Andrew D Ellington

Summary

Affiliation: University of Texas
Country: USA

Publications

  1. ncbi request reprint Evolution. Changing the cofactor diet of an enzyme
    Andrew D Ellington
    Departments of Chemistry and Integrative Biology, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Science 310:454-5. 2005
  2. pmc Deoxyribozymes that recode sequence information
    Jeffrey J Tabor
    Center for Systems and Synthetic Biology and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Nucleic Acids Res 34:2166-72. 2006
  3. doi request reprint In vitro selection of RNA aptamers to a protein target by filter immobilization
    Bradley Hall
    Department of Chemistry and Biochemistry, University of Texas, Austin, Texas, USA
    Curr Protoc Mol Biol . 2009
  4. doi request reprint In vitro selection using modified or unnatural nucleotides
    Scott M Knudsen
    University of Texas, Austin, Texas, USA
    Curr Protoc Nucleic Acid Chem . 2002
  5. doi request reprint Technical and biological issues relevant to cell typing with aptamers
    Na Li
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
    J Proteome Res 8:2438-48. 2009
  6. pmc Transiently transfected purine biosynthetic enzymes form stress bodies
    Alice Zhao
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 8:e56203. 2013
  7. pmc Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization
    Matthew Levy
    Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78751, USA
    RNA 11:1555-62. 2005
  8. pmc Engineering stochasticity in gene expression
    Jeffrey J Tabor
    Center for Systems and Synthetic Biology and Institute for Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Mol Biosyst 4:754-61. 2008
  9. doi request reprint Design, synthesis, and amplification of DNA pools for in vitro selection
    Bradley Hall
    Department of Chemistry and Biochemistry, University of Texas, Austin, Texas, USA
    Curr Protoc Mol Biol . 2009
  10. doi request reprint An in vitro autogene
    Eric A Davidson
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
    ACS Synth Biol 1:190-6. 2012

Collaborators

Detail Information

Publications77

  1. ncbi request reprint Evolution. Changing the cofactor diet of an enzyme
    Andrew D Ellington
    Departments of Chemistry and Integrative Biology, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Science 310:454-5. 2005
  2. pmc Deoxyribozymes that recode sequence information
    Jeffrey J Tabor
    Center for Systems and Synthetic Biology and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Nucleic Acids Res 34:2166-72. 2006
    ..The binary deoxyribozyme ligases could potentially be used in a variety of applications, including the detection of single nucleotide polymorphisms in genomic DNA or the identification of short nucleic acids such as microRNAs...
  3. doi request reprint In vitro selection of RNA aptamers to a protein target by filter immobilization
    Bradley Hall
    Department of Chemistry and Biochemistry, University of Texas, Austin, Texas, USA
    Curr Protoc Mol Biol . 2009
    ..Bound complexes are separated from unbound reagents by filtration, and the RNA:protein complexes are amplified by a combination of reverse transcription, PCR, and in vitro transcription...
  4. doi request reprint In vitro selection using modified or unnatural nucleotides
    Scott M Knudsen
    University of Texas, Austin, Texas, USA
    Curr Protoc Nucleic Acid Chem . 2002
    ..It includes a discussion of when to use modified nucleotides; protocols for preparing a modified RNA pool and verifying its suitability for in vitro selection; and protocols for selecting and amplifying a functionally enriched pool...
  5. doi request reprint Technical and biological issues relevant to cell typing with aptamers
    Na Li
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
    J Proteome Res 8:2438-48. 2009
    ..Better understanding and controlling for the role of background and nonspecific binding to cells should open the way to using arrays of aptamers for describing and quantifying the cell surface proteome...
  6. pmc Transiently transfected purine biosynthetic enzymes form stress bodies
    Alice Zhao
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 8:e56203. 2013
    ....
  7. pmc Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization
    Matthew Levy
    Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78751, USA
    RNA 11:1555-62. 2005
    ....
  8. pmc Engineering stochasticity in gene expression
    Jeffrey J Tabor
    Center for Systems and Synthetic Biology and Institute for Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Mol Biosyst 4:754-61. 2008
    ..These results demonstrate that synthetic genetic constructs can significantly affect the noise profile of a living cell and, importantly, that operons are a facile genetic strategy for buffering against noise...
