Conformational analysis of the telomerase RNA pseudoknot hairpin by Raman spectroscopy

RNA

Volumn 13, Issue 1, 2007, Pages 108-115

  Reipa, Vytas ^a   Niaura, Gediminas ^b   Atha, Donald H ^a  

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

^b CENTER FOR PHYSICAL SCIENCES AND TECHNOLOGY   (Lithuania)

Author keywords

Raman spectroscopy; RNA conformation; RNA pseudoknot hairpin; Telomerase

Indexed keywords

OLIGONUCLEOTIDE; RIBOSE; TELOMERASE; URIDINE;

ARTICLE; HUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; RAMAN SPECTROMETRY; RNA CONFORMATION; RNA SEQUENCE; RNA STABILITY; RNA STRUCTURE; TEMPERATURE DEPENDENCE; THERMODYNAMICS;

BASE SEQUENCE; DYSKERATOSIS CONGENITA; HUMANS; MUTATION; NUCLEIC ACID CONFORMATION; RIBONUCLEOTIDES; RNA; RNA STABILITY; SPECTRUM ANALYSIS, RAMAN; TELOMERASE; THERMODYNAMICS; TRANSITION TEMPERATURE;

EID: 33845871717     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.182607     Document Type: Article

References (27)

1. Abdelkafi, M., Leulliot, N., Ghomi, M., Herve du Penhoat, C., Namane, A., Gouyette, C., Huynh-Dinh, T., Baumruk, V., and Turpin, P.Y. 1997a. Thermodynamic and structural properties of r(ACC) as revealed by ultraviolet electronic absorption, circular dichroism, 1H-NMR spectroscopy and Monte Carlo simulations. J. Biomol. Struct. Dyn. 409: 241-245.
2. Abdelkafi, M., Ghomi, M., Turpin, P.Y., Baumruk, V., Herve du Penhoat, C., Lampire, O., Bouchemal-Chibani, N., Goyer, P., Namane, A., Gouyette, C., et al. 1997b. Common structural features of UUCG and UACG tetraloops in very short hairpins determined by UV absorption, Raman, IR and NMR spectroscopies. J. Biomol. Struct. Dyn. 14: 579-593.
3. Abdelkafi, M., Leulliot, N., Baumruk, V., Bednarova, L., Turpin, P.Y., Namane, A., Gouyette, C., Huynh-Dinh, T., and Ghomi, M. 1998. Structural features of the UCCG and UGCG tetraloops in very short hairpins as evidenced by optical spectroscopy. Biochemistry 37: 7878-7884.
4. Allsopp, R.C., Vaziri, H., Patterson, C., Goldstein, S., Yonglai, E.V., Futcher, A.B., Greider, C.W., and Harley, C.B. 1992. Telomere length predicts replicative capacity of human fibroblasts. Proc. Natl. Acad. Sci. 89: 10114-10118.
5. Baumruk, V., Gouyette, C., Huyh-Dinh, T., Sun, J.S., and Ghomi, M. 2001. Comparison between CUUG and UUCG tetraloops: Thermodynamic stability and structural features analyzed by UV absorption and vibrational spectroscopy. Nucleic Acids Res. 29: 4089-4096.
6. 2O solutions and application to B, Z and A-DNA. Nucleic Acids Res. 11: 5747-5761.
7. Blackburn, E.H. 1991. Structure and function of telomeres. Nature 350: 569-573.
8. Chen, H.-L. and Greider, C.W. 2005. Functional analysis of the pseudoknot structure in human telomerase RNA. Proc. Natl. Acad. Sci. 102: 8080-8085.
9. Chen, H.-L., Blasco, M.A., and Greider, C.W. 2000. Secondary structure of vertebrate telomerase RNA. Cell 100: 503-514.
10. Comolli, L.R., Smirnov, I., Xu, L., Blackburn, E.H., and James, T.L. 2002. A molecular switch underlies a human telomerase disease. Proc. Natl. Acad. Sci. 99: 16998-17003.
