Chemical and Biomolecular Engineering

Top 20 Doctoral Program — National Research Council

Faculty

Dr. Richard C. Willson
Dr. Richard C. Willson

Huffington-Woestemeyer Professor of Chemical and Biomolecular Engineering
Professor of Biochemical & Biophysical Sciences

Office Location: S229, Engineering Building 1
Phone: 713-743-4308   |   Fax: 713-743-4323
Email: willson [at] uh [dot] edu
Willson's research

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 & Honors: 

2014 Elected to Phi Kappa Phi and as Fellow, American Chemical Society
2013-present Huffington-Woestemeyer Professor
2012 Co-organizer, AACC Oak Ridge Conference on Emerging Diagnostics, San Jose, CA
2011-present Fellow, American Association for the Advancement of Science
2010-2013 John and Rebecca Moores Professor (UH campus-wide competitive)
2009 Fluor-Daniel Award (highest faculty award of the UH Cullen College of Engineering)
2008-present Theme Leader, Diagnostics, NIH Western Regional Center of Excellence
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: 

2008-present: Editorial Board, PLOS ONE

2008-present: Affiliate, SCBMB Program, Baylor College of Medicine

2008-present: Editorial Board, Journal of Biophysics

2007-present: Senior Affiliate Member, The Methodist Hospital Research Institute

2006-present: Member, Faculty of 1000

2004-2007: President, International Society for Molecular Recognition (Program of 2005 and 2007 meetings)

2003-present: Editorial board, Biotechnology Progress

2001-present: Editorial board, Journal of Molecular Recognition

1999: Member/Past Chair, UH Intellectual Property Committee

1998-2002: Council on Chemical Research (CCR) Vision 2020 Roadmap committee on Bioprocessing

Selected Publications

  1. Kisley L, Chen J, Mansur AP, Shuang B, Kourentzi K, Poongavanam MV, Chen WH, Dhamane S, Willson RC, Landes CF,

    Unified superresolution experiments and stochastic theory provide mechanistic insight into protein ion-exchange adsorptive separations. Proc Natl Acad Sci 111: p. 2075-2080.

    , 2014
  2. Paterson AS, Raja B, Garvey G, Kolhatkar A, Hagstrom AE, Kourentzi K, Lee TR, Willson RC,

    Persistent Luminescence Strontium Aluminate Nanoparticles as Reporters in Lateral Flow Assays. Anal Chem. p.9481-9499

    , 2014
  3. Adhikari M, Dhamane S, Hagstrom AEV, Garvey G, Chen WH, Kourentzi K, Strych U, Willson RC,

    “Functionalized viral nanoparticles as ultrasensitive reporters in lateral-flow assays”, Analyst, DOI: 10.1039/c3an00891f

    , 2013
  4. Cacao EC, Sherlock T, Nasrullah A, Kemper S, Knoop J, Kourentzi K, Ruchhoeft P, Stein GE, Atmar RL, Willson RC,

    “Helium-beam shadowing for high spatial resolution patterning of antibodies on microstructured diagnostic surfaces”, Biointerphases, 8(9)

    , 2013
  5. Kanakaraj I, Chen WH, Poongavanam M, Dhamane S, Stagg LG, Ladbury JE, Kourentzi K, Strych U, Willson RC,

    “Biophysical characterization of VEGF-aHt DNA aptamer interactions. Int. J. Biol. Macromol.”,  57:69-75

    , 2013
  6. Chen, W. H.; Fu, J. Y.; Kourentzi, K.; Willson, R. C.,

    Nucleic acid affinity of clustered-charge anion exchange adsorbents: Effects of ionic strength and ligand density. Journal of Chromatography A 2011, 1218 (2), 258-262.

    , 2011
  7. Daniels, C. R.; Reznik, C.; Kilmer, R.; Felipe, M. J.; Tria, M. C. R.; Kourentzi, K.; Chen, W. H.; Advincula, R. C.; Willson, R. C.; Landes, C. F.,

    Permeability of anti-fouling PEGylated surfaces probed by fluorescence correlation spectroscopy. Colloids and Surfaces B-Biointerfaces 2011, 88 (1), 31-38.

    , 2011
  8. Gijavanekar, C.; Anez-Lingerfelt, M.; Feng, C.; Putonti, C.; Fox, G. E.; Sabo, A.; Fofanov, Y.; Willson, R. C.,

    PCR detection of nearly any dengue virus strain using a highly sensitive primer 'cocktail'. Febs Journal 2011, 278 (10), 1676-1687.

    , 2011
  9. 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
  10. Kanakaraj, I.; Jewell, D. L.; Murphy, J. C.; Fox, G. E.; Willson, R. C.,

    Removal of PCR Error Products and Unincorporated Primers by Metal-Chelate Affinity Chromatography. Plos One 2011, 6 (1).

    , 2011
  11. Sherlock, T.; Nasrullah, A.; Litvinov, J.; Cacao, E.; Knoop, J.; Kemper, S.; Kourentzi, K.; Kar, A.; Ruchhoeft, P.; Willson, R.,

    Suspended, micron-scale corner cube retroreflectors as ultra-bright optical labels. Journal of Vacuum Science & Technology B 2011, 29 (6).

    , 2011
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. Jackson GW, McNichols RJ, Fox GE, Willson RC.,

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

    , 2008
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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 Spectrometry261(2-3):218-226

    , 2007
  29. 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
  30. 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,” Biochemistry46(48):13864-73

    , 2007
  31. 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
  32. 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
  33. 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
  34. Jackson GW, McNichols RJ, Fox GE, Willson RC.,

    “Bacterial genotyping by 16S rRNA mass cataloging,” BMC Bioinformatics7:321

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

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

    , 2006
  36. 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
  37. 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
  38. Zhang Z, Jackson GW, Fox GE, Willson RC.,

    “Microbial identification by mass cataloging,”BMC Bioinformatics7:117

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

    “Separation of Genomic DNA from Plasmid DNA by selective renaturation with IMAC capture,” Biotechnology Progress21: 1472-1477

    , 2005
  40. 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
  41. 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 Chemistry5(4); 121-128

    , 2005
  42. 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 CrystallographyD61, 628-633

    , 2005
  43. 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
  44. Jandhyala DM, Willson RC, Sewell BT, and Benedik MJ,

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

    , 2005
  45. 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
  46. 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
  47. 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 Virology78(17):9306-16

    , 2004
  48. 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 Letters25:1111-1116

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

    “Compaction Agent Clarification of Microbial Lysates,” Protein Expression and Purification28(2) 220 – 223

    , 2003
  50. 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

Research partially sponsored by:

National Science Foundation       CHEMYX

BioDefense