  9. doi request reprint Design, synthesis, and amplification of DNA pools for in vitro selection
    Bradley Hall
    Department of Chemistry and Biochemistry, University of Texas, Austin, Texas, USA
    Curr Protoc Mol Biol . 2009
    ..Support protocols describe determination of the complexity and skewing of the pool, and optimization of amplification conditions...
  10. doi request reprint An in vitro autogene
    Eric A Davidson
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
    ACS Synth Biol 1:190-6. 2012
    ..Compartmentalization of individual templates within a water-in-oil emulsion links genotype and phenotype, allowing evolution...
  11. pmc DNA circuits as amplifiers for the detection of nucleic acids on a paperfluidic platform
    Peter B Allen
    University of Texas at Austin, Chemistry and Biochemistry Dept, 1 University Station, A4800, USA
    Lab Chip 12:2951-8. 2012
    ..By bridging the gap between the low concentrations of LAMP amplicons and the limits of fluorescence detection, the non-enzymatic amplifier allowed us to detect as few as 1200 input templates in a paperfluidic format...
  12. doi request reprint Gene synthesis: methods and applications
    Randall A Hughes
    Applied Research Laboratories, The University of Texas at Austin, Austin, Texas, USA
    Methods Enzymol 498:277-309. 2011
    ..Finally, an example of automated gene synthesis from our own laboratory is provided...
  13. pmc Direct selection for ribozyme cleavage activity in cells
    Xi Chen
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    RNA 15:2035-45. 2009
    ..More importantly, these results have led us to develop a quantitative, kinetic model that can be used to assess the stringency of the hybrid selection scheme and to direct future experiments...
  14. pmc Arginine-rich motifs present multiple interfaces for specific binding by RNA
    Travis S Bayer
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    RNA 11:1848-57. 2005
    ....
  15. pmc Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response
    Yariv Wine
    Department of Chemical Engineering, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712 1062, USA
    Proc Natl Acad Sci U S A 110:2993-8. 2013
    ..The ability to deconvolute the polyclonal serum response is likely to be of key importance for analyzing antibody responses after vaccination and for more completely understanding adaptive immune responses in health and disease...
  16. pmc Identification and characterization of the constituent human serum antibodies elicited by vaccination
    Jason J Lavinder
    Department of Chemical Engineering, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, Center for Systems and Synthetic Biology, Department of Biomedical Engineering, Department of Chemistry and Biochemistry, and Applied Research Laboratories, University of Texas at Austin, Austin, TX 78712 1062
    Proc Natl Acad Sci U S A 111:2259-64. 2014
    ..Collectively, our results reveal the nature and dynamics of the serological response to vaccination with direct implications for vaccine design and evaluation. ..
  17. pmc novel modifications on C-terminal domain of RNA polymerase II can fine-tune the phosphatase activity of Ssu72
    Yonghua Luo
    Department of Chemistry and Biochemistry and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
    ACS Chem Biol 8:2042-52. 2013
    ..Overall, we report the first case of structural and kinetic effects of phosphorylated Thr4 on CTD modifying enzymes. Our results support a model in which a combinatorial cascade of CTD modification can modulate transcription. ..
  18. ncbi request reprint Functional RNA microarrays for high-throughput screening of antiprotein aptamers
    James R Collett
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Anal Biochem 338:113-23. 2005
    ..Integrating RNA aptamer microarray production with the maturing technology for automated in vitro selection of antiprotein aptamers should result in the high-throughput production of proteome chips...
  19. doi request reprint Evolutionary origins and directed evolution of RNA
    Andrew D Ellington
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
    Int J Biochem Cell Biol 41:254-65. 2009
    ..Self-replication would have inexorably led to life...
  20. pmc Antibody repertoires in humanized NOD-scid-IL2Rγ(null) mice and human B cells reveals human-like diversification and tolerance checkpoints in the mouse
    Gregory C Ippolito
    Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 7:e35497. 2012
    ..Overall, our results provide evidence that key features of the primary repertoire are shaped by genetic factors intrinsic to human B cells and are principally unaltered by differences between mouse and human stromal microenvironments...
