Andrew Ellington

Summary

Affiliation: University of Texas
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. pmc Aptamer antagonists of myelin-derived inhibitors promote axon growth
    Yuxuan Wang
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 5:e9726. 2010
  5. pmc Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA
    Randall A Hughes
    Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
    Nucleic Acids Res 38:6813-30. 2010
  6. 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
  7. pmc Inhibition of cell proliferation by an anti-EGFR aptamer
    Na Li
    AM Biotechnologies, Houston, Texas, United States of America
    PLoS ONE 6:e20299. 2011
  8. 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
  9. 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
  10. 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

Research Grants

  1. MicroRNA Profiles of Pathogen Infection
    Andrew Ellington; Fiscal Year: 2005
  2. T7 RNA polymerase engineering and RNA amplification
    Andrew Ellington; Fiscal Year: 2007
  3. Design and Selection of Aptamer Beacons
    Andrew Ellington; Fiscal Year: 2006
  4. Transducing Tumor Cell Antigens to Amplicons
    Andrew Ellington; Fiscal Year: 2006
  5. Genetic circuits based on allosteric ribozymes
    Andrew Ellington; Fiscal Year: 2007
  6. Design and Selection of Aptamer Beacons
    Andrew Ellington; Fiscal Year: 2007
  7. Genetic circuits based on allosteric ribozymes
    Andrew Ellington; Fiscal Year: 2009
  8. Site-specific incorporation of FRET pairs into intracellular proteins
    Andrew Ellington; Fiscal Year: 2009
  9. Genetic circuits based on allosteric ribozymes
    Andrew D Ellington; Fiscal Year: 2010
  10. Amorphous computation with transcription logic gates
    Andrew D Ellington; Fiscal Year: 2010

