Chemical & Biomolecular Engineering

Top 20 Doctoral Program—National Research Council

Faculty

Dr. Richard C. Willson

Professor of Chemical and Biomolecular Engineering
Professor of Biochemical & Biophysical Sciences

Office Location: S229, Engineering Building 1

Tel: (713) 743-4308 | Fax: (713) 743-4323

Email: willson [at] uh [dot] edu

Education

  • B.S. Chemical Engineering, California Institute of Technology (1981; honors)
  • M.S. Chemical Engineering, California Institute of Technology (1982)
  • Ph.D. Chemical Engineering, Massachusetts Institute of Technology (1988)

Research Interests

Richard Willson's laboratory works on biomolecular recognition, and its applications in separations and molecular diagnostics.

Biomolecular recognition

We’re interested in the structural determinants of molecular recognition in complexes of proteins with recognition agents such as monoclonal antibodies and aptamers. Our primary techniques are expression, mutagenesis, fluorescence anisotropy (kinetics) and titration calorimetry. Topics of current interest include the recognition of hen egg lysozyme by a “homologous series” of antibodies differing in combining site rigidity and cross-reactivity (with S. Smith-Gill of NIH), and the biophysical chemistry of aptamer/protein recognition (with A. Ellington of UT-Austin).

Biomolecular separations

New chemistries for DNA/RNA purification
One example is metal-chelate affinity, also known as Immobilized Metal Affinity Chromatography, IMAC. IMAC is famous for its use in the purification of hexa-histidine tagged recombinant proteins, as well as large-scale purification of pharmaceutical proteins. We have found that the same chemistry binds purines in single-stranded RNA and DNA (which is quite useful for capturing RNA, polyA mRNA, primers, etc). We have combined the ideas of condensation conformational control and DNA metal affinity into a selective renaturation scheme in which genomic DNA is endowed with kinetically-trapped single-stranded "purification handles" that allow it to be captured by metal chelates while plasmid DNA renatures completely and does not bind. This method allows remarkable (million-fold) selectivity between plasmid (e.g., a DNA vaccine) and contaminating genomic DNA despite their chemical similarity.

Nanostructured adsorbents
Conventional bioseparations adsorbents (e.g., ion exchangers) are derivitized with functional groups (e.g., charges), randomly distributed over their surface area. This produces a functional polyclonality or heterogeneity, in that there are some places where several charges are close together, and many where a smaller number are clustered. So the binding properties are heterogeneous, and the selectivity for purification (e.g., of protein pharmaceuticals) or analysis (e.g., proteomics) is inherently limited. We are controlling the distribution of charges on a nanometer scale by immobilizing groups of charges all at once. This reduces the heterogeneity of adsorption, and confers interesting new specificity for proteins displaying clusters of charges on their surfaces. We are now also exploring nanoclustered metal-chelates for DNA/RNA separations.

Molecular diagnostics and sensors

Ribosomal RNA-based identification of bacteria and viruses
One project, with UH's George Fox (co-discoverer of the Archae), is funded by NASA's National Space Biomedical Research Institute. This project centers on the development of molecular labels and computationally-derived probes for organisms of interest to crew health in long-duration space flight. Other applications include terrestrial infectious disease diagnosis, and biodefense. The Fox lab identifies signature sequences associated with different regions of the phylogenetic tree, and we believe an array of probes to these can allow approximate classification of nearly any organism even if it has not been seen before. This last part is a substantial advance, and the work has been written up in The Scientist, Lancet Infectious Diseases, etc.

Genome-based identification of microorganisms
As hundreds of microbial, viral, and metazoan genome sequences become available, it is increasingly possible to use this base of knowledge to design DNA probe/primer sets for organisms of interest known not to interact with background sequences (e.g., environmental background, human sequences, etc.). This HSARPA-funded project, with George Fox and Yuriy Fofanov of UH Computer Science, relies on the remarkable computational prowess of the Fofanov group in identifying sequences of interest by exhaustive calculation. We use these results in several ways: 1. Custom DNA arrays for identification of pathogens; 2. Developing custom cocktails of RT-PCR primers rigorously known not to interact with each other, or with any human sequence or known SNP, with at least two mismatches and designed to amplify e.g., viral sequences against an overwhelming background of human DNA; 3. Engineering of hybridization-responsive fluorescent probes for these sequences. These resemble molecular beacons, but we directly incorporate environment-sensitive fluorescent nucleotide analogs such as 2-aminopurine during synthesis, etc.

