Taking femtosecond snapshots of RNA conformational dynamics and complexity

Current Opinion in Chemical Biology

Volumn 12, Issue 6, 2008, Pages 604-611

  Xia, Tianbing ^a  

^a UNIVERSITY OF TEXAS AT DALLAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

BIOPHYSICS; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; FLUORESCENCE RESONANCE ENERGY TRANSFER; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PROTEIN RNA BINDING; REVIEW; SPECTROSCOPY; THERMODYNAMICS; TIME RESOLVED SPECTROSCOPY;

BACTERIOPHAGE LAMBDA; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA; TIME FACTORS; VIRAL PROTEINS;

EID: 57549085374     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2008.08.033     Document Type: Review

References (54)

1. Crothers D.M. RNA Conformational Dynamics. In: Soll D., Nishimura S., and Moore P.B. (Eds). RNA (2001), Elsevier Science Ltd.
2. Williamson J.R. Induced fit in RNA-protein recognition. Nat Struct Biol 7 (2000) 834-837
3. Leulliot N., and Varani G. Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 40 (2001) 7947-7956
4. Al-Hashimi H.M. Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy. ChemBioChem 6 (2005) 1506-1519
5. Al-Hashimi H.M., and Walter N.G. RNA dynamics: it is about time. Curr Opin Struct Biol 18 (2008) 321-329
6. Xia T., Becker H.C., Wan C., Frankel A., Roberts R.W., and Zewail A.H. The RNA-protein complex: direct probing of the interfacial recognition dynamics and its correlation with biological functions. Proc Natl Acad Sci U S A 100 (2003) 8119-8123. First paper describing use of femtosecond time-resolved fluorescence spectroscopy probing an RNA-protein complex that identified multiple conformations of the boxB/N complex.
7. Xia T., Wan C.Z., Roberts R.W., and Zewail A.H. RNA-protein recognition: single-residue ultrafast dynamical control of structural specificity and function. Proc Natl Acad Sci U S A 102 (2005) 13013-13018. Analysis of the physical nature of interactions between boxB RNA and N peptide that determine the population distributions, by combination of femtosecond time-resolved fluorescence and transient absorbance spectroscopy.
8. Zhao L., and Xia T. Direct revelation of multiple conformations in RNA by femtosecond dynamics. J Am Chem Soc 129 (2007) 4118-4119. First example of application of femtosecond time-resolved spectroscopy to capture multiple conformations of an RNA motif.
9. Liu J.D., Zhao L., and Xia T. The dynamic structural basis of differential enhancement of conformational stability by 5′- and 3′-dangling ends in RNA. Biochemistry 47 (2008) 5962-5975. Quantitative analysis of the correlation between the population distribution of stacking structures of dangling end bases with thermodynamic stability enhancement.
10. Wan C., Fiebig T., Schiemann O., Barton J.K., and Zewail A.H. Femtosecond direct observation of charge transfer between bases in DNA. Proc Natl Acad Sci U S A 97 (2000) 14052-14055
11. Fiebig T., Wan C., and Zewail A.H. Femtosecond charge transfer dynamics of a modified DNA base: 2-aminopurine in complexes with nucleotides. ChemPhysChem 3 (2002) 781-788
12. O'Neill M.A., Becker H.C., Wan C., Barton J.K., and Zewail A.H. Ultrafast dynamics in DNA-mediated electron transfer: base gating and the role of temperature. Angew Chem Int Ed Engl 42 (2003) 5896-5900
13. Wan C.Z., Xia T.B., Becker H.C., and Zewail A.H. Ultrafast unequilibrated charge transfer: a new channel in the quenching of fluorescent biological probes. Chem Phys Lett 412 (2005) 158-163
