Ignacio Tinoco

Summary

Affiliation: Lawrence Berkeley National Laboratory
Country: USA

Publications

  1. pmc Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods
    Pan T X Li
    Department of Chemistry, University of California, Berkeley, California, USA
    Biophys J 90:250-60. 2006
  2. ncbi request reprint Force as a useful variable in reactions: unfolding RNA
    Ignacio Tinoco
    Department of Chemistry, University of California, Berkeley, California 94720 1460, USA
    Annu Rev Biophys Biomol Struct 33:363-85. 2004
  3. pmc Determination of thermodynamics and kinetics of RNA reactions by force
    Ignacio Tinoco
    Department of Chemistry, University of California, Berkeley, CA 94720 1460, USA
    Q Rev Biophys 39:325-60. 2006
  4. pmc RNA reactions one molecule at a time
    Ignacio Tinoco
    Department of Chemistry, University of California, Berkeley, California 94720 1460, USA
    Cold Spring Harb Perspect Biol 2:a003624. 2010
  5. pmc The effect of force on thermodynamics and kinetics: unfolding single RNA molecules
    I Tinoco
    Chemistry Department, University of California, Berkeley, CA 94720 1460, USA
    Biochem Soc Trans 32:757-60. 2004
  6. doi request reprint Simulation and analysis of single-ribosome translation
    Ignacio Tinoco
    Department of Chemistry, University of California, Berkeley, CA 94720 1460, USA
    Phys Biol 6:025006. 2009
  7. ncbi request reprint Physical chemistry of nucleic acids
    Ignacio Tinoco
    Department of Chemistry, University of California and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 1460, USA
    Annu Rev Phys Chem 53:1-15. 2002
  8. ncbi request reprint The effect of force on thermodynamics and kinetics of single molecule reactions
    Ignacio Tinoco
    Department of Chemistry, University of California, Berkeley, CA 94720 1460, USA
    Biophys Chem 101:513-33. 2002
  9. pmc Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results
    Jin Der Wen
    Department of Chemistry, University of California, Berkeley, California, USA
    Biophys J 92:2996-3009. 2007
  10. doi request reprint The ribosome uses two active mechanisms to unwind messenger RNA during translation
    Xiaohui Qu
    Jason L Choy Laboratory of Single Molecule Biophysics and QB3 Institute, University of California, Berkeley, California 94720, USA
    Nature 475:118-21. 2011

Research Grants

  1. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2002
  2. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2003
  3. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2007
  4. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2009
  5. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2010
  6. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 1980
  7. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2011