Nano- and micro-scale molecular labels
Many methods in diagnostics, genomic technology, and proteomics rely upon the sensitive detection of labels added to target or reporter molecules, to facilitate the detection of an analyte or a binding event. With Paul Ruchhoeft of UH, we are making 1-micron cubic retroreflectors (small-scale analogs of the lunar retroreflectors which are possibly the most detectable objects ever produced by mankind) for use as labels and in one-step assays based on self-assembly. With Dmitri Litvinov of UH (formerly Seagate) we are seeking to adapt the GMR technology which has radically improved data-storage hard disk drive performance, to produce a biosensor array of extremely high feature density and number (millions), capable of single-molecule detection (using 50 nm magnetic particle labels) and magnetic pull-off “melting curves” for each spot to ensure high data quality.

Awards and Honors

  • 2011 Fellow, American Association for the Advancement of Science
  • 2010 John and Rebecca Moores Professor, UH
  • 2005 Senior Faculty Research Excellence Award, UH College of Engineering
  • 2001 van Lanen Award, ACS
  • 1999-present Fellow, American Institute of Medical and Biological Engineering
  • 1997-2002 Shell/UH Interdisciplinary Scholar
  • 1993 3M Young Faculty Award (Life Sciences Division)
  • 1990-1995 NSF Presidential Young Investigator
  • 1984-present Sigma Xi
  • 1983-1984 Pfizer Predoctoral Fellowship in Biochemical Engineering
  • 1982-1983 Shell Predoctoral Fellowship
  • 1981 Robert Noland Leadership Award
  • 1977-1981 Adolph Coors Foundation Frontiers of Science Scholarship

Professional Activities

Selected Publications

  1. Kanakaraj I, Jewell DL, Murphy JC, Fox GE, Willson RC.,

    “Removal of PCR Error Products and Unincorporated Primers by Metal-Chelate Affinity Chromatography,” PLoS One, 6(1):e14512

    , 2011
  2. Chen WH, Fu JY, Kourentzi K, Willson RC.,

    “Nucleic acid affinity of clustered-charge anion exchange adsorbents: effects of ionic strength and ligand density,” J Chromatogr A., 1218(2):258-62

    , 2011
  3. Potty AS, Kourentzi K, Fang H, Schuck P, Willson RC.,

    “Biophysical characterization of DNA and RNA aptamer interactions with hen egg lysozyme,” Int J Biol Macromol. (ePub)

    , 2010
  4. Liu Y, Stepanov VG, Strych U, Willson RC, Jackson GW, Fox GE.,

    “DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli,” BMC Biotechnol., 10:85

    , 2010
  5. Zuo G,Roberts DJ,Lehman SG,Jackson GW,Fox GE, Willson RC.,

    “Molecular assessment of salt-tolerant, perchlorate- and nitrate-reducing microbial cultures,” Water Sci Technol., 60(7):1745-1756

    , 2009
  6. Zhang X, Potty AS, Jackson GW, Stepanov V, Tang A, Liu Y, Kourentzi K, Strych U, Fox GE, Willson RC.,

    “Engineered 5S ribosomal RNAs displaying aptamers recognizing vascular endothelial growth factor and malachite green,” J Mol Recognit., 22(2):154-61

    , 2009
  7. Mohan S, Kourentzi K, Schick KA, Uehara C, Lipschultz CA, Acchione M, Desantis ME, Smith-Gill SJ, Willson RC.,

    “Association Energetics of Cross-Reactive and Specific Antibodies,” Biochemistry

    , 2009
  8. Potty AS, Kourentzi K, Fang H, Jackson GW, Zhang X, Legge GB, Willson RC.,

    “Biophysical characterization of DNA aptamer interactions with vascular endothelial growth factor,” Biopolymers., 91(2):145-56

