Life at Berkeley for the past 57 years involved research on the thermodynamics, kinetics, and spectroscopic properties of RNA to better understand its structures, interactions, and functions. We (myself and all the graduate students and postdocs who shared in the fun) began with dinucleoside phosphates and slowly worked our way up to megadalton-sized RNA molecular motors. We used UV absorption, circular dichroism, circular intensity differential scattering, fluorescence, NMR, and single-molecule methods. We learned a lot and had fun doing it.


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Literature Cited

  1. Banks RE. 1.  1960. Transstar. Galaxy Science Fiction. Jun. 108–34
  2. Borer PN, Dengler B, Tinoco I Jr, Uhlenbeck OC. 2.  1974. Stability of ribonucleic acid double-stranded helices. J. Mol. Biol. 86:843–53 [Google Scholar]
  3. Cantor CR, Tinoco I Jr. 3.  1965. Absorption and optical rotatory dispersion of seven trinucleoside diphosphates. J. Mol. Biol. 13:65–77 [Google Scholar]
  4. Cheong C, Varani G, Tinoco I Jr. 4.  1990. Solution structure of an unusually stable RNA hairpin, 5′GGAC(UUCG)GUCC. Nature 346:680–82 [Google Scholar]
  5. Comstock MJ, Ha T, Chemla YR. 5.  2011. Ultrahigh-resolution optical trap with single-fluorophore sensitivity. Nat. Methods 8:335–40 [Google Scholar]
  6. Hall K, Cruz P, Tinoco I Jr, Jovin TM, van de Sande JH. 6.  1984. ‘Z-RNA’—a left-handed RNA double helix. Nature 311:584–86Discovery and characterization of Z-RNA. [Google Scholar]
  7. James JK, Tinoco I Jr. 7.  1993. The solution structure of a d[C(TTCG)G] DNA hairpin and comparison to the unusually stable RNA analogue. Nucleic Acids Res. 21:3287–93 [Google Scholar]
  8. Jarzynski C. 8.  1997. Equilibrium free-energy differences from nonequilibrium measurements: a master-equation approach. Phys. Rev. E 56:5018–35 [Google Scholar]
  9. Kang H, Hines JV, Tinoco I Jr. 9.  1996. Conformation of a non-frameshifting RNA pseudoknot from mouse mammary tumor virus. J. Mol. Biol. 259:135–47 [Google Scholar]
  10. Kirkwood JG. 10.  1937. On the theory of optical rotatory power. J. Chem. Phys. 5:479–91 [Google Scholar]
  11. Lee CH, Tinoco I Jr. 11.  1977. Studies of the conformation of modified dinucleoside phosphates containing 1,N6-ethenoadenosine and 2′-O-methylcytidine by 360-MHz 1H nuclear magnetic resonance spectroscopy. Investigation of the solution conformations of dinucleoside phosphates. Biochemistry 16:5403–14 [Google Scholar]
  12. Liphardt J, Dumont S, Smith SB, Tinoco I Jr, Bustamante C. 12.  2002. Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science 296:1832–35 [Google Scholar]
  13. Liphardt J, Onoa B, Smith SB, Tinoco I Jr, Bustamante C. 13.  2001. Reversible unfolding of single RNA molecules by mechanical force. Science 292:733–37 [Google Scholar]
  14. Maestre MF, Bustamante C, Hayes TL, Subirana JA, Tinoco I Jr. 14.  1982. Differential scattering of circularly polarized light by the helical sperm head from the octopus Eledone cirrhosa. Nature 298:773–74 [Google Scholar]
  15. Mickols W, Maestre MF, Tinoco I Jr, Embury SH. 15.  1985. Visualization of oriented hemoglobin S in individual erythrocytes by differential extinction of polarized light. Proc. Natl. Acad. Sci. USA 82:6527–31 [Google Scholar]
  16. Mickols W, Tinoco I Jr, Katz JE, Maestre MF, Bustamante C. 16.  1985. Imaging differential polarization microscope with electronic readout. Rev. Sci. Instrum. 56:2228–36 [Google Scholar]
  17. Moore D, Tinoco I Jr. 17.  1980. The circular dichroism of large helices. A free particle on a helix. J. Chem. Phys. 72:3396–400 [Google Scholar]
  18. Oncley JL. 18.  1959. Biophysical science—a study program. Rev. Mod. Phys. 31:1–563 [Google Scholar]
  19. Patterson D, Schnell M, Doyle JM. 19.  2013. Enantiomer-specific detection of chiral molecules via microwave spectroscopy. Nature 497:475–77 [Google Scholar]