  21. pmc Modelling amorphous computations with transcription networks
    Zack Booth Simpson
    Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
    J R Soc Interface 6:S523-33. 2009
    ..1038/msb4100099)). The hairpin transcriptional gates are uniquely suited to the design of a complementary NAND gate that can serve as an underlying basis of molecular computing that can output matter rather than electronic information...
  22. pmc Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits
    Bingling Li
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    J Am Chem Soc 134:13918-21. 2012
    ..These findings highlight the potential impacts of DNA circuitry on DNA nanotechnology and provide new tools for further development of these fields...
  23. pmc Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires
    Brandon J DeKosky
    Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
    Proc Natl Acad Sci U S A 113:E2636-45. 2016
    ..The data reported here address several longstanding questions regarding antibody repertoire selection and development and provide a benchmark for future repertoire-scale analyses of antibody responses to vaccination and disease...
  24. pmc Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness
    Michael J Hammerling
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
    Nat Chem Biol 10:178-80. 2014
    ....
  25. pmc G-quadruplex-generating polymerase chain reaction for visual colorimetric detection of amplicons
    Sanchita Bhadra
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Anal Biochem 445:38-40. 2014
    ..Furthermore, primer design considerations for the G-quadruplex-generating PCR system have allowed us to visually distinguish SNPs associated with Mycobacterium tuberculosis drug resistance alleles. ..
  26. doi request reprint Directed evolution of proteins in vitro using compartmentalization in emulsions
    Eric A Davidson
    University of Texas at Austin, Austin, Texas, USA
    Curr Protoc Mol Biol . 2009
    ....
  27. doi request reprint Kinetic optimization of a protein-responsive aptamer beacon
    Bradley Hall
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
    Biotechnol Bioeng 103:1049-59. 2009
    ..By integrating these various interactions, we were ultimately able to design aptamer beacons that were activated by threefold within 1 min of the addition of thrombin...
  28. ncbi request reprint The robustness of naturally and artificially selected nucleic acid secondary structures
    Lauren Ancel Meyers
    Section of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA
    J Mol Evol 58:681-91. 2004
    ..The thermostability of RNA molecules bred in the laboratory is probably not constrained by a lack of suitable variation in the sequence pool but, rather, by intrinsic biases in the selection process...
  29. pmc Design principles for ligand-sensing, conformation-switching ribozymes
    Xi Chen
    Department of Chemistry and Biochemistry, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
    PLoS Comput Biol 5:e1000620. 2009
    ..The robust theoretical framework and identified optimization parameters should now enable the precision design of aptazymes for biotechnological and clinical applications...
  30. ncbi request reprint Ribozyme-mediated signal augmentation on a mass-sensitive biosensor
    Scott M Knudsen
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    J Am Chem Soc 128:15936-7. 2006
    ..Aptazyme activity was observed in real time, and low-molecular-weight analyte detection has been successfully demonstrated with both aptazymes...
  31. pmc Engineering antibody fragments to fold in the absence of disulfide bonds
    Min Jeong Seo
    Department of Chemical Engineering, University of Texas, Austin, 78712, USA
    Protein Sci 18:259-67. 2009
    ..Using this approach, we isolated scFv antibody variants that are fully active when expressed in the cytoplasm or when the four Cys residues that normally form disulfides are substituted by Ser residues...
  32. doi request reprint Structure-based design of supercharged, highly thermoresistant antibodies
    Aleksandr E Miklos
    Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
    Chem Biol 19:449-55. 2012
    ..Such supercharged antibodies should prove useful for assays in resource-limited settings and for developing reagents with improved shelf lives...
  33. ncbi request reprint Developing RNA tools for engineered regulatory systems
    Jeffrey J Tabor
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712 0159, USA
    Biotechnol Genet Eng Rev 22:21-44. 2006
  34. doi request reprint Coupling two different nucleic acid circuits in an enzyme-free amplifier
    Yu Jiang
    Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Molecules 17:13211-20. 2012
    ..The modular circuit connections also allowed the output reporter to be readily modified to a G-quadruplex-DNAzyme that yielded a fluorescent signal...
  35. pmc Spatial control of DNA reaction networks by DNA sequence
    Peter B Allen
    Institute of Cell and Molecular Biology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712 0159, USA
    Molecules 17:13390-402. 2012
    ..The ability to program at the nanoscale so as to produce patterns at the macroscale is a step towards programmable, synthetic chemical systems for generating defined spatiotemporal patterns...