Collaborators

Detail Information

Publications85

  1. 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...
  2. 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...
  3. 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...
  4. pmc Aptamer antagonists of myelin-derived inhibitors promote axon growth
    Yuxuan Wang
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 5:e9726. 2010
    ..This first demonstration that aptamers can directly influence neuronal function suggests that aptamers may prove useful for not only healing spinal cord and other neuronal damage, but may be more generally useful as neuromodulators...
  5. pmc Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA
    Randall A Hughes
    Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
    Nucleic Acids Res 38:6813-30. 2010
    ..Our results provide insight into the role of tRNA flexibility in molecular recognition and the engineering and evolution of tRNA specificity...
  6. 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%...
  7. pmc Inhibition of cell proliferation by an anti-EGFR aptamer
    Na Li
    AM Biotechnologies, Houston, Texas, United States of America
    PLoS ONE 6:e20299. 2011
    ..In addition, Aptamer E07 is readily internalized into EGFR-expressing cells, raising the possibility that it might be used to escort other anti-tumor or contrast agents...
  8. 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...
  9. 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...
  10. 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...
  11. pmc Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes
    Rammohan Narayanaswamy
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, 2500 Speedway, University of Texas, Austin, TX 78712, USA
    Genome Biol 7:R6. 2006
    ..Besides morphology assays, cell microarrays should be valuable for high-throughput in situ hybridization and immunoassays, enabling new classes of genetic assays based on cell imaging...
  12. pmc Anticipatory evolution and DNA shuffling
    Jamie M Bacher
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Genome Biol 3:REVIEWS1021. 2002
    ..A mix of theoretical and applied research has now provided insights into how recombination can be guided to more efficiently generate proteins and even organisms with altered functions...
  13. pmc Evolution of phage with chemically ambiguous proteomes
    Jamie M Bacher
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    BMC Evol Biol 3:24. 2003
    ..The evolution of a small bacteriophage proteome to accommodate an unnatural amino acid analogue can provide insights into the number and type of substitutions that individual proteins will require to retain functionality...
  14. pmc A combined in vitro/in vivo selection for polymerases with novel promoter specificities
    J Chelliserrykattil
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, USA
    BMC Biotechnol 1:13. 2001
    ..Following RT / PCR amplification in vitro, the most numerous polymerase genes are preferentially cloned and carried into subsequent rounds of selection...
  15. pmc Group I aptazymes as genetic regulatory switches
    Kristin M Thompson
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    BMC Biotechnol 2:21. 2002
    ..We attempted to generate Group I self-splicing introns that were activated by a small organic effector, theophylline, and to show that such Group I aptazymes could mediate theophylline-dependent splicing in vivo...
  16. pmc The scene of a frozen accident
    A D Ellington
    Department of Chemistry and Biochemistry, University of Texas at Austin, 78712, USA
    RNA 6:485-98. 2000
    ..We argue that the suggested connections between modern motifs and ancient sequences are logically tenuous, and show that there is no statistically meaningful association between motifs found in aptamers and codons...
  17. 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...
  18. 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
  19. ncbi request reprint What's so great about RNA?
    Andrew D Ellington
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
    ACS Chem Biol 2:445-8. 2007
  20. pmc Aptamer-targeted gold nanoparticles as molecular-specific contrast agents for reflectance imaging
    David J Javier
    Department of Bioengineering, Rice University, Houston, Texas 77005, USA
    Bioconjug Chem 19:1309-12. 2008
    ..This design strategy can easily be modified to incorporate multifunctional agents as part of a multimodal platform for reflectance imaging applications...
  21. 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
    ....
  22. ncbi request reprint Optimization of the biological component of a bioelectrochemical cell
    Eun Jeong Cho
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Bioelectrochemistry 70:165-72. 2007
    ..We are further exploring whether this increase was due to metabolic adaptations or to genetic mutations, and examining additional ways to evolve electrogenic organisms...
  23. 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
  24. doi request reprint Applications of aptamers as sensors
    Eun Jeong Cho
    The Institute for Drug and Diagnostic Development, University of Texas at Austin, Austin, Texas 78712, USA
    Annu Rev Anal Chem (Palo Alto Calif) 2:241-64. 2009
    ..However, application of aptamers without a basic knowledge of their biochemistry or technical requirements can cause serious analytical difficulties...
  25. 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...
  26. 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...
  27. pmc Multiple RNA binding domains of Bruno confer recognition of diverse binding sites for translational repression
    Brad Reveal
    Section of Molecular Cell and Developmental Biology, The University of Texas at Austin, Austin, TX, USA
    RNA Biol 8:1047-60. 2011