14. Cate J.H., Gooding A.R., Podell E., Zhou K.H., Golden B.L., Kundrot C.E., Cech T.R., and Doudna J.A. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273 (1996) 1678-1685
15. Jucker F.M., Heus H.A., Yip P.F., Moors E.H., and Pardi A. A network of heterogeneous hydrogen bonds in GNRA tetraloops. J Mol Biol 264 (1996) 968-980
16. Davis J.H., Tonelli M., Scott L.G., Jaeger L., Williamson J.R., and Butcher S.E. RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. J Mol Biol 351 (2005) 371-382
17. Menger M., Eckstein F., and Porschke D. Dynamics of the RNA hairpin GNRA tetraloop. Biochemistry 39 (2000) 4500-4507
18. Sorin E.J., Engelhardt M.A., Herschlag D., and Pande V.S. RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. J Mol Biol 317 (2002) 493-506
19. Krasilnikov A.S., Yang X.J., Pan T., and Mondragon A. Crystal structure of the specificity domain of ribonuclease P. Nature 421 (2003) 760-764
20. Pley H.W., Flaherty K.M., and McKay D.B. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature 372 (1994) 111-113
21. Cheong C.J., Varani G., and Tinoco I. Solution structure of an unusually stable RNA hairpin, 5'ggac(UUCG)Gucc. Nature 346 (1990) 680-682
22. SantaLucia J., Kierzek R., and Turner D.H. Context dependence of hydrogen-bond free-energy revealed by substitutions in an RNA hairpin. Science 256 (1992) 217-219
23. Moody E.M., Feerrar J.C., and Bevilacqua P.C. Evidence that folding of an RNA tetraloop hairpin is less cooperative than its DNA counterpart. Biochemistry 43 (2004) 7992-7998
24. Butcher S.E., Dieckmann T., and Feigon J. Solution structure of a GAAA tetraloop receptor RNA. EMBO J 16 (1997) 7490-7499
25. Cate J.H., Gooding A.R., Podell E., Zhou K.H., Golden B.L., Szewczak A.A., Kundrot C.E., Cech T.R., and Doudna J.A. RNA tertiary structure mediation by adenosine platforms. Science 273 (1996) 1696-1699
26. Qin P.Z., Feigon J., and Hubbell W.L. Site-directed spin labeling studies reveal solution conformational changes in a GAAA tetraloop receptor upon Mg2+-dependent docking of a GAAA tetraloop. J Mol Biol 351 (2005) 1-8
27. Hodak J.H., Fiore J.L., Nesbitt D.J., Downey C.D., and Pardi A. Docking kinetics and equilibrium of a GAAA tetra loop-receptor motif probed by single-molecule FRET. Proc Natl Acad Sci U S A 102 (2005) 10505-10510
28. Sattint B.D., Zhao W., Travers K., Chut S., and Herschlag D. Direct measurement of tertiary contact cooperativity in RNA folding. J Am Chem Soc 130 (2008) 6085-6087
29. Chauhan S., and Woodson S.A. Tertiary interactions determine the accuracy of RNA folding. J Am Chem Soc 130 (2008) 1296-1303
30. Yang X.J., Gerczei T., Glover L., and Correll C.C. Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping. Nat Struct Biol 8 (2001) 968-973
31. Turner D.H., Sugimoto N., and Freier S.M. RNA Structure Prediction. Annu Rev Biophys Biophys Chem 17 (1988) 167-192
32. Freier S.M., Alkema D., Sinclair A., Neilson T., and Turner D.H. Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes. Biochemistry 24 (1985) 4533-4539
33. Burkard M.E., Kierzek R., and Turner D.H. Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs. J Mol Biol 290 (1999) 967-982
34. Isaksson J., and Chattopadhyaya J. A uniform mechanism correlating dangling-end stabilization and stacking geometry. Biochemistry 44 (2005) 5390-5401
35. Bommarito S., Peyret N., and SantaLucia J. Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res 28 (2000) 1929-1934
36. Legault P., Li J., Mogridge J., Kay L.E., and Greenblatt J. NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell 93 (1998) 289-299