    , 2009
  9. Añez-Lingerfelt M, Fox GE, Willson RC.,

    “Reduction of DNA contamination in RNA samples for reverse transcription-polymerase chain reaction using selective precipitation by compaction agents,” Anal Biochem., 384(1):79-85

    , 2009
  10. Basile LJ, Willson RC, Sewell BT, Benedik MJ.,

    “Genome mining of cyanide-degrading nitrilases from filamentous fungi,” Appl Microbiol Biotechnol., 80(3):427-35

    , 2008
  11. Vu BV, Litvinov D, Willson RC.,

    “Gold nanoparticle effects in polymerase chain reaction: favoring of smaller products by polymerase adsorption,” Anal Chem., 80(14):5462-7

    , 2008
  12. Nick Taylor J, Darugar Q, Kourentzi K, Willson RC, Landes CF.,

    “Dynamics of an anti-VEGF DNA aptamer: a single-molecule study,” Biochem Biophys Res Commun., 373(2):213-8

    , 2008
  13. Peterson KJ, Sadowsky JD, Scheef EA, Pal S, Kourentzi KD, Willson RC, Bresnick EH, Sheibani N, Gellman SH.,

    “A fluorescence polarization assay for identifying ligands that bind to vascular endothelial growth factor,” Anal Biochem., 378(1):8-14

    , 2008
  14. Kourentzi K, Srinivasan M, Smith-Gill SJ, Willson RC.,

    “Conformational flexibility and kinetic complexity in antibody-antigen interactions,” J Mol Recognit., 21(2):114-21

    , 2008
  15. Jackson GW, McNichols RJ, Fox GE, Willson RC.,

    “Toward Universal Flavivirus Identification by Mass Cataloging,” J Mol Diagn., 10(2):135-141

    , 2008
  16. Añez M, Putonti C, Fox GE, Fofanov Y, Willson RC.,

    “Exhaustive computational identification of pathogen sequences far-distant from background genomes: Identification and experimental verification of human-blind dengue PCR primers,” J Biotechnol., 133(3):267-76

    , 2008
  17. Ortego BC, Whittenton JJ, Li H, Tu SC, Willson RC.,

    “In vivo translational inaccuracy in Escherichia coli: missense reporting using extremely low activity mutants of Vibrio harveyi luciferase,” Biochemistry, 46(48):13864-73

    , 2007
  18. Fu JY, Balan S, Potty A, Nguyen V, Willson RC.,

    “Enhanced protein affinity and selectivity of clustered-charge anion-exchange adsorbents,” Anal Chem., 79(23):9060-5

    , 2007
  19. Larios-Sanz M, Kourentzi KD, Warmflash D, Jones J, Pierson DL, Willson RC, Fox GE.,

    “16S rRNA beacons for bacterial monitoring during human space missions,” Aviat Space Environ Med., 78(4 Suppl):A43-7

    , 2007
  20. Jackson GW, McNichols RJ, Fox GE, and Willson RC.,

    “Universal bacterial identification by mass spectrometry of 16S ribosomal RNA cleavage products,” International Journal of Mass Spectrometry, 261(2-3):218-226

    , 2007
  21. Tucker DL, Ott CM, Huff S, Fofanov Y, Pierson DL, Willson RC, Fox GE.,

    “Characterization of Escherichia coli MG1655 grown in a low-shear modeled microgravity environment,” BMC Microbiol., 7(1):15

    , 2007
  22. Cano T, Offringa N, Willson RC.,

    “The effectiveness of three multi-component binding models in describing the binary competitive equilibrium adsorption of two cytochrome b(5) mutants,” J Chromatogr A., 1144(2):197-202

    , 2007
  23. Svitel J, Boukari H, Van Ryk D, Willson RC, Schuck P.,

    “Probing the functional heterogeneity of surface binding sites by analysis of experimental binding traces and the effect of mass transport limitation,” Biophys J., 92(5):1742-58

    , 2007
  24. Jackson GW, McNichols RJ, Fox GE, Willson RC.,

    “Bacterial genotyping by 16S rRNA mass cataloging,” BMC Bioinformatics, 7:321

    , 2006
  25. Fu JY, Potty AS, Fox GE, Willson RC.,

    “Water-elutability of nucleic acids from metal-chelate affinity adsorbents: enhancement by control of surface charge density,” J Mol Recognit., 19(4):348-53

