A quantitative study of the flexibility contributed to RNA structures by nicks and single-stranded gaps

RNA

Volumn 4, Issue 10, 1998, Pages 1179-1185

  Cohen, Scott B ^a   Cech, Thomas R ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

2' amine; Crosslinking; Disulfide; Flexibility; Thermal motion; Two helix junction

Indexed keywords

ARTICLE; CROSS LINKING; DISULFIDE BOND; MOLECULAR INTERACTION; PRIORITY JOURNAL; QUANTITATIVE ASSAY; RNA CONFORMATION; RNA STRUCTURE;

CROSS-LINKING REAGENTS; DISULFIDES; NUCLEIC ACID CONFORMATION; OLIGORIBONUCLEOTIDES; RNA; RNA, DOUBLE-STRANDED;

EID: 0031666950     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838298001010     Document Type: Article

References (19)

1. Benseler F, Williams DM, Eckstein F. 1992. Synthesis of suitably-protected phosphoramidites of 2′-fluoro-2′-deoxyguanosine and 2′-amino-2′-deoxyguanosine for incorporation into oligoribonu-cleotides. Nucleosides & Nucleotides 11:1333-1351.
2. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA. 1996. Crystal structure of a Group I ribozyme domain: Principles of RNA packing. Science 273:1625-1764.
3. Cech TR, Damberger SH, Gutell RR. 1994. Representation of the secondary and tertiary structure of group I introns. Nature Struc Biol 1:273-280.
4. Cohen SB, Cech TR. 1997. Dynamics of thermal motions within a large catalytic RNA investigated by cross-linking with thiol-disulfide interchange. J Am Chem Soc 119:6259-6268.
5. Forster AC, Symons RH. 1987. Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site. Cell 50:9-16.
6. Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH. 1986a. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci USA 83:9373-9377.
7. Freier SM, Sugimoto N, Sinclair A, Alkema D, Neilson T, Kierzek R, Caruthers MH, Turner DH. 1986b. Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: An empirical estimate of the energetics of hydrogen bonds in nucleic acids. Biochemistry 25:3214-3219.
8. Guthrie C, Patterson B. 1988. Spliceosomal snRNAs. Annu Rev Genet 22:387-419.
9. Hampel A, Tritz R, Hicks M, Cruz P. 1990. Hairpin catalytic RNA model: Evidence for helices and sequence requirement for substrate RNA. Nucleic Acids Res 18:299-304.
10. Hertel KJ, Herschlag D, Uhlenbeck OC. 1994. A kinetic and thermodynamic framework for the Hammerhead ribozyme reaction. Biochemistry 33:3374-3384.
11. James BD, Olsen FJ, Liu J, Pace NR. 1988. The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme. Cell 52:19-26.
12. Lehnert V, Jaeger L, Michel F, Westhof E. 1996. New loop-loop tertiary interactions in self-splicing introns of subgroup 1C and 1D: A complete 3D model of the Tetrahymena thermophila ribozyme. Chemistry & Biology 3:993-1009.
13. Mills JB, Cooper JP, Hagerman PJ. 1994. Electrophoretic evidence that single-stranded regions of one or more nucleotides dramatically increase the flexibility of DNA. Biochemistry 33:1797-1803.
14. Norberg J, Nilsson L 1995. Stacking free energy profiles for all 16 natural ribodinucleoside monophosphates in aqueous solution. J Am Chem Soc 117:10832-10840.
15. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: A laboratory manual, 2nd ed. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
16. Sigurdsson ST, Tuschl T, Eckstein F. 1995. Probing RNA tertiary structure: Interhelical crosslinking of the hammerhead ribozyme. RNA 1:575-583.
17. Sollner-Webb B, Tyc K, Steitz JA. 1993. Ribosomal RNA processing in eukaryotes. In: Dahlberg AE, Zimmermann RA, eds. Ribosomal RNA: Structure, evolution, processing, and function in protein synthesis. Boca Raton, Florida: CRC Press.
18. Verheyden JPH, Wagner D, Moffatt JG. 1971. Synthesis of some pyrimidine 2′-amino-deoxynucleosides. J Org Chem 36:250-254.
19. Wincott F, DiRenzo A, Shaffer C, Grimm S, Tracz D, Workman C, Sweedler D, Gonzalez C, Scaringe S, Usman N. 1995. Synthesis, deprotection, analysis, and purification of RNA and ribozymes. Nucleic Acids Res 23:2677-2684.