Collaborators

Detail Information

Publications33

  1. pmc Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods
    Pan T X Li
    Department of Chemistry, University of California, Berkeley, California, USA
    Biophys J 90:250-60. 2006
    ..Thus, we find that folding of RNA hairpins can be more complex than a simple single-step reaction, and that application of several methods can improve understanding of reaction mechanisms...
  2. ncbi request reprint Force as a useful variable in reactions: unfolding RNA
    Ignacio Tinoco
    Department of Chemistry, University of California, Berkeley, California 94720 1460, USA
    Annu Rev Biophys Biomol Struct 33:363-85. 2004
    ..The main purpose of the review is to describe the simple experiments that have been done so far, and to encourage more people to enter a field that is new and full of opportunities...
  3. pmc Determination of thermodynamics and kinetics of RNA reactions by force
    Ignacio Tinoco
    Department of Chemistry, University of California, Berkeley, CA 94720 1460, USA
    Q Rev Biophys 39:325-60. 2006
    ..Unfolding of RNA in biological cells by helicases, or ribosomes, has similarities to unfolding by force...
  4. pmc RNA reactions one molecule at a time
    Ignacio Tinoco
    Department of Chemistry, University of California, Berkeley, California 94720 1460, USA
    Cold Spring Harb Perspect Biol 2:a003624. 2010
    ..Single-molecule FRET experiments yielded important information on ribosome conformational changes and tRNA dynamics during translation. Overall, single-molecule experiments have been very valuable for understanding RNA reactions...
  5. pmc The effect of force on thermodynamics and kinetics: unfolding single RNA molecules
    I Tinoco
    Chemistry Department, University of California, Berkeley, CA 94720 1460, USA
    Biochem Soc Trans 32:757-60. 2004
    ..The rate of unfolding was decreased and the rate of folding was increased by argininamide...
  6. doi request reprint Simulation and analysis of single-ribosome translation
    Ignacio Tinoco
    Department of Chemistry, University of California, Berkeley, CA 94720 1460, USA
    Phys Biol 6:025006. 2009
    ..Two rate-determining steps were only obtained at low concentrations of elongation factors. These analyses can be used to design new single-molecule experiments to better understand the kinetics and mechanism of translation...
  7. ncbi request reprint Physical chemistry of nucleic acids
    Ignacio Tinoco
    Department of Chemistry, University of California and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 1460, USA
    Annu Rev Phys Chem 53:1-15. 2002
    ....
  8. ncbi request reprint The effect of force on thermodynamics and kinetics of single molecule reactions
    Ignacio Tinoco
    Department of Chemistry, University of California, Berkeley, CA 94720 1460, USA
    Biophys Chem 101:513-33. 2002
    ..Force changes the thermodynamic stability of a molecule; it can thus increase or decrease the free energy change for the reaction. Force can also speed or slow rates of reactions; it changes the free energy of activation of the reaction...
  9. pmc Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results
    Jin Der Wen
    Department of Chemistry, University of California, Berkeley, California, USA
    Biophys J 92:2996-3009. 2007
    ..In the companion article on pages 3010-3021, we analyze how the measured kinetics parameters differ from the intrinsic molecular rates of the RNA, and thus how to obtain the molecular rates...
  10. doi request reprint The ribosome uses two active mechanisms to unwind messenger RNA during translation
    Xiaohui Qu
    Jason L Choy Laboratory of Single Molecule Biophysics and QB3 Institute, University of California, Berkeley, California 94720, USA
    Nature 475:118-21. 2011
    ..Our results establish a quantitative mechanical basis for understanding the mechanism of regulation of the elongation rate of translation by structured mRNAs...
  11. pmc Following translation by single ribosomes one codon at a time
    Jin Der Wen
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 452:598-603. 2008
    ..Translocation and RNA unwinding are strictly coupled ribosomal functions...
  12. pmc NS3 helicase actively separates RNA strands and senses sequence barriers ahead of the opening fork
    Wei Cheng
    QB3 Institute, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:13954-9. 2007
    ..Instead, we find that NS3 destabilizes the duplex before separating the strands. Failure to do so before a strong barrier leads to helicase dissociation and limits the processivity of the enzyme...
  13. pmc Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA
    Gang Chen
    Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
    RNA 13:2175-88. 2007
    ..Possible nonnative structures and folding pathways are discussed...
  14. ncbi request reprint Characterization of the mechanical unfolding of RNA pseudoknots
    Lisa Green
    Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
    J Mol Biol 375:511-28. 2008
    ..The greater mechanical stability of pseudoknots compared to hairpins, and their kinetic insensitivity to force supports the hypothesis that -1 frameshifting depends on the difficulty of unfolding the mRNA...
  15. pmc Ribosomal protein S1 unwinds double-stranded RNA in multiple steps
    Xiaohui Qu
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 109:14458-63. 2012
    ..Unwinding by multiple small substeps is much less rate limited by thermal breathing than unwinding in a single step. Thus, a multistep scheme greatly expedites S1 unwinding of an RNA structure compared to a single-step mode...
  16. pmc Temperature control methods in a laser tweezers system
    Hanbin Mao
    Lawrence Berkeley National Laboratory, California 94720, USA
    Biophys J 89:1308-16. 2005
    ..The utility of the second method was demonstrated in single-molecule experiments by measuring the mechanical stretch of a 41 kbp lambda double-stranded DNA at temperatures ranging from 8.4 degrees C to 45.6 degrees C...
  17. pmc Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting
    Gang Chen
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 106:12706-11. 2009
    ..Better understanding of the molecular determinants of frameshifting efficiency may facilitate the development of anti-virus therapeutics targeting frameshifting...
  18. pmc Measurement of the effect of monovalent cations on RNA hairpin stability
    Jeffrey Vieregg
    Department of Physics, University of California, Berkeley, California 94720, USA
    J Am Chem Soc 129:14966-73. 2007
    ..Surprisingly, the U.C.U bulge of TAR was found to be equally stable in all conditions tested. We also report a new estimate for the elastic parameters of single-stranded RNA...
  19. pmc Real-time control of the energy landscape by force directs the folding of RNA molecules
    Pan T X Li
    Department of Chemistry, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:7039-44. 2007
    ..Controlling folding pathways at the single-molecule level provides a way to survey the manifold of folding trajectories and intermediates, a capability that previously was available only to theoretical studies...
  20. pmc Unusual mechanical stability of a minimal RNA kissing complex
    Pan T X Li
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 103:15847-52. 2006
    ..The strong mechanical stability of even a minimal kissing complex indicates the importance of such loop-loop interactions in initiating and stabilizing RNA dimers in retroviruses...
  21. pmc RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP
    Sophie Dumont
    Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
    Nature 439:105-8. 2006
    ..The assay developed here should be useful in investigating a broad range of nucleic acid translocation motors...
  22. ncbi request reprint Reversible unfolding of single RNA molecules by mechanical force
    J Liphardt
    Department of Chemistry, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
    Science 292:733-7. 2001
    ..We determine the force-dependent equilibrium constants for folding/unfolding these single RNA molecules and the positions of their transition states along the reaction coordinate...
  23. pmc Biological mechanisms, one molecule at a time
    Ignacio Tinoco
    Department of Chemistry, University of California at Berkeley, USA
    Genes Dev 25:1205-31. 2011
    ....
  24. ncbi request reprint Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
    Jan Liphardt
    Department of Chemistry, Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
    Science 296:1832-5. 2002
    ..This work also extends the thermodynamic analysis of single molecule manipulation data beyond the context of equilibrium experiments...
  25. pmc Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments
    M Manosas
    Department of Chemistry, University of California at Berkeley, Berkeley, California, USA
    Biophys J 92:3010-21. 2007
    ..03 pN/nm) represent the best conditions to obtain the intrinsic molecular rates. The methodology and rationale presented here can be applied to other experimental setups and other molecules...
  26. ncbi request reprint Structural and thermodynamic studies on mutant RNA motifs that impair the specificity between a viral replicase and its promoter
    C H Kim
    Department of Chemistry, University of California Berkeley, CA, 94720-1460, USA
    J Mol Biol 307:827-39. 2001
    ..Based on this study, we conclude that the key structural motif in the triloop recognized by the replicase is a solution-exposed, 5'-adenine base in the triloop that is clamped to the stem helix, which is called a clamped adenine motif...
  27. pmc Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA
    M Schmitz
    Department of Chemistry, University of California, Berkeley 94720 1460, USA
    RNA 6:1212-25. 2000
    ..The change of the metal-ion binding site provides a possible explanation for changes in catalytic activity of the mutant RNase P in the presence of Ca2+...
  28. pmc Formation of a GNRA tetraloop in P5abc can disrupt an interdomain interaction in the Tetrahymena group I ribozyme
    M Zheng
    Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
    Proc Natl Acad Sci U S A 98:3695-700. 2001
    ..This study shows that the P5abc RNA subdomain containing a GNRA tetraloop in P5c (in contrast to the five-nucleotide loop P5c in the tertiary folded ribozyme) can disrupt the base-paired interdomain (P14) interaction between P5c and P2...
  29. ncbi request reprint A characteristic bent conformation of RNA pseudoknots promotes -1 frameshifting during translation of retroviral RNA
    X Chen
    Department of Chemistry, University of California, Berkeley 94720, USA
    J Mol Biol 260:479-83. 1996
    ..The requirement for a precise pseudoknot conformation for efficient frameshifting strongly implies that a specific interaction occurs between the viral RNA pseudoknot and the host protein-synthesizing machinery...
  30. ncbi request reprint Biophysical analysis of nucleic acids
    I Tinoco
    University of California, Lawrence Berkeley National Laboratory, Berkeley, California, USA
    Curr Protoc Nucleic Acid Chem . 2001
    ..Advantages and disadvantages of the methods are compared...
  31. pmc Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme
    Bibiana Onoa
    Department of Physics and Department of Molecular and Cell Biology and Howard Hughes Medical Institute
    Science 299:1892-5. 2003
    ..The response of complex RNA structures to locally applied mechanical forces may be analogous to the responses of RNA during translation, messenger RNA export from the nucleus, and viral replication...
  32. ncbi request reprint RNA folding and unfolding
    Bibiana Onoa
    DuPont Central Research and Development Experimental Station, PO Box 80328, Wilmington, Delaware 19880 0328, USA
    Curr Opin Struct Biol 14:374-9. 2004
    ..The hierarchical nature of RNA folding - first secondary structure, then tertiary structure - makes the process susceptible to analysis and prediction...
  33. doi request reprint How RNA unfolds and refolds
    Pan T X Li
    Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
    Annu Rev Biochem 77:77-100. 2008
    ..We also review the applications of fluorescence and fluorescence resonance energy transfer to measure RNA dynamics...

