The Gonzalez Laboratory

Publications


2011

  • Fei, J., Richard, A.C., Bronson, J.E. and Gonzalez, R.L., Jr. (2011) Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis. Nat Struct Mol Biol, (in press).
  • MacDougall, D.D. Fei, J. and Gonzalez, R.L., Jr. (2011) Single-molecule fluorescence resonance energy transfer investigations of ribosome-catalyzed protein synthesis. Molecular Machines in Biology: Workshop of the Cell, ed. J. Frank, New York, Cambridge University Press. (in press).
  • MacDougall, D.D. and Gonzalez, R.L., Jr. (2011) Exploring the structural dynamics of the translational machinery using single-molecule fluorescence resonance energy transfer. Ribosomes: Structure, Function, and Dynamics, eds. M. Rodnina, R. Green, W. Wintermeyer, New York, Springer-Verlag. (in press).
  • Tinoco, I., Jr. and Gonzalez, R.L., Jr. (2011) Biological mechanisms, one molecule at a time. Gene Dev, 25, 1205-1231. [PDF]
  • Palma, M.m Abramson, J.J., Gorodetsky, A.A., Penzo, E., Gonzalez, R.L., Jr., Sheetz, M.P., Nuckolls, C., Hone, J. and Wind, S.J. (2011) Selective biomolecular nanoarrays for parallel single-molecule investigations. J Am Chem Soc, 133, 7656-7659. [PDF] [Supp Mat]
  • Sorgenfrei, S., Chiu, C.Y., Gonzalez, R.L., Jr., Yu, Y.J., Kim, P., Nuckolls, C. and Shepard, K.L. (2011) Label-free single-molecule detection of DNA hybridization kinetics with a carbon nanotube field effect transistor. Nat Nanotechnol, 6, 126-132. [PDF] [Supp Mat]
  • Wang, B., Ho, J., Fei, J., Gonzalez, R.L., Jr. and Lin, Q. (2011) A microfluidic approach for investigating the temperature dependence of biomolecular activity with single-molecule resolution.. Lab Chip, 11, 274-281. [PDF] [Supp Mat]

 

2010

  • Bronson, J.E., Hofman, J.M., Fei, J., Gonzalez, R.L., Jr. and Wiggins, C. (2010) Graphical models for inferring single molecule dynamics. BMC Bioinformatics, 11, Supp 8, S2. [PDF]
  • Frank, J. and Gonzalez,R.L, Jr. (2010). Structure and dynamics of a processive Brownian motor: the translating ribosome. Ann Rev Biochem, 79, 381-412. [PDF]
  • Fei, J., Wang, J., Sternberg, S.H., MacDougall, D.D., Elvekrog, M.M., Pulukkunat, D., Englander, M.T. and Gonzalez, R.L., Jr. (2010). A highly-purified, fluorescently-labeled in vitro translation system for single molecule studies of protein synthesis. Methods Enzymol, 472, 221-259. [PDF]

 

2009

  • Bronson, J.E., Fei, J., Hofman, J.M. Gonzalez,R.L, Jr.* and Wiggins, C.H.* (2009). Learning rates and states from biophysical time series: A Bayesian approach to model selection and single-molecule FRET data. Biophys J,  97, 3196-3205. (*Co-corresponding authors) [PDF] [Supp Mat] [Download vbFRET Software]
    • Featured as one of the Top 5 Most Accessed Articles in Biophys J for December 2009
     