    , 2006
  26. Potty AS, Fu JY, Balan S, Haymore BL, Hill DJ, Fox GE, Willson RC.,

    “Neutral additives enhance the metal-chelate affinity adsorption of nucleic acids: role of water activity,” J Chromatogr A., 1115(1-2):88-92

    , 2006
  27. Murphy JC, Cano T, Fox GE, Willson RC.,

    “Compaction agent protection of nucleic acids during mechanical lysis,” Biotechnol Prog., 22(2):519-22

    , 2006
  28. Zhang Z, Jackson GW, Fox GE, Willson RC.,

    “Microbial identification by mass cataloging,” BMC Bioinformatics, 7:117

    , 2006
  29. Putonti C, Chumakov S, Mitra R, Fox GE, Willson RC, and Fofanov Y.,,

    “Human-blind probes and primers for dengue virus identification,” FEBS J., 273(2):398-408

    , 2006
  30. Cano T, Murphy JC, Fox GE, & Willson R.C.,

    “Separation of Genomic DNA from Plasmid DNA by selective renaturation with IMAC capture,” Biotechnology Progress, 21: 1472-1477

    , 2005
  31. Jackson GW, and Willson R,

    “Preparative electrophoresis with on-column optical fiber monitoring and direct elution into a minimized volume,” Biotechnol Lett., 27(22):1739-43

    , 2005
  32. Cano T, Offringa ND, and Willson RC,

    “Competitive ion-exchange adsorption of proteins: isotherms with controlled competitor concentration,” J Chromatogr A., 24;1079(1-2):116-26

    , 2005
  33. Chumakov, S., Belapurkar, C., Putonti, C., Li, T.-B., Pettitt, B.M., Fox, G.E., Willson, R.C. and Fofanov, Y.,

    “Theoretical Basis for Universal Identification Systems for Bacteria and Viruses,” Journal of Biological Physics and Chemistry, 5(4); 121-128

    , 2005
  34. Mulder BA, Anaya S, Yu P, Lee KW, Nguyen A, Murphy J, Willson R, Briggs JM, Gao X, and Hardin SH,

    “Nucleotide modification at the gamma-phosphate leads to the improved fidelity of HIV-1 reverse transcriptase,” Nucleic Acids Res., 33(15):4865-73

    , 2005
  35. Tucker DL, Karouia F, Wang J, Luo Y, Li TB, Willson RC, Fofanov Y, and Fox GE,

    “Effect of an artificial RNA marker on gene expression in Escherichia coli,” Appl Environ Microbiol., 71(7):4156-9

    , 2005
  36. Jandhyala DM, Willson RC, Sewell BT, and Benedik MJ,

    “Comparison of cyanide-degrading nitrilases,” Appl Microbiol Biotechnol., 68(3):327-35

    , 2005
  37. Cohen, G.H., Silverton, E.W., Padlan, E.A., Dyda, F., Wibbenmeyer, J.A., Willson, R.C., and Davies, D.R.,

    “Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 Å resolution: comparison with results from isothermal titration calorimetry,” Acta Crystallographica Section D: Biological Crystallography, D61, 628-633

    , 2005
  38. Forsman, Z.H., Lednicky, J.A., Fox, G.E., Willson, R.C., White, Z.S., Halvorson, S.J., Wong, C., Lewis, A.M. Jr, and Butel, J.S.,

    “Phylogenetic analysis of polyomavirus simian virus 40 from monkeys and humans reveals genetic variation,” Journal of Virology, 78(17):9306-16

    , 2004
  39. Gibbs, P.R., Riddle, R.R., Marchal, M., Benedik, M.J. and Willson, R.C.,

    “Purification and characterization of 2'aminobiphenyl-2,3-diol 1,2-dioxygenase from Pseudomonas sp. LD2,” Protein Expression and Purification, 32:35-43

    , 2003
  40. Jandhyala, D., Berman, M., Meyers, P.R., Sewell, B.T., Willson, R.C., and Benedik, M.J.,

