Xi Chen

Summary

Affiliation: University of Texas
Country: USA

Publications

  1. 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
  2. pmc Expanding the rule set of DNA circuitry with associative toehold activation
    Xi Chen
    Department of Chemistry and Biochemistry, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin Texas 78712, USA
    J Am Chem Soc 134:263-71. 2012
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

  • Andrew D Ellington
  • Na Li
  • Matthew Levy
  • Yan Zhang
  • Bingling Li
  • Peter B Allen
  • Yu Jiang
  • Steven M Chirieleison
  • Mengmeng Zhang
  • Zack Booth Simpson
  • Zack B Simpson
  • Yonghua Luo
  • Felicia A Etzkorn
  • Xiaodong J Wang
  • Joseph P Noel
  • Seyed A Arshad
  • Marianne E Bowman
  • Nam Nguyen
  • Timothy L Tsai

Detail Information

Publications17

  1. 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...
  2. pmc Expanding the rule set of DNA circuitry with associative toehold activation
    Xi Chen
    Department of Chemistry and Biochemistry, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin Texas 78712, USA
    J Am Chem Soc 134:263-71. 2012
    ....
  3. 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...
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  8. 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...
  9. 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...
  10. 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...
  11. 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...
  12. pmc Structural and kinetic analysis of prolyl-isomerization/phosphorylation cross-talk in the CTD code
    Mengmeng Zhang
    Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
    ACS Chem Biol 7:1462-70. 2012
    ..These data exemplify for the first time how modulation of proline isomerization can kinetically impact signal transduction in transcription regulation...
  13. 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...
  14. doi request reprint 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. ..
  15. pmc Shaping up nucleic acid computation
    Xi Chen
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Curr Opin Biotechnol 21:392-400. 2010
    ..Into the future, the chemical dynamics of nucleic acids may prove as useful as hybridization for computation...
  16. pmc Stacking nonenzymatic circuits for high signal gain
    Xi Chen
    Department of Chemistry and Biochemistry, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 110:5386-91. 2013
    ..Implementation of these unique methods and design principles should greatly empower molecular programming in general and DNA-based molecular diagnostics in particular...
  17. 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
    ....