    Effraim, P.R., Wang, J., Englander, M.T., Avins, J., Leyh, T.S.*, Gonzalez, R.L., Jr.* and Cornish, V.W.* (2009). Natural amino acids do not require their native tRNAs for efficient selection by the ribosome. Nat Chem Biol, 5, 947-953. (*Co-corresponding authors) [PDF] [Supp Mat]  
  • Fei, J., Bronson, J.E., Hofman, J.M., Srinivas, R.L., Wiggins, C.H. and Gonzalez, R.L., Jr. (2009). Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc Natl Acad Sci, USA,106, 15702-15707.  [PDF] [Supp Mat]
    • Featured as a Science and Technology News Item in Chem. Engn. News, 87, 29 [PDF]
  • Sternberg, S., Fei, J., Prywes, N., McGrath, K. and Gonzalez, R.L., Jr. (2009). Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling. Nat Struct Mol Biol, 16, 861-868. [PDF] [Supp Mat]
    • Featured as a Research Highlight in Nat Chem Biol, 5, 540 [PDF]
    • Featured as a Science and Technology News Item in Chem. Engn. News, 87, 29 [PDF]

 

2008

  • Gonzalez, R.L., Jr. (2008). Navigating the RNA folding landscape. Nat Chem Biol, 4, 451-452. [PDF] 
  • Fei, J., Kosuri, P., MacDougall, D. and Gonzalez, R.L., Jr. (2008). Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol Cell, 30, 348-359. [PDF] [Supp Mat] 

 

2007

  • Wang, B., Fei, J., Nguyen,T., Gonzalez, R.L., Jr. and Lin, Q. (2007) Translocation of the ribosome in temperature-controlled microfluidic channels," Int. Conf. on Miniaturized Chemical and Biochemical Analysis Systems (MicroTAS '07), pp. 796-798, Paris, France. [PDF]
  • Wang, B., Fei, J., Nguyen, T., Gonzalez, R.L., Jr. and Lin, Q. (2007) Single-molecule detection in temperature-controlled microchannels," IEEE Int. Conf. Nano/Micro Engineered and Molecular Systems (NEMS '07), pp. 972-976, Bangkok, Thailand. [PDF]
  • Gonzalez, R.L., Jr., Chu, S. and Puglisi, J.D. (2007). Thiostrepton inhibition of tRNA delivery to the ribosome. RNA, 13, 348-359. [PDF]

 

2004

  • Dorywalska, M., Blanchard, S.C., Gonzalez, R.L., Jr., Chu, S. and Puglisi, J.D. (2004). Site-specific labeling of 16S rRNA for single-molecule spectroscopy. Nucleic Acids Res. 31, 182-189. [PDF]
  • Blanchard, S.C., Gonzalez, R.L., Jr., Kim, H.D., Chu, S. and Puglisi, J.D. (2004). tRNA selection and proofreading in translation. Nat Struct Mol Biol, 11, 1008-1014. [PDF] [Supp Mat]
    Blanchard, S.C.*, Kim, H.D.*, Gonzalez, R.L., Jr.*, Puglisi, J.D. and Chu, S. (2004). tRNA dynamics on the ribosome during translation. Proc Natl Acad Sci USA, 101, 12893-12898. (*Equal Authorship). [PDF] [Supp Mat]  

 

2003

    Lynch, S.R., Gonzalez, R.L., Jr. and Puglisi, J.D. (2003). Comparison of X-Ray crystal structure of the 30S subunit-antibioticc omplex with NMR structure of decoding site oligonucleotide paromomycin complex. Structure, 11, 43-53. [PDF]

 

2000

  • Gonzalez, R.L., Jr. and Tinoco, I. Jr. (2000). NMR spectroscopic techniques for the identification and characterization of metal ion binding sites in RNA. Methods Enzymol, 338, 421-443. [PDF]
  • Yuen, H-W., Tinoco, I. Jr. and Gonzalez, R.L., Jr. (2000). The effect of magnesium (II) ion and cobalt (III) hexammine ion on an RNA pseudoknot. Berkeley Scientific, 4, 139-143.

 

1999

  • Gonzalez, L.R.,Jr and Tinoco, I. Jr. (1999). Solution Structure and Thermodynamics of a Divalent Metal Ion Binding Site in an RNA Pseudoknot. J Mol Biol, 289, 1267-1282. [PDF]