  36. pmc Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals
    Bo Wang
    a Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
    MAbs 8:1035-44. 2016
    ..The new antibodies represent well-characterized reagents for biodefense diagnostics and therapeutics development. ..
  37. pmc Generalized bacterial genome editing using mobile group II introns and Cre-lox
    Peter J Enyeart
    Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Mol Syst Biol 9:685. 2013
    ..No selectable markers need to be placed in the genome, and the efficiency of Cre-mediated manipulations typically approaches 100%...
  38. doi request reprint Directed evolution of genetic parts and circuits by compartmentalized partnered replication
    Jared W Ellefson
    1 Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA 2
    Nat Biotechnol 32:97-101. 2014
    ..In both cases, the CPR-evolved parts were more orthogonal and/or more active than variants evolved using other methods. CPR should be useful for evolving any genetic part or circuit that can be linked to Taq DNA polymerase expression. ..
  39. pmc Real-time detection of isothermal amplification reactions with thermostable catalytic hairpin assembly
    Yu Sherry Jiang
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    J Am Chem Soc 135:7430-3. 2013
    ..These methods have been condensed into a set of general rules for the design of thermostable CHA circuits with high signals and low noise...
  40. doi request reprint Abiotic self-replication
    Adam J Meyer
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
    Acc Chem Res 45:2097-105. 2012
    ..The eventual outsourcing of metabolic functions (including the replication of nucleic acids) to more competent protein enzymes would complete the journey from an abiotic world to the molecular biology we see today...
  41. pmc Directed evolution of streptavidin variants using in vitro compartmentalization
    Matthew Levy
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Chem Biol 15:979-89. 2008
    ..The methods we have developed should prove to be generally useful for generating a variety of novel SA reagents and for evolving other extremely high-affinity protein:ligand couples...
  42. pmc Real-time PCR detection of protein analytes with conformation-switching aptamers
    Litao Yang
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Anal Biochem 380:164-73. 2008
    ..The method has advantages relative to both immunoPCR (because no signal is produced by background binding) and the proximity ligation assay (PLA) (because only one epitope, rather than two epitopes, on a protein surface must be bound)...
  43. doi request reprint Design and assembly of large synthetic DNA constructs
    Aleksandr E Miklos
    The University of Texas at Austin, Applied Research Laboratories, Department of Chemistry and Biochemistry, Center for Systems and Synthetic Biology, Austin, Texas, USA
    Curr Protoc Mol Biol . 2012
    ....
  44. pmc Analysis of DNA-guided self-assembly of microspheres using imaging flow cytometry
    Hao Tang
    Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
    J Am Chem Soc 134:15245-8. 2012
    ..The analysis demonstrated that self-assembly of 50 bp microspheres can be driven nearly to completion by stoichiometric excess in a manner similar to Le Chatelier's principle in common chemical equilibrium...
  45. doi request reprint Residue-specific incorporation of unnatural amino acids into proteins in vitro and in vivo
    Amrita Singh-Blom
    Department of Molecular Genetics and Microbiology, The University of Texas at Austin, Austin, TX, USA
    Methods Mol Biol 978:93-114. 2013
    ..Special attention is paid to obtaining high levels of incorporation while maintaining high yields of protein expression...
  46. ncbi request reprint Ribozyme catalysis of metabolism in the RNA world
    Xi Chen
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Chem Biodivers 4:633-55. 2007
    ....
  47. ncbi request reprint Synthetic RNA circuits
    Eric A Davidson
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, 1 University Station A4800, University of Texas at Austin, Austin, Texas 78712, USA
    Nat Chem Biol 3:23-8. 2007
    ....
  48. pmc Adapting enzyme-free DNA circuits to the detection of loop-mediated isothermal amplification reactions
    Bingling Li
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA
    Anal Chem 84:8371-7. 2012
    ..The AND-GATE detector will act as a simultaneous, specific readout of the LAMP product, rather than of competing and parasitic amplicons...
  49. ncbi request reprint Aptamer:toxin conjugates that specifically target prostate tumor cells
    Ted C Chu
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
    Cancer Res 66:5989-92. 2006
    ..These results validate the notion that "escort aptamers" may be useful for the treatment of specific tumors expressing unique antigen targets...