    ..Other proteins with multiple RRMs may employ combinatorial binding to achieve high levels of specificity and affinity...
  28. 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
    ....
  29. 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
    ....
  30. doi request reprint In vitro selection of RNA aptamers to a small molecule target
    Vlad Codrea
    Department of Chemistry and Biochemistry, University of Texas, Austin, Texas, USA
    Curr Protoc Nucleic Acid Chem . 2010
    ..This unit describes two modes of selection, one by column filtration and one by batch selection...
  31. ncbi request reprint Peptide-templated nucleic acid ligation
    Matthew Levy
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, 78712, USA
    J Mol Evol 56:607-15. 2003
    ..These results support the possibility that life could have originated with peptide replicators and transitioned to nucleic acid replicators or that peptide and nucleic acid replicators could have been interdependent...
  32. 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
  33. 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...
  34. 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
    ....
  35. ncbi request reprint Simultaneous detection of diverse analytes with an aptazyme ligase array
    Jay R Hesselberth
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, 78712, USA
    Anal Biochem 312:106-12. 2003
    ....
  36. pmc 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...
  37. ncbi request reprint Engineering regulatory RNAs
    Eric A Davidson
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Trends Biotechnol 23:109-12. 2005
    ..A recent paper by Isaacs et al. describes the engineering and in vivo activity of a small RNA that removes translation inhibition by binding the 5' untranslated region of its target mRNA and making the ribosome-binding site accessible...
  38. ncbi request reprint ATP-dependent allosteric DNA enzymes
    Matthew Levy
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Chem Biol 9:417-26. 2002
    ..This novel allosteric mechanism has not previously been observed for nucleic-acid catalysts and is rare even in protein catalysts...
  39. pmc Synthesis and evaluation of quinoxaline derivatives as potential influenza NS1A protein inhibitors
    Lei You
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Bioorg Med Chem Lett 21:3007-11. 2011
    ..The most active compounds (35 and 44) had IC(50) values in the range of low micromolar concentration without exhibiting significant dsRNA intercalation. Compound 44 was able to inhibit influenza A/Udorn/72 virus growth...
  40. ncbi request reprint Molecular optical imaging of therapeutic targets of cancer
    Konstantin Sokolov
    Department of Imaging Physics, MD Anderson Cancer Center, Houston, Texas 77030, USA
    Adv Cancer Res 96:299-344. 2007
    ....
  41. ncbi request reprint Increasing the thermal stability of an oligomeric protein, beta-glucuronidase
    Humberto Flores
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology ICMB a4800 MBB 3 424, University of Texas at Austin, 26th and Speedway, Austin, TX 78712, USA
    J Mol Biol 315:325-37. 2002
    ....
  42. 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...
  43. 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...
  44. 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...
  45. 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...
  46. 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
    ....
  47. 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...
  48. 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...
  49. pmc Aptamer database
    Jennifer F Lee
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712, USA
    Nucleic Acids Res 32:D95-100. 2004
    ..The database is updated monthly and is publicly available at http://aptamer. icmb.utexas.edu/...
  50. 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
    ....
  51. ncbi request reprint Aptamers as potential diagnostic reagents for diabetes
    Amy Yan
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
    Diabetes Technol Ther 4:339-46. 2002
  52. ncbi request reprint Selecting nucleic acids for biosensor applications
    Manjula Rajendran
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Comb Chem High Throughput Screen 5:263-70. 2002
    ..Nucleic acid biosensor arrays for non-nucleic acid targets could likely be generated with the same facility as DNA chips...
  53. ncbi 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
    ....
  54. ncbi 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...
  55. pmc Exponential growth by cross-catalytic cleavage of deoxyribozymogens
    Matthew Levy
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas, Austin 78712, USA
    Proc Natl Acad Sci U S A 100:6416-21. 2003
    ..Seeding the system with a pool of linear catalysts resulted not only in amplification of function but in sequence selection and represents an in vitro selection experiment conducted in the absence of any protein enzymes...
  56. ncbi 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...
  57. ncbi 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...
  58. 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...
  59. 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...
  60. 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
    ....
  61. pmc Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer
    J Colin Cox
    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Nucleic Acids Res 30:e108. 2002
    ..These results not only reveal a potential path to the high throughput generation of aptamers, but also yield insights into the incredible specificity of the U1A protein for its natural RNA ligands...
  62. 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
  63. ncbi request reprint Autogene selections
    Jijumon Chelliserrykattil