    “CynD, the Cyanide Dihydratase from Bacillus pumilus: Gene Cloning and Structural Studies,” Applied and Environmental Microbiology, 69:4794-4805

    , 2003
  41. Kourentzi, K.D., George E. Fox, G.E. and Willson. R.C.,

    “Hybridization-responsive fluorescent DNA probes containing the adenine analog 2-aminopurine,” Analytical Biochemistry, 322(1), 124-126

    , 2003
  42. Gibbs, P.R., Uehara, C.S., Nguyen, P.T., and Willson, R.C.,

    “Imaging Polarimetry for High Throughput Chiral Screening,” Biotechnology Progress, 19(4); 1329-1334

    , 2003
  43. Murphy, J. C., Jewell, D. L., White, K. I., Fox, G. E., and Willson, R. C.,

    “Nucleic Acid Separations Utilizing Immobilized Metal Affinity Chromatography,” Biotechnology Progress, 19: 982-986

    , 2003
  44. DeWalt, B., Murphy, J. C., Fox, G. E., and Willson, R. C.,

    “Compaction Agent Clarification of Microbial Lysates,” Protein Expression and Purification, 28(2) 220 – 223

    , 2003
  45. Balan, S. E., Murphy, J. C., Galaev, I., Kumar, A., Fox, G. E., Mattiasson, B., and Willson, R. C.,

    “Metal Chelate Affinity Precipitation of Nucleic Acids,” Biotechnology Letters, 25:1111-1116

    , 2003
  46. D’Souza, L.M., Larios-Sanz, M., Setterquist, R. A., Willson, R. C., and Fox, G. E.,

    “Small RNA Sequences are readily stabilized by inclusion in a carrier rRNA,” Biotechnology Progress, 19: 734-738

    , 2003
  47. Riddle, R. R., Gibbs, P. R., Willson, R.C., and Benedik, M. J.,

    “Recombinant carbazole-degrading strains for enhanced petroleum processing,” J. Ind. Microbiol. Biotechnol., 30: 6-12

    , 2003
  48. Riddle, R., P.R. Gibbs, R.C. Willson and M.J. Benedik,

    “Purification and Properties of 2-hydroxy-6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoic acid Hydrolase Involved with Microbial Degradation of Carbazole,” Protein Expression and Purification, 28:182-189

    , 2003
  49. Murphy J.C., Fox G.E., and Willson, R.C.,

    “Enhancement of anion-exchange chromatography of DNA using compaction agents,” J. Chromatogr. A., 984: 215-21

    , 2003
  50. Shick, K.A., S. Mohan, S.J. Smith-Gill and R.C. Willson,

    “Calorimetric Study of Monoclonal Antibody HyHEL-10 Association with Hen and Japanese Quail-Egg Lysozymes,” Biochimica et Biophysica Acta

    , 2002
  51. Murphy, J.C., G.E. Fox and R.C. Willson,

    “Compaction Agents Enhance Anion-Exchange Adsorption of Nucleic Acids,” Journal of Chromatography

    , 2002
  52. Kourentzi, K.D., G.E. Fox and R.C. Willson,

    “Microbial Identification by Immunohybridization Assay of Artificial RNA Labels,” J. Microbiol. Methods, 49(3), 301-306

    , 2002
  53. Zhang, Z., R.C. Willson and G.E. Fox,

    “Identification of Characteristic Oligonucleotides in the 16S Ribosomal RNA Sequence Dataset,” Bioinformatics, 18, 244-250

    , 2002
  54. Kourentzi, K.D., G.E. Fox and R.C. Willson,

    “Microbial Detection with Low-Molecular-Weight RNA,” Current Microbiology, 43(6), 444-447

    , 2001
  55. Kourentzi, K.D., G.E. Fox and R.C. Willson,

    “Rapid Identification of Microorganisms using 5S rRNA Specific Molecular Beacons,” Current Microbiology, 43, 444

    , 2001
  56. Murphy, J.C., G.E. Fox and R.C. Willson,

    “RNA Isolation and Fractionation using Compaction Agents,” Analytical Biochemistry, 295, 143

    , 2001
  57. D’Souza, L.M., R.C. Willson and G.E. Fox,

    “Expression of Marker RNAs in Pseudomonas Putida,” Current Microbiology, 40, 91-95

