2-Aminopurine labelled RNA bulge loops. Synthesis and thermodynamics

Biochimie

Volumn 78, Issue 2, 1996, Pages 123-130

  Zagorowska I ^a   Adamiak, R W ^a  

^a INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

Author keywords

2 aminopurine; chemical synthesis; RNA bulge loops; thermodynamics

Indexed keywords

2 AMINOPURINE; RNA;

ARTICLE; RNA ANALYSIS; RNA CONFORMATION; RNA SYNTHESIS; SPECTROFLUOROMETRY; STRUCTURE ANALYSIS; THERMODYNAMICS;

EID: 0029762376     PISSN: 03009084     EISSN: None     Source Type: Journal    
DOI: 10.1016/0300-9084(96)82644-7     Document Type: Article

References (27)

1. 1 Wyatt JR, Tinoco Jr I (1993) RNA structural elements and RNA function. In: The RNA World (Gesteland RF, Atkins JF, eds) Cold Spring Harbor Laboratory Press, 465-496
2. 2 Longfellow CE, Kierzek R, Turner DH (1990) Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides. Biochemistry 29, 278-285
3. 3 van den Hoogen YT, van Beuzekon AA, de Vroom E, van der Marel GA, van Boom JH, Altona C (1988) Bulge-out structures in the single stranded trimer AUA and in the duplex (CUGGUGCGG) (CCGCCCAG). Nucleic Acids Res 16, 5013-5030
4. 4 Zhang P, Popieniek P, Moore PB (1989) Physical studies of 5S RNA variants at position 66. Nucleic Acids Res 17, 8645-8657
5. 5 Puglisi JD, Tan R, Calnan BJ, Frankel AD, Williamson JR (1992) Conformation of the TAR RNA-arginine complex by NMR. Science 257, 76-80
6. 6 Bhattacharyya A, Murchie AIH, Lilley DMJ (1990) RNA bulges and the helical periodicity of double-stranded RNA. Nature 343, 484-487
7. 7 Tang CK, Draper DE (1990) Bulge loops used to measure the helical twist of RNA in solution. Biochemistry 29, 5232-5237
8. 8 Sharp PA (1987) Splicing of messenger RNA precursors. Science 235, 766-771
9. 9 Frankel AD (1992) Activation of HIV transcription by Tat. Curr Opin Genet Dev 2, 293-298
10. 10 Gerster JS, Jones JW, Robins RK (1963) Purine nucleosides IV. The synthesis of 6-halogenated 9-(β-D-ribofuranosyl)-purines from inosine and guanosine. J Org Chem 28, 945-948
11. 11 Usman N, Ogilvie KK, Jiang MJ, Cedergren RJ (1987) Automated chemical synthesis of long oligoribonucleotides using 2′-O-sililated ribonucleoside 3′-O-phosphoramidites on a controlled-pore glass support: synthesis of a 43-nucleotide sequence similar to the 3′-half molecule of an Escherichia coli formylmethionine tRNA. J Am Chem Soc 109, 7845-7854
12. 31P NMR study of 2′-O-tBDMSi group migration during nucleoside 3′-OH phosphorylation and phosphitylation reactions. Nucleosides Nucleotides 8, 463-472
13. 13 Rigler R, Claesens F, Kristensen O (1985) Picosecond fluorescence spectroscopy in the analysis of structure and motion of biopolymers. Anal Instrument 14, 525-546
14. 14 Nordlund TM, Andersson S, Nilsson L, Rigler R, Graslund A, McLaughlin LW (1989) Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies. Biochemistry 28, 9095-9103
15. 15 Borer PN (1975) In: CRC Handbook of Biochemistry and Molecular Biology (Fasman GD, ed) CRC Press, Cleveland, vol 1, p 589
16. 16 Santa Lucia Jr J, Kierzek R, Turner DH (1991) Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops. J Am Chem Soc 113, 4313-4322
17. 17 Petersheim M, Turner DH (1983) Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp and ACCGGUp. Biochemistry 22, 256-263
18. 18 Freier SM, Burger BJ, Alkema D, Neilson T, Turner DH (1983) Effects of 3′ dangling end stacking on the stability of GGCC and CCGG double helices. Biochemistry 22, 6198-6206
19. 19 Borer PN, Dengler B, Tinoco Jr I, Uhlenbeck OC (1974) Stability of ribonucleic acid double stranded helices. J Mol Biol 86, 843-853
20. 20 Doudna JA, Szostak W, Rich A, Usman N (1990) Chemical synthesis of oligoribonucleotides containing 2-aminopurine: substrates for the investigation of ribozyme function. J Org Chem 55, 5547-5549
21. 21 Tuschl T, Ng MMP, Pieken W, Benseler F, Eckstein F (1993) Importance of exocyclic base functional groups of central core guanosines for hammerhead ribozyme activity. Biochemistry 32, 11658-11668
22. 22 Fox JJ, Wempen I, Hampton A, Doerr IL (1958) Thiation of nucleosides. I. Synthesis of 2-amino-6-mercapto-9-β-D-ribofuranosylpurine ('thioguanosine') and related purine nucleosides. J Am Chem Soc 80, 1669-1675
23. 1H NMR analysis of isomeric 2′(3′)-O-trialkylsilyl and 2′(3′)-O-methyl ribonucleosides. Polish J Chem 68, 275-280
24. 13C)methyl- and 5-methyl-analogs of ribo-CGCGCG. Acta Biochim Pol 40, 521-530
25. 25 Santa Lucia Jr J, Kierzek R, Turner DH (1992) Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. Science 256, 217-219
26. 26 Rychlik W (1994) OLIGO 5.0 primer analysis software for Windows. National Biosciences Inc USA
27. 27 Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci USA 83, 9373-9377