    Department of Chemistry and Biochemistry, University of Texas, Austin, TX, USA
    Methods Mol Biol 230:27-43. 2003
  64. ncbi request reprint Selection of fluorescent aptamer beacons that light up in the presence of zinc
    Manjula Rajendran
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, 2500 Speedway, Austin, TX 78712, USA
    Anal Bioanal Chem 390:1067-75. 2008
    ..Such biosensors could potentially be used for continuous monitoring of metals in environmental samples...
  65. doi request reprint Using RNA aptamers and the proximity ligation assay for the detection of cell surface antigens
    Supriya S Pai
    Department of Microbiology, University of Texas at Austin, Austin, TX, USA
    Methods Mol Biol 504:385-98. 2009
    ....
  66. 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...
  67. ncbi request reprint Electrospray ionization of nucleic acid aptamer/small molecule complexes for screening aptamer selectivity
    Karin M Keller
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin TX 78712, USA
    J Mass Spectrom 40:1327-37. 2005
    ..These results indicate that in at least some cases, mass spectrometric data on aptamer/ligand binding affinities should be used in conjunction with complementary techniques to fully assess aptamer molecular recognition properties...
  68. pmc Mistakes in translation don't translate into termination
    Randall A Hughes
    Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 102:1273-4. 2005
  69. 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
  70. 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
    ....
  71. ncbi request reprint Aptamer-based sensor arrays for the detection and quantitation of proteins
    Romy Kirby
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    Anal Chem 76:4066-75. 2004
    ..The aptamer chips proved to be useful for screening aptamers from in vitro selection experiments and for sensitively quantitating the biothreat agent ricin...
  72. 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...
  73. pmc In vitro selection of molecular beacons
    Manjula Rajendran
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Nucleic Acids Res 31:5700-13. 2003
    ..The ability to select molecular beacons may prove useful for identifying available sites on complex targets, such as mRNAs, while the method for selection can be easily generalized to other, non-nucleic acid target classes...
  74. 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)...
  75. ncbi request reprint The importance of prebiotic chemistry in the RNA world
    Randall A Hughes
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Curr Opin Chem Biol 8:629-33. 2004
    ..4 billion years ago are tenuous at best. Thus, perhaps the best way to understand origins is not by examining relatively unconstrained sequence information, but by examining the inherent constraints imposed by prebiotic chemistry...
  76. ncbi request reprint A modified consensus approach to mutagenesis inverts the cofactor specificity of Bacillus stearothermophilus lactate dehydrogenase
    Humberto Flores
    Instituto de Biotecnologia UNAM, Apartado Postal 510 3, Cuernavaca, Morelos, 62271, Mexico
    Protein Eng Des Sel 18:369-77. 2005
    ....
  77. pmc In vitro selection of ribozymes dependent on peptides for activity
    Michael P Robertson
    University of California Santa Cruz, Santa Cruz, CA 95064, USA
    RNA 10:114-27. 2004
    ..These results have important implications for the development of aptazymes that can be used in arrays for the detection and quantitation of multiple cellular proteins (proteome arrays)...
  78. ncbi request reprint Q &A. Andrew D. Ellington
    Andrew D Ellington
    Curr Biol 18:R184-5. 2008
  79. ncbi request reprint Ribozyme déjà vu
    Scott M Knudsen
    Nat Struct Mol Biol 11:301-3. 2004
  80. ncbi request reprint Synthetic biology: engineering Escherichia coli to see light
    Anselm Levskaya
    Biophysics Program, University of California, San Francisco, California 94143, USA
    Nature 438:441-2. 2005
    ..This spatial control of bacterial gene expression could be used to 'print' complex biological materials, for example, and to investigate signalling pathways through precise spatial and temporal control of their phosphorylation steps...
  81. ncbi request reprint A (ribo) switch in the paradigms of genetic regulation
    Jay R Hesselberth
    Nat Struct Biol 9:891-3. 2002
  82. pmc Binding of herpes simplex virus-1 US11 to specific RNA sequences
    Kevin F Bryant
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
    Nucleic Acids Res 33:6090-100. 2005
    ..The results define a relatively short specific sequence that binds US11 with high affinity and indicate that dsRNA alone does not confer high-affinity binding...
  83. ncbi request reprint Global incorporation of unnatural amino acids in Escherichia coli
    Jamie M Bacher
    The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
    Methods Mol Biol 352:23-34. 2007
    ..Here we describe protocols to characterize the effects of such proteome-wide perturbations...
  84. ncbi request reprint Evolution of a T7 RNA polymerase variant that transcribes 2'-O-methyl RNA
    Jijumon Chelliserrykattil
    Nat Biotechnol 22:1155-60. 2004
    ..Most important, our method allows the selection of polymerases that have good processivities and can be combined to simultaneously incorporate several different modified nucleotides in a transcript...
  85. ncbi request reprint Protein-dependent ribozymes report molecular interactions in real time
    Jörg S Hartig
    Kekule Institut fur Organische Chemie und Biochemie, University of Bonn, Gerhard Domagk Strasse 1, 53121 Bonn, Germany
    Nat Biotechnol 20:717-22. 2002
    ..The rapid identification of interactions between proteins or of compounds that disrupt such interactions should have substantial utility for the drug-discovery process...