  50. pmc Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation
    Rammohan Narayanaswamy
    Department of Chemistry and Biochemistry, University of Texas, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Austin, TX 78712 1064, USA
    Proc Natl Acad Sci U S A 106:10147-52. 2009
    ..Thus, upon nutrient depletion we observe widespread protein assemblies displaying nutrient-specific formation and dissolution...
  51. ncbi request reprint Production and processing of aptamer microarrays
    James R Collett
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Methods 37:4-15. 2005
    ....
  52. doi request reprint In vitro selection of RNA aptamers to a protein target by filter immobilization
    Bradley Hall
    Department of Chemistry and Biochemistry, University of Texas, Austin, Texas, USA
    Curr Protoc Nucleic Acid Chem . 2010
    ..Bound complexes are separated from unbound reagents by filtration, and the RNA:protein complexes are amplified by a combination of reverse transcription, PCR, and in vitro transcription...
  53. doi request reprint Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells
    Sai T Reddy
    Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
    Nat Biotechnol 28:965-9. 2010
    ..Antibodies generated in this manner from six mice, each immunized with one of three antigens were overwhelmingly antigen specific (21/27 or 78%). Those generated from a mouse with high serum titers had nanomolar binding affinities...
  54. pmc A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Glucometers
    Yan Du
    Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
    Sci Rep 5:11039. 2015
    ..The method describes has potential for accelerating point-of-care applications, in that biological samples could be applied to a transducer that would then directly interface with an off-the-shelf, approved medical device. ..
  55. pmc Pattern transformation with DNA circuits
    Steven M Chirieleison
    Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
    Nat Chem 5:1000-5. 2013
    ..We believe these strategies will provide programmable platforms on which to prototype CRNs, discover bottom-up construction principles and generate patterns in materials. ..
  56. pmc Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers
    Sanchita Bhadra
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
    Nucleic Acids Res 42:e58. 2014
    ..Taken together, these results validate an entirely new chemistry for the implementation of nucleic acid circuits. ..
  57. doi request reprint In vitro selection of proteins via emulsion compartments
    Wei Cheng Lu
    Institute of Cellular and Molecule Biology, University of Texas at Austin, TX 78712, USA
    Methods 60:75-80. 2013
    ....
  58. pmc AANT: the Amino Acid-Nucleotide Interaction Database
    Michael M Hoffman
    Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712 0159, USA
    Nucleic Acids Res 32:D174-81. 2004
    ..Moreover, by modularly representing the fundamental interactions that govern binding specificity it may prove possible to better engineer nucleic acid binding proteins...
  59. ncbi request reprint Using a deoxyribozyme ligase and rolling circle amplification to detect a non-nucleic acid analyte, ATP
    Eun Jeong Cho
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
    J Am Chem Soc 127:2022-3. 2005
    ..Cooperative ATP activation of the deoxyribozyme was faithfully mimicked by RCA, yielding an amplified "switch" that was responsive to ATP concentration...
  60. ncbi request reprint Tuning the specificity of a synthetic receptor using a selected nucleic acid receptor
    Joseph C Manimala
    The University of Texas at Austin, Institute for Cellular and Molecular Biology 1 University Station, A5300, University of Texas, Austin, Texas 78712, USA
    J Am Chem Soc 126:16515-9. 2004
    ..The RNA conformation changed upon the introduction of the synthetic host, consistent with an induced-fit mechanism for binding...
  61. ncbi request reprint Quantum-dot aptamer beacons for the detection of proteins
    Matthew Levy
    Institute for Cellular and Molecular Biology, University of Texas, Austin, Austin TX 78712, USA
    Chembiochem 6:2163-6. 2005
  62. pmc Aptamer mediated siRNA delivery
    Ted C Chu
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Nucleic Acids Res 34:e73. 2006
    ..These results suggest new venues for the therapeutic delivery of siRNAs and for the development of reagents that can be used to probe cellular physiology...
  63. ncbi request reprint Computational selection of nucleic acid biosensors via a slip structure model
    Bradley Hall
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Biosens Bioelectron 22:1939-47. 2007
    ....
