couplings
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Chemical shift ranges in nucleic acids H2 ,H2 ’’ 15 10 5 0 NH (G, T, U) NH 2 (G, C, A) DNA RNA A-U A-T G-C G-C Loops, MM Loops, MM H2, H8, H6 H2, H8, H6 H1 H1 H3 H2 ,H3 ,H4 ,H5 ,H5 ’’ H4 ,H5 ,H5 ’’
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H1' 5-6 H2' 2.3-2.9(A,G) 1.7-2.3(T,C) H2'' 2.4-3.1(A,G) 2.1-2.7(T,C) H3' 4.4-5.2 H4' 3.8-4.3 H5' 3.8-4.3 H5'' 3.8-4.3 H1' 5-6 H2' 4.4-5.0 H3' 4.4-5.2 H4' 3.8-4.3 H5' 3.8-4.3 H5'' 3.8-4.3 C1' 83-89 C2' 35-38 C3' 70-78 C4' 82-86 C5' 63-68 C1' 87-94 C2' 70-78 C3' 70-78 C4' 82-86 C5' 63-68 RNA DNA
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9R-Borano DNA•RNA 5’-d(A T G G T G C T C) (u a c c a c g a g)r-5’
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Adenine Guanine H2 7.5-8 C2 152-156 - - C2 156 H8 7.7-8.5 C8 137-142 H8 7.5-8.3 C8 131-138 N6H 5-6/7-8 N6 82-84 N1H 12-13.6 N1 146-149 - - - N2H 5-6/8-9 N2 72-76 C4 149-151 C4 152-154 C5 119-121 C5 117-119 C6 157-158 C6 161 N1 214-216 N1 146-149 N3 220-226 N3 167 N7 224-232 N7 228-238 N9 166-172 N9 166-172 Thymidine Uridine Cytidine H6 6.9-7.9 C6 137-142 H6 6.9-7.9 C6 137-142 H6 6.9-7.9 C6 136-1 Me5 1.0-1.9 Me5 15-20 H5 5.0-6.0 C5 102-107 H5 5.0-6.0 C5 94-99 N3H 13-14 N3 156 N3H 13-14 N3 156-162 - - N3 210 - - - - - - - N4H 6.7-7/81-8.8 N4 94-98 C2 154 C2 154 C2 159 C4 169 C4 169 C4 166-1 C5 95-112 C5 102-107 C5 94-99 N1 144 N1 142-146 N1 150-1
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No Structure Required!
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This note was uploaded on 11/07/2011 for the course CHEM 8853R taught by Professor Gelbaum during the Fall '11 term at Georgia Institute of Technology.

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NMR_10_mwgLecture1 - Nucleic Acids NMR Spectroscopy Markus...

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