11. Dohy, D., Ghomi, M., and Taillandier, E. 1989. Interpretation of DNA vibration modes: III-The behaviour of the sugar pucker vibration modes as a function of its pseudorotation parameters. J. Biomol. Struct. Dyn. 6: 741-754.
12. Kim, N.W., Piatyszek, M.A., Prowse, K.R., Harley, C.B., West, M.D., Ho, P.L., Coviello, G.M., Wright, W.E., Weinrich, S.L., and Shay, J.W. 1994. Specific association of human telomerase activity with immortal cells and cancer. Science 266: 2011-2015.
13. Leulliot, N., Baumruk, V., Abdelkafi, M., Turpin, P.Y., Namane, A., Gouyette, C., Tam, H.D., and Ghomi, M. 1999a. Unusual nucleotide conformations in GNRA and UNCG type tetraloop hairpins: Evidence from Raman markers assignments. Nucleic Acids Res. 27: 1398-1404.
14. Leulliot, N., Ghomi, M., Jobic, H., Bouloussa, O., Baumruk, V., and Coulombeau, C. 1999b. Ground state properties of the nucleic acid constituents studied by density functional calculations. 2. Comparison between calculated and experimental vibrational spectra of Uridine and Cytidine. J. Phys. Chem. B. 103: 10934-10944.
15. Li, T., Johnson, J.E., and Thomas, Jr., G.J. 1993. Raman dynamic probe of hydrogen exchange in Bean Pod Mottle virus: Base-specific retardation of exchange in packaged ssRNA. Biophys. J. 65: 1963-1972.
16. Martin-Rivera, L. and Blasco, M.A. 2001. Identification of functional domains and dominant negative mutations in vertebrate telomerase RNA using an in vivo reconstitution system. J. Biol. Chem. 276: 5856-5865.
17. Peticolas, W.L. 1995. Raman spectroscopy of DNA and proteins. Methods Enzymol. 246: 389-416.
18. Scaringe, S.A., Wincott, F.E., and Caruthers, M.H. 1998. Novel RNA synthesis method using 5′-silyl-2′-orthoester protecting groups. J. Chem. Soc. 120: 11820-11821.
19. Small, E.W., Brown, K.G., and Peticolas, W.L. 1972. Structural changes in t-RNA from changes in the Raman scattering intensities. Biopolymers 11: 1209-1215.
20. Theimer, C.A., Finger, L.D., and Feigon, J. 2003a. YNMG tetraloop formation by a dyskeratosis congenital mutation in human telomerase RNA. RNA 9: 1446-1455.
21. Theimer, C.A., Finger, L.D., Trantirek, L., and Feigon, J. 2003b. Mutations linked to dyskeratosis congenital cause changes in the structural equilibrium in telomerase RNA. Proc. Natl. Acad. Sci. 100: 449-454.
22. Theimer, C.A., Blois, C.A., and Feigon, J. 2005. Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol. Cell 17: 671-682.
23. Thomas, G.A. and Peticolas, W.L. 1983. Fluctuations in nucleic acid conformations 2. Raman spectroscopic evidence of varying ring pucker in A-T Polynucleotides. J. Am. Chem. Soc. 105: 993-996.
24. Thomas, G.J. 1999. Raman spectroscopy of protein and nucleic acid assemblies. Annu. Rev. Biophys. Biomol. Struct. 28: 1-27.
25. Thomas, G.J. and Tsuboi, M. 1993. Raman spectroscopy of nucleic acids and their complexes. Adv. Biophys. Chem. 3: 1-70.
26. Trulson, M.A., Cruz, P., Puglisi, J.D., Tinoco, Jr., I., and Mathies, R.A. 1987. Raman spectroscopic study of left-handed Z-RNA. Biochemistry 26: 8624-8630.
27. Yingling, Y.G. and Shapiro, B.A. 2005. Dynamic behavior of the telomerase RNA hairpin structure and its relationship to dyskeratosis congenita. J. Mol. Biol. 348: 27-42.