  20. Puglisi JD, Wyatt JR, Tinoco I Jr. 20.  1988. A pseudoknotted RNA oligonucleotide. Nature 331:283–86First NMR structure of an RNA pseudoknot. [Google Scholar]
  21. Qu X, Wen JD, Lancaster L, Noller HF, Bustamante C, Tinoco I Jr. 21.  2011. The ribosome uses two active mechanisms to unwind messenger RNA during translation. Nature 475:118–21 [Google Scholar]
  22. Shen LX, Tinoco I Jr. 22.  1995. The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus. J. Mol. Biol. 247:963–78 [Google Scholar]
  23. Tinoco I Jr. 23.  1955. Conversion of fibrinogen to fibrin XVI. Electrical birefringence of fibrinogen and activated fibrinogen. J. Am. Chem. Soc. 77:3476–80 [Google Scholar]
  24. Tinoco I Jr. 24.  1957. The change of optical activity of poly-γ-benzyl-l-glutamate in an electric field. J. Am. Chem. Soc. 79:4248–49 [Google Scholar]
  25. Tinoco I Jr. 25.  1959. The optical rotation of oriented helices I. Electrical orientation of poly-γ-benzyl-l-glutamate in ethylene dichloride. J. Am. Chem. Soc. 81:1540–44 [Google Scholar]
  26. Tinoco I Jr. 26.  1960. Hypochromism in polynucleotides. J. Am. Chem. Soc. 82:4785–90 [Google Scholar]
  27. Tinoco I Jr. 27.  2013. The Medical Research Council Laboratory of Molecular Biology, January to July, 1964. Memories and Consequences: Visiting Scientists at the MRC Laboratory of Molecular Biology H Huxley 79–84 London: Icon Books [Google Scholar]
  28. Tinoco I Jr, Borer PN, Dengler B, Levine MD, Uhlenbec OC. 28.  et al. 1973. Improved estimation of secondary structure in ribonucleic acids. Nat. New Biol. 246:40–41 [Google Scholar]
  29. Tinoco I Jr, Ferry JD. 29.  1954. The site of attack by thrombin on fibrinogen. J. Am. Chem. Soc. 76:5573–74 [Google Scholar]
  30. Tinoco I Jr, Freeman MP. 30.  1957. The optical activity of oriented copper helices. I. Experimental. J. Phys. Chem. 61:1196–200First measurement of the optical rotary dispersion and circular dichroism in the microwave region of oriented helices. [Google Scholar]
  31. Tinoco I Jr, Gonzalez RL Jr. 31.  2011. Biological mechanisms, one molecule at a time. Genes Dev. 25:1205–31 [Google Scholar]
  32. Tinoco I Jr, Hammerle WG. 32.  1956. The influence of an external electric field on the optical activity of fluids. J. Phys. Chem. 60:1619–23 [Google Scholar]
  33. Tinoco I Jr, Uhlenbeck OC, Levine MD. 33.  1971. Estimation of secondary structure in ribonucleic acids. Nature 230:362–67Prediction of RNA structure from sequence. [Google Scholar]
  34. Tinoco I Jr, Woody RW. 34.  1960. Optical rotation of oriented helices. II. Calculation of the rotatory dispersion of the alpha-helix. J. Chem. Phys. 32:461–67 [Google Scholar]
  35. Tinoco I Jr, Woody RW. 35.  1964. Optical rotation of oriented helices. IV. Free electron on a helix. J. Chem. Phys. 40:160–64 [Google Scholar]
  36. Turner DH, Tinoco I Jr, Maestre MF. 36.  1975. Fluorescence detected circular dichroism study of the anticodon loop of yeast tRNAPhe. Biochemistry 14:3794–99 [Google Scholar]
  37. Warshaw MM, Tinoco I Jr. 37.  1966. Optical properties of sixteen dinucleoside phosphates. J. Mol. Biol. 20:29–38 [Google Scholar]
  38. Watson JD, Crick FH. 38.  1953. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737–38 [Google Scholar]
  39. Wen JD, Lancaster L, Hodges C, Zeri AC, Yoshimura SH. 39.  et al. 2008. Following translation by single ribosomes one codon at a time. Nature 452:598–603Translation of a single messenger RNA by a single ribosome. [Google Scholar]
  40. Zheng M, Wu M, Tinoco I Jr. 40.  2001. Formation of a GNRA tetraloop in P5abc can disrupt an interdomain interaction in the Tetrahymena group I ribozyme. Proc. Natl. Acad. Sci. USA 98:3695–700 [Google Scholar]

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