Enhanced NMR signal detection of imino protons in RNA molecules containing 3′ dangling nucleotides

Journal of Biomolecular NMR

Volumn 40, Issue 3, 2008, Pages 183-188

  Amborski, Andrew N ^a   Johnson, Philip E ^a  

^a YORK UNIVERSITY   (Canada)

Author keywords

NMR spectroscopy; RNA NMR; RNA stability; RNA structure

Indexed keywords

ADENOSINE; CYTIDINE; GUANOSINE; IMINO ACID; MESSENGER RNA; NUCLEOTIDE; PROTON; RNA; URIDINE; WATER;

ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN INTERACTION; QUALITY CONTROL; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; TEMPERATURE DEPENDENCE; THERMODYNAMICS; WILD TYPE;

3' UNTRANSLATED REGIONS; BASE SEQUENCE; IMINES; MOLECULAR SEQUENCE DATA; MOVEMENT; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; PROTONS; RNA; SEQUENCE ANALYSIS, RNA; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 41149111291     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-008-9220-z     Document Type: Article

References (24)

1. Beribisky AV, Tavares TJ, Amborski AN, Motamed M, Johnson AE, Mark TL, Johnson PE (2007) The three-dimensional structure of the Moorella thermoacetica selenocysteine insertion sequence RNA hairpin and its interaction with the elongation factor SelB. RNA 13:1948-1956
2. Bommarito S, Peyret N, SantaLucia Jr J (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res 28:1929-1934
3. Burkard ME, Kierzek R, Turner DH (1999) Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs. J Mol Biol 290:967-982
4. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277-293
5. Flinders J, Dieckmann T (2006) NMR spectroscopy of ribonucleic acids. Prog NMR Spec 48:137-159
6. Fourmy D, Guittet E, Yoshizawa S (2002) Structure of prokaryotic SECIS mRNA hairpin and its interaction with elongation factor SelB. J Mol Biol 324:137-150
7. Furtig B, Richter C, Wohnert J, Schwalbe H (2003) NMR Spectroscopy of RNA. ChemBioChem 4:936-962
8. Huang H, Alexandrov A, Chen X, Barnes III TW, Zhang H, Dutta K, Pascal SM (2001) Structure of an RNA Hairpin from HRV-14. Biochemistry 40:8055-8064
9. Huttenhofer A, Westhof E, Böck A (1996) Solution structure of mRNA hairpins promoting selenocysteine incorporation in Escherichia coli and their base-specific interaction with special elongation factor SelB. RNA 2:354-366
10. Isaksson J, Chattopadhyaya J (2005) A uniform mechanism correlating dangling-end stabilization and stacking geometry. Biochemistry 44:5390-5401
11. Jeener J, Meier BH, Bachmann P, Ernst RR (1979) Investigation of exchange processes by two-dimensional NMR spectroscopy. J Chem Phys 71:4546-4553
12. Johnson BA, Blevins RA (1994) NMR view: A computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603-614
13. Kromayer M, Wilting R, Tormay P, Böck A (1996) Domain structure of the prokaryotic selenocysteine-specific elongation factor SelB. J Mol Biol 262:413-420
14. Macura S, Ernst RR (1980) Elucidation of cross relaxation in liquids by two-dimensional NMR spectroscopy. Mol Phys 41:95-117
15. Milligan JF, Uhlenbeck OC (1989) Synthesis of small RNAs using T7 RNA polymerase. Meth Enzymol 180:51-62
16. Mollova ET, Pardi A (2000) NMR solution structure determination of RNAs. Curr Opin Struct Biol 10:298-302
17. Neilson T, Romaniuk PJ, Alkema D, Hughes DW, Everett JR, Bell RA (1980) The effects of base sequence and dangling bases on the stability of short ribonucleic acid duplexes. Nucleic Acids Symp. Ser 293-311
18. Piotto M, Saudek V, Sklenar V (1992) Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J Biomol NMR 2:661-665
19. Plateau P, Maurice G (1982) Exchangeable proton NMR without base-line distortion using new strong-pulse sequences. J Am Chem Soc 104:7310-7311
20. Puglisi EV, Puglisi JD (1998) Nuclear Magnetic Resonance of RNA. In: Simons RW, Grunberg-Manago M (eds) RNA structure and function, Cold Spring Harbor Laboratory Press, Cold Spring Harbor
21. Romaniuk PJ, Hughes DW, Gregoire RJ, Neilson T, Bell RA (1978) Stabilizing effect of dangling bases on a short RNA double helix as determined by proton nuclear magnetic resonance spectroscopy. J Am Chem Soc 100:3971-3972
22. Varani G, Aboul-ela F, Allain FHT (1996) NMR investigation of RNA structure. Prog NMR Spect 29:51-127
23. Wyatt JR, Chastain M, Puglisi JD (1991) Synthesis and purification of large amounts of RNA oligonucleotides. Biotechniques 11:764-769
24. Zidek L, Stefl R, Sklenar V (2001) NMR methodology for the study of nucleic acids. Curr Opin Struct Biol 11:275-281