  64. doi request reprint Nucleic acid pool preparation and characterization
    Shawn K Piasecki
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
    Methods Mol Biol 535:3-18. 2009
    ..The following protocol takes the reader through the steps necessary for the preparation of a pool of known complexity...
  65. pmc Infrared multiphoton dissociation of small-interfering RNA anions and cations
    Myles W Gardner
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712 0165, USA
    J Am Soc Mass Spectrom 21:580-91. 2010
    ..With longer irradiation times, however, the individual single-strands underwent secondary dissociation to yield informative sequence ions not obtained by CID...
  66. pmc Sequential injection analysis for optimization of molecular biology reactions
    Peter B Allen
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, United States
    Anal Chem 83:2194-200. 2011
    ..The device and method should now be amenable to much more complex molecular biology reactions whose variable spaces are correspondingly larger...
  67. pmc Aptamers that recognize drug-resistant HIV-1 reverse transcriptase
    Na Li
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Nucleic Acids Res 36:6739-51. 2008
    ..M3 and WT HIV-1 RTs could be distinguished using an aptamer-based microarray. By probing protein conformation as a correlate to drug resistance we introduce an additional and useful measure for determining HIV-1 drug resistance...
  68. pmc Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods
    Bingling Li
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Nucleic Acids Res 39:e110. 2011
    ..Overall, these data demonstrate that catalyzed hairpin assembly is suitable for analyte detection and signal amplification in a 'plug-and-play' fashion...
  69. doi request reprint Identification of influenza virus inhibitors targeting NS1A utilizing fluorescence polarization-based high-throughput assay
    Eun Jeong Cho
    Texas Institute for Drug and Diagnostic Development, University of Texas at Austin, Austin, TX 78712, USA
    J Biomol Screen 17:448-59. 2012
    ..Overall, the FP-based binding assay demonstrated its superior capability for simple, rapid, inexpensive, and robust identification of NS1A inhibitors and validation of their activity targeting NS1A...
  70. pmc Bioinformatic analysis of the contribution of primer sequences to aptamer structures
    Matthew C Cowperthwaite
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    J Mol Evol 67:95-102. 2008
    ....
  71. pmc Dynamic reorganization of metabolic enzymes into intracellular bodies
    Jeremy D O'Connell
    Center for Systems and Synthetic Biology, University of Texas, Austin, Texas 78712, USA
    Annu Rev Cell Dev Biol 28:89-111. 2012
    ..The panoply of intracellular protein bodies also raises interesting questions regarding their evolution and maintenance within cells. We speculate on models for how such structures form in the first place and why they may be inevitable...
  72. doi request reprint Enrichment of error-free synthetic DNA sequences by CEL I nuclease
    Randall A Hughes
    The University of Texas at Austin, Applied Research Laboratories, Department of Chemistry and Biochemistry, Center for Systems and Synthetic Biology, Austin, Texas, USA
    Curr Protoc Mol Biol . 2012
    ..This method is a straightforward and quick way of reducing the error content of synthetic DNA pools and reliably reduces the error rates by >6-fold per round of treatment...
  73. ncbi request reprint Feature multiplexing--improving the efficiency of microarray devices
    Matthew J Schmid
    Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
    Angew Chem Int Ed Engl 45:3338-41. 2006
  74. pmc Man versus machine versus ribozyme
    Andrew D Ellington
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
    PLoS Biol 6:e132. 2008
  75. pmc Identification of novel specific allosteric modulators of the glycine receptor using phage display
    Megan E Tipps
    Section of Neurobiology, University of Texas, A4800, 2500 Speedway, MBB 1 148, Austin, TX 78712, USA
    J Biol Chem 285:22840-5. 2010
    ..This approach can readily be adapted for use with other channels that currently lack specific allosteric modulators...
  76. ncbi request reprint Using aptamers to identify and enter cells
    Ted Chu
    University of Texas at Austin, Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, Austin, TX 78712, USA
    Curr Opin Mol Ther 9:137-44. 2007
    ..The generation of anti-cell aptamers has important implications for identifying disease-specific biomarkers, generating diagnostics, and developing novel drug delivery strategies...
  77. pmc Motifs from the deep
    Tony W Hwang
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas, Austin, TX78712, USA
    J Biol 8:72. 2009
    ....