    , 2000
  58. K.A. Xavier, S.M. McDonald, J.A. McCammon, and R.C. Willson,

    “Association and dissociation kinetics of Bobwhite quail lysozyme with monoclonal antibody HyHEL-5,” Protein Engineering, 12(1), 79-83

    , 1999
  59. Wibbenmeyer, J.A., Xavier, K.A., Smith-Gill, S.J. and Willson, R.C.,

    “Cloning, Expression, and Characterization of the Fab Fragment of the Anti-Lysozyme Antibody HyHEL-5,” BBA, 1430, 191-202

    , 1999
  60. Singh, N. and Willson, R.C.,

    “Boronate affinity adsorption of RNA: possible role of conformational changes,” Journal of Chromatography, 840, 205-213

    , 1999
  61. Riddle, R.R., Willson, R.C., and Benedik, M.J.,

    “Temperature- and solvent-tolerant mutants of filamentous bacteriophage helper M13 KO7,” Biotechnology Letters, 21(1):87-90

    , 1999
  62. Li, H., Ortego, B.C., Maillard, K.I., Willson, R.C., and Tu, S.-C.,

    “Effects of mutations of the alpha His-45 residue of Vibrio harveyi luciferase on the yield and reactivity of flavin peroxide intermediate,” Biochemistry, 38(14), 4409-4415

    , 1999
  63. Murphy, J.C., Wibbenmeyer, J.A., Fox, G.E. and Willson, R.C.,

    “Purification of plasmid DNA using selective precipitation by compaction agents,” Nature Biotechnology, 17, 822

    , 1999
  64. Wibbenmeyer, J.A., P. Schuck, S.J. Smith-Gill, and R.C. Willson,

    “Salt Links Dominate Affinity of Antibody HyHEL-5 for Lysozyme Through Enthalpic Contributions,” Journal of Biological Chemistry, 274(38), 26838-42

    , 1999
  65. Xavier, K.A., Shick, K.A., and Willson, R.C.,

    “Association and Dissociation kinetics of anti-hen egg lysozyme monoclonal antibodies HyHEL-5 and HyHEL-10,” Biophys. J., 74, 2036-2045

    , 1998
  66. Benedik, M.J., Gibbs, P.R., Riddle, R.R., and Willson, R.C.,

    “Microbial denitrogenation of fossil fuels,” Trends Biotechnol., 16, 390-395

    , 1998
  67. Shick, K.A., Xavier, K.A., Rajpal, A., Smith-Gill, S.J. and Willson, R.C.,

    “Association of the anti-hen egg lysozyme monoclonal antibody HyHEL-5 with avian species variant and mutant lysozymes,” Biochim. Biophys. Acta, 1340, 205-214

    , 1997
  68. Xavier, K.A., Shick, K.A., Smith-Gill, S.J. and Willson, R.C.,

    “Involvement of water molecules in the association of monoclonal antibody HyHEL-5 with Bobwhite quail lysozyme,” Biophys. J., 73, 2116-2125

    , 1997
  69. Maillard, K.I., Benedik, M.J. and Willson, R.C.,

    “Rapid detection of mutagens by induction of luciferase-bearing prophages in E. coli,” Environmental Science and Technology, 30(8), 2478-2483

    , 1996
  70. Chacko, S., Silverton, E.W., Smith-Gill, S.J., Davies, D.R., Shick, K.A., Xavier, K.A., Willson, R.C., Jeffrey, P.D., Chang, C.Y.Y., Sieker, L.C., and Sheriff, S.,

    “Refined structures of Bobwhite quail lysozyme uncomplexed and complexed with the HyHEL-5 Fab fragment,” Proteins: Structure, Function, and Genetics, 26, 55-65

    , 1996
  71. Moates, F.C., Somani, M., Annamalai, J., Richardson, J.T, Luss, D. and Willson, R.C.,

    “Infrared Thermographic Screening of Combinatorial Libraries of Heterogeneous Catalysts,” Industrial and Engineering Chemistry Research, 35(12), 4801-4803

    , 1996

Research partially sponsored by:

National Science Foundation       CHEMYX

BioDefense