Research Grants29

  1. MicroRNA Profiles of Pathogen Infection
    Andrew Ellington; Fiscal Year: 2005
    ..3. Apply these methods to the detection of changes in microRNA expression during influenza infection. 4. Apply these methods to the detection of changes in microRNA expression with other infectious agents. ..
  2. T7 RNA polymerase engineering and RNA amplification
    Andrew Ellington; Fiscal Year: 2007
    ..This will enable microarray gene analysis with as little as 1 ng of total RNA with a single round of amplification or microarray profiling from a single cell (-10 pg of total RNA) after two rounds of amplification. ..
  3. Design and Selection of Aptamer Beacons
    Andrew Ellington; Fiscal Year: 2006
    ..abstract_text> ..
  4. Transducing Tumor Cell Antigens to Amplicons
    Andrew Ellington; Fiscal Year: 2006
    ..abstract_text> ..
  5. Genetic circuits based on allosteric ribozymes
    Andrew Ellington; Fiscal Year: 2007
    ....
  6. Design and Selection of Aptamer Beacons
    Andrew Ellington; Fiscal Year: 2007
    ..abstract_text> ..
  7. Genetic circuits based on allosteric ribozymes
    Andrew Ellington; Fiscal Year: 2009
    ....
  8. Site-specific incorporation of FRET pairs into intracellular proteins
    Andrew Ellington; Fiscal Year: 2009
    ..This will allow us to follow and track proteins in a cell, and to determine where, when, and how proteins reside next to one another, in either normal or malformed complexes. ..
  9. Genetic circuits based on allosteric ribozymes
    Andrew D Ellington; Fiscal Year: 2010
    ....
  10. Amorphous computation with transcription logic gates
    Andrew D Ellington; Fiscal Year: 2010
    ..The results of these inquiries should help understand development, including how development sometimes goes awry during disease formation, and may assist with building nanoscale devices for therapy and diagnostics. ..
  11. APTAMER BASED DETECTOR TO QUANTIFY MACROMOLECULES
    Andrew Ellington; Fiscal Year: 2006
    ....
  12. Genetic circuits based on allosteric ribozymes
    Andrew Ellington; Fiscal Year: 2006
    ....
  13. REV DECOYS FOR GENE THERAPY AND DRUG DEVELOPMENT
    Andrew Ellington; Fiscal Year: 1999
    ..In particular, the peptide motifs identified by physical mapping and selection studies should provide information essential to the synthesis of peptidomimetic drugs. ..
  14. REV DECOYS FOR GENE THERAPY AND DRUG DEVELOPMENT
    Andrew Ellington; Fiscal Year: 2001
    ....
  15. Ribozymes for Peptide- and Protein- Sensing Chip Arrays
    Andrew Ellington; Fiscal Year: 2001
    ..1.-D.3), and (2)Adapting peptide and protein-activated aptazymes to function in chip arrays (D.4). ..
  16. REV DECOYS FOR GENE THERAPY AND DRUG DEVELOPMENT
    Andrew Ellington; Fiscal Year: 2002
    ....
  17. Ribozymes for Peptide- and Protein- Sensing Chip Arrays
    Andrew Ellington; Fiscal Year: 2002
    ..1.-D.3), and (2)Adapting peptide and protein-activated aptazymes to function in chip arrays (D.4). ..
  18. REV DECOYS FOR GENE THERAPY AND DRUG DEVELOPMENT
    Andrew Ellington; Fiscal Year: 2003
    ....
  19. Ribozymes for Peptide- and Protein- Sensing Chip Arrays
    Andrew Ellington; Fiscal Year: 2003
    ..1.-D.3), and (2)Adapting peptide and protein-activated aptazymes to function in chip arrays (D.4). ..
  20. REV DECOYS FOR GENE THERAPY AND DRUG DEVELOPMENT
    Andrew Ellington; Fiscal Year: 2004
    ....
  21. Auto Selection of aptamers binding to pX01 proteome
    Andrew Ellington; Fiscal Year: 2004
    ..abstract_text> ..
  22. Design and Selection of Aptamer Beacons
    Andrew Ellington; Fiscal Year: 2005
    ..abstract_text> ..
  23. DNA circuits for point-of-care diagnostics
    Andrew D Ellington; Fiscal Year: 2010
    ..The selfsame DNA circuitry can be readily redesigned for the detection of other mRNAs and alleles, and should therefore find great use in first world clinical settings, as well. ..
  24. Ribozymes for Peptide- and Protein- Sensing Chip Arrays
    Andrew Ellington; Fiscal Year: 2004
    ..1.-D.3), and (2)Adapting peptide and protein-activated aptazymes to function in chip arrays (D.4). ..