37. Scharpf M., Sticht H., Schweimer K., Boehm M., Hoffmann S., and Rosch P. Antitermination in bacteriophage lambda. The structure of the N36 peptide-boxB RNA complex. Eur J Biochem 267 (2000) 2397-2408
38. Greenblatt J., Nodwell J.R., and Mason S.W. Transcriptional antitermination. Nature 364 (1993) 401-406
39. Franklin N.C. Clustered arginine residues of bacteriophage lambda N protein are essential to antitermination of transcription, but their locale cannot compensate for boxB loop defects. J Mol Biol 231 (1993) 343-360
40. Xia T., Frankel A., Takahashi T.T., Ren J., and Roberts R.W. Context and conformation dictate function of a transcription antitermination switch. Nat Struct Biol 10 (2003) 812-819
41. Millar D.P., Robbins R.J., and Zewail A.H. Direct observation of the torsional dynamics of DNA and RNA by picosecond spectroscopy. Proc Natl Acad Sci U S A 77 (1980) 5593-5597
42. Pal S.K., Zhao L., and Zewail A.H. Water at DNA surfaces: ultrafast dynamics in minor groove recognition. Proc Natl Acad Sci U S A 100 (2003) 8113-8118. Probed the ultrafast hydration of the minor groove of DNA using a minor groove-binding drug.
43. Pal S.K., Zhao L., Xia T., and Zewail A.H. Site- and sequence-selective ultrafast hydration of DNA. Proc Natl Acad Sci U S A 100 (2003) 13746-13751. Identified hydration dynamics on two different ultrafast timescales that represent bulk and layered water molecules in the major and minor grooves of DNA.
44. Andreatta D., Lustres J.L.P., Kovalenko S.A., Ernsting N.P., Murphy C.J., Coleman R.S., and Berg M.A. Power-law solvation dynamics in DNA over six decades in time. J Am Chem Soc 127 (2005) 7270-7271. Used three different techniques to cover a broad time-range (40 fs-40 ns) of the time-resolved emission spectrum and demonstrated the DNA dynamics distribute broadly.
45. Berg M.A., Coleman R.S., and Murphy C.J. Nanoscale structure and dynamics of DNA. Phys Chem Chem Phys 10 (2008) 1229-1242
46. Pal S.K., Peon J., Bagchi B., and Zewail A.H. Biological water: femtosecond dynamics of macromolecular hydration. J Phys Chem B 106 (2002) 12376-12395
47. Pal S.K., and Zewail A.H. Dynamics of water in biological recognition. Chem Rev 104 (2004) 2099-2123
48. Ma H.R., Wan C.Z., and Zewail A.H. Ultrafast T-jump in water: studies of conformation and reaction dynamics at the thermal limit. J Am Chem Soc 128 (2006) 6338-6340. Demonstrated the first temperature jump (20 °C) with ultrafast time-resolution.
49. Ma H.R., Wan C.Z., Wu A.G., and Zewail A.H. DNA folding and melting observed in real time redefine the energy landscape. Proc Natl Acad Sci U S A 104 (2007) 712-716. Application of ultrafast temperature jump to monitor the energy landscape of the folding and unfolding of a DNA hairpin.
50. Hochstrasser R.M. Two-dimensional spectroscopy at infrared and optical frequencies. Proc Natl Acad Sci U S A 104 (2007) 14190-14196. Reviewed the state-of-the-art ultrafast 2D IR and its applications and challenges.
51. Rist M.J., and Marino J.P. Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions. Curr Org Chem 6 (2002) 775-793
52. Batey R.T., Gilbert S.D., and Montange R.K. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432 (2004) 411-415
53. Serganov A., Yuan Y.-R., Pikovskaya O., Polonskaia A., Malinina L., Phan A.T., Hobartner C., Micura R., Breaker R.R., and Patel D.J. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem Biol 11 (2004) 1729-1741
54. Gilbert S.D., and Batey R.T. Riboswitches: fold and function. Chem Biol 13 (2006) 805-807