Research Grants24

  1. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2002
    ..This information will lead to improved prediction of RNA structure from sequence alone. RNA structures will help in understanding function, and in controlling the RNA role in viral and genetic diseases. ..
  2. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2003
    ..This information will lead to improved prediction of RNA structure from sequence alone. RNA structures will help in understanding function, and in controlling the RNA role in viral and genetic diseases. ..
  3. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2007
    ..This information will lead to improved understanding of RNA structure, stability, and dynamics. It will help in understanding RNA function, and in controlling the role of RNA in viral and genetic diseases ..
  4. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2009
    ..Malfunctioning RNAs that occur naturally in humans can also cause diseases. Investigation of RNA structure will provide better understanding of RNA function, and can lead to better drugs to cure or prevent human disease. ..
  5. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2010
    ..Malfunctioning RNAs that occur naturally in humans can also cause diseases. Investigation of RNA structure will provide better understanding of RNA function, and can lead to better drugs to cure or prevent human disease. ..
  6. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 1980
    ..The affect of mutagens on the conformations and stabilities of nucleic acid helices is under investigation...
  7. STRUCTURE AND FUNCTION OF NUCLEIC ACIDS
    Ignacio Tinoco; Fiscal Year: 2011
    ..Malfunctioning RNAs that occur naturally in humans can also cause diseases. Investigation of RNA structure will provide better understanding of RNA function, and can lead to better drugs to cure or prevent human disease. ..