Research Topics
| Ignacio TinocoSummaryAffiliation: Lawrence Berkeley National Laboratory Country: USA Publications
Research Grants
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Detail Information
Publications
Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methodsPan 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...
Force as a useful variable in reactions: unfolding RNAIgnacio 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...- Determination of thermodynamics and kinetics of RNA reactions by forceIgnacio 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... - RNA reactions one molecule at a timeIgnacio 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... - The effect of force on thermodynamics and kinetics: unfolding single RNA moleculesI 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... 
Simulation and analysis of single-ribosome translationIgnacio 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...- Physical chemistry of nucleic acidsIgnacio 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.... - The effect of force on thermodynamics and kinetics of single molecule reactionsIgnacio 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... - Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured resultsJin 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... - The ribosome uses two active mechanisms to unwind messenger RNA during translationXiaohui 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... - Following translation by single ribosomes one codon at a timeJin 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... - NS3 helicase actively separates RNA strands and senses sequence barriers ahead of the opening forkWei 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... - Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNAGang 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... - Characterization of the mechanical unfolding of RNA pseudoknotsLisa 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... - Ribosomal protein S1 unwinds double-stranded RNA in multiple stepsXiaohui 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... - Temperature control methods in a laser tweezers systemHanbin 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... - Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshiftingGang 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... - Measurement of the effect of monovalent cations on RNA hairpin stabilityJeffrey 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... - Real-time control of the energy landscape by force directs the folding of RNA moleculesPan 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... - Unusual mechanical stability of a minimal RNA kissing complexPan 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... - RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATPSophie 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... - Reversible unfolding of single RNA molecules by mechanical forceJ 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... - Biological mechanisms, one molecule at a timeIgnacio Tinoco
Department of Chemistry, University of California at Berkeley, USA
Genes Dev 25:1205-31. 2011.... - Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equalityJan 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... - Force unfolding kinetics of RNA using optical tweezers. II. Modeling experimentsM 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... - Structural and thermodynamic studies on mutant RNA motifs that impair the specificity between a viral replicase and its promoterC 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... - Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNAM 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+... - Formation of a GNRA tetraloop in P5abc can disrupt an interdomain interaction in the Tetrahymena group I ribozymeM 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... - A characteristic bent conformation of RNA pseudoknots promotes -1 frameshifting during translation of retroviral RNAX 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... - Biophysical analysis of nucleic acidsI 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... - Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozymeBibiana 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... - RNA folding and unfoldingBibiana 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... - How RNA unfolds and refoldsPan 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 Grants
- STRUCTURE AND FUNCTION OF NUCLEIC ACIDSIgnacio 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. ..
- STRUCTURE AND FUNCTION OF NUCLEIC ACIDSIgnacio 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. ..
- STRUCTURE AND FUNCTION OF NUCLEIC ACIDSIgnacio 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 ..
- STRUCTURE AND FUNCTION OF NUCLEIC ACIDSIgnacio 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. ..
- STRUCTURE AND FUNCTION OF NUCLEIC ACIDSIgnacio 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. ..
- STRUCTURE AND FUNCTION OF NUCLEIC ACIDSIgnacio Tinoco; Fiscal Year: 1980..The affect of mutagens on the conformations and stabilities of nucleic acid helices is under investigation...
- STRUCTURE AND FUNCTION OF NUCLEIC ACIDSIgnacio 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. ..