Structural Energetics of the Adenine Tract from an Intrinsic Transcription Terminator

Journal of Molecular Biology

Volumn 397, Issue 3, 2010, Pages 677-688

  Huang, Yuegao ^a   Weng, Xiaoli ^a   Russu, Irina M ^a  

^a Molecular Biophysics Program   (United States)

Author keywords

adenine tracts; base pair opening; intrinsic transcription termination; proton exchange; RNA DNA hybrids

Indexed keywords

ADENINE; DNA; RNA; RNA POLYMERASE; URACIL;

ARTICLE; BACTERIOPHAGE LAMBDA; BASE PAIRING; CONTROLLED STUDY; DNA RNA HYBRIDIZATION; DNA TRANSCRIPTION; MOLECULAR STABILITY; NONHUMAN; PRIORITY JOURNAL; RNA TRANSCRIPTION; TRANSCRIPTION TERMINATION;

ENTEROBACTERIA PHAGE LAMBDA;

EID: 77649339290     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.01.068     Document Type: Article

References (34)

1. Nudler E., Mustaev A., Lukhtanov E., and Goldfarb A. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89 (1997) 33-41
2. Korzheva N., Mustaev A., Kozlov M., Malhotra A., Nikiforov V., Goldfarb A., and Darst S.A. A structural model of transcription elongation. Science 289 (2000) 619-625
3. Lesnik E.A., Sampath R., Levene H.B., Henderson T.J., McNeil J.A., and Ecker D.J. Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Res. 29 (2001) 3583-3594
4. d'Aubenton Carafa Y., Brody E., and Thermes C. Prediction of Rho-independent Escherichia coli transcription terminators. a statistical analysis of their RNA stem-loop structures. J. Mol. Biol. 216 (1990) 835-858
5. Yarnell W.S., and Roberts J.W. Mechanism of intrinsic transcription termination and antitermination. Science 284 (1999) 611-615
6. von Hippel P.H. An integrated model of the transcription complex in elongation, termination, and editing. Science 281 (1998) 660-665
7. Greive S.J., and von Hippel P.H. Thinking quantitatively about transcription regulation. Nat. Rev. Mol. Cell Biol. 6 (2005) 221-232
8. Gusarov I., and Nudler E. The mechanism of intrinsic transcription termination. Mol. Cell 3 (1999) 495-504
9. Nudler E., and Gottesman M.E. Transcription termination and anti-termination in E. Coli. Genes Cells 7 (2002) 755-768
10. Komissarova N., Becker J., Solter S., Kireeva M., and Kashlev M. Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol. Cell 10 (2002) 1151-1162
11. Martin F.H., and Tinoco I.J. RNA-DNA hybrid duplexes containing oligo (dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription. Nucleic Acids Res. 8 (1980) 2295-2299
12. Wilson K.S., and von Hippel P.H. Transcription termination at intrinsic terminators: the role of the RNA hairpin. Proc. Natl Acad. Sci. USA 92 (1995) 8793-8797
13. Huang Y., Chen C., and Russu I.M. Dynamics and stability of individual base pairs in two homologous RNA-DNA hybrids. Biochemistry 48 (2009) 3988-3997
14. Epshtein V., Cardinale C.J., Ruckenstein A.E., Borukhov S., and Nudler E. An allosteric path to transcription termination. Mol. Cell 28 (2007) 991-1001
15. Datta K., and von Hippel P.H. Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework. J. Biol. Chem. 283 (2008) 3537-3549
16. Gueron M., and Leroy J.-L. Studies of base pair kinetics by NMR measurement of proton exchange. Methods Enzymol. 261 (1995) 383-413
17. Russu I.M. Probing site-specific energetics in proteins and nucleic acids by hydrogen exchange and NMR spectroscopy. Methods Enzymol. 379 (2004) 152-175
18. Yager T.D., and von Hippel P.H. A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli. Biochemistry 30 (1991) 1097-1118
19. Toulokhonov I., Artsimovitch I., and Landick R. Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science 292 (2001) 730-733
20. Leroy J.L., Charretier E., Kochoyan M., and Gueron M. Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature. Biochemistry 27 (1988) 8894-8898
21. Moe J.G., and Russu I.M. Proton exchange and base pair opening kinetics in 5′-d (CGCGAATTCGCG)-3′ and related dodecamers. Nucleic Acids Res. 18 (1990) 821-827
22. 3 tract. Nucleic Acids Res. 23 (1995) 1984-1989
23. Tadigotla V.R., Maoileidigh D.O., Sengupta A.M., Epshtein V., Ebright R.H., Nudler E., and Ruckenstein A.E. Thermodynamic and kinetic modeling of transcriptional pausing. Proc. Natl Acad. Sci. USA 103 (2006) 4439-4444
24. 15N-labeled, N-alkyl, and N-amino nucleosides via N-nitration of uridines and inosines. J. Am. Chem. Soc. 117 (1995) 3665-3673
25. Pitsch S., Weiss P.A., Jenny L., Stutz A., and Wu X.L. Reliable chemical synthesis of oligoribonucleotides (RNA) with 2′-O-[(triisopropylsilyl)oxy]methyl(2′-O-tom)-protected phosphoramidites. Helv. Chim. Acta 84 (2001) 3773-3795
26. 15N-labeled 2′-O-{[(triisopropylsilyl)oxy]methyl}(=tom)-protected ribonucleoside phosphoramidites and their incorporation into a bistable 32mer RNA sequence. Helv. Chim. Acta 86 (2003) 3955-3974
27. Milligan J.F., Groebe D.R., Witherell G.W., and Uhlenbeck O.C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15 (1987) 8783-8798
28. Chen C., and Russu I.M. Sequence-dependence of the energetics of opening of AT base pairs in DNA. Biophys. J. 87 (2004) 1-7
29. Plateau P., and Gueron M. Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences. J. Am. Chem. Soc. 104 (1982) 7310-7311
30. Mori S., Abeygunawardana C., Johnson M.O., and van Zijl P.C.M. Improved sensitivity of HSQC spectra of exchanging protons at short interscan delays using a new fast HSQC (FHSQC) detection scheme that avoids water saturation. J. Magn. Reson. B 108 (1995) 94-98
31. Chen C., Jiang L., Michalczyk R., and Russu I.M. Structural energetics and base-pair opening dynamics in sarcin-ricin domain RNA. Biochemistry 45 (2006) 13606-13613
32. Lippens G., Dhalluin C., and Wieruszeski J.-M. Use of a water flip-back pulse in the homonuclear NOESY experiment. J. Biomol. NMR 5 (1995) 327-331
33. Englander S.W., and Kallenbach N.R. Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 16 (1984) 521-655
34. Weast R.C. CRC Handbook of Chemistry and Physics. 67th edit. (1987), CRC Press, Boca Raton, FL