Mitchel J. Doktycz

Mitchel J. Doktycz

Biological and Nanoscale Systems
BioSciences Division
Oak Ridge National Laboratory
Oak Ridge, TN 37831-6445
Phone: (865) 574-6204
Fax: (865) 574-5345
doktyczmj@ornl.gov

Mitchel J. Doktycz is a Distinguished Staff Scientist and Leader of the Biological and Nanoscale Systems Group in the Biosciences Division at the Oak Ridge National Laboratory. He is also the Laboratory Research Manager for the Plant-Microbe Interfaces Scientific Focus Area, a member of the Research Staff at ORNL’s Center for Nanophase Materials Sciences and has a joint appointments with the University of Tennessee’s Bredesen Center for Interdisciplinary Research and Graduate Education and Graduate School of Genome Science and Technology.  He received his B.S. in Biology and Chemistry in 1985 and Ph.D. in Chemistry in 1991 from the University of Illinois at Chicago. His research interests focus on the intersection of natural and synthetic systems. His laboratory is involved in the development of analytical technologies for post-genomics studies with specific emphases on molecular and cellular imaging techniques and the use of nanomaterials to study and mimic biological systems.

 

Publications

  1. Kumar, A., Karig, D., Neethirajan, S., Suresh, A. K., Srijanto, B. R., Mukherjee, P. P., Retterer, S. T., Doktycz, M.J. (2012) “Adhesion and formation of biofilms in complex microfluidic devices”, Proc ASME-MNHMT2012, Paper # MNHMT2012-75207
  2. Weston, D.J., Pelletier, D. A., Morrell-Falvey, J. L., Tschaplinski, T. J., Jawdy, S.S., Lu, T.-Y., Melton, S. J., Martin, M., Schadt, C. W., Karve, A. A., Chen, J.-G., Doktycz, M. J., Tuskan, G. A. (2012) “Pseudomonas fluorescens induces strain-dependent and strain-independent host plant responses in defense networks, primary metabolism and photosynthesis” Molecular Plant-Microbe Interactions, 25(6) 765–778.
  3. Brown, S. D., Klingeman, D. M, Lu, T.-Y. S., Johnson, C., Utturkar, S., Land, M., Schadt, C. W., Doktycz, M. J., and Pelletier, D. A. (2012) “Draft Genome Sequence of Rhizobium sp. PDO1-076, a bacterium isolated from Populus deltoides, Journal of Bacteriology, 194(9), 2383.
  4. Suresh, A. K., Pelletier, D. A., Wang, W., Morrell-Falvey, J. L., Gu, B., and Doktycz, M. J. (2012) “Cytotoxicity Induced by Engineered Silver Nanocrystallites is Dependent on Surface Coatings and Cell Types” Langmuir, 28(5) 2727-2735.
  5. Siuti, P., Retterer, S. T., Choi, C.-K., Doktycz, M. J. (2012) “Enzyme reactions in picoliter, nanoporous containers”, Analytical Chemistry, Analytical Chemistry, 84(2) 1092-1097.
  6. Karig, D. K., Iyer, S., Simpson, M. L., Doktycz, M. J. (2011) “Expression Optimization and Inducible Negative Feedback in Cell-Free Systems”, Nucleic Acids Research, 40(8) 3763-3774.
  7. Siuti, P., Green, C., Edwards, A. N., Doktycz, M. J., Alexandre, G. (2011) “Nitrogen availability modulates surface attachment of Azospirillum brasilense while changes in adhesive cell surface properties regulated by the chemotaxis-like pathway Che1 have an indirect role”, FEMS Microbiology Letters, 323(2) 105-112.
  8. Suresh, A. K., Doktycz, M. J., Wang, W., Moon, J.-W., Gu, B., Meyer III, H. M., Hensley, D. K., Allison, D. P., Phelps, T. J., Pelletier, D. A. (2011) “Monodispersed Biocompatible Silver Sulfide Nanoparticles: Facile Extracellular Biofabrication using the γ-proteobacterium, Shewanella oneidensis”, ActaBiomaterialia, 7(12), 4253–4258.
  9. Siuti, P., Retterer, S. T., Doktycz, M. J. (2011) “Continuous protein production in nanoporous, picoliter volume containers”, Lab on a Chip, 11(20), 3523-3529.
  10. Gottel, N.R., Castro, H. F., Kerley, M, Yang, Z., Pelletier, D. A., Podar, M., Karpinets, T., Uberbacher, E., Tuskan, G. A., Vilgalys, R., Doktycz, M. J., Schadt, C. W. (2011) “Populus deltoides roots harbor distinct microbial communities within the endosphere and rhizosphere across contrasting soil types”, Applied and Environmental Microbiology, 77(17), 5934-5944.
  11. Kumar, A., Mortensen, N. P., Mukherjee, P., Retterer, S. T. and Doktycz, M. J. (2011) “Electric field induced bacterial flocculation of Enteroaggregative Escherichia coli 042”, Applied Physics Letters, 98, 253701.
  12. Mortensen, N. P., Fowlkes, J. D., Maggert, M., Treviño-Dopatka, S., Boisen, N., Doktycz, M. J., Nataro, J. P., Allison, D. P. (2011) “Effects of sub-minimum inhibitory concentrations of ciprofloxacin on enteroaggregative Escherichia coli and the role of the surface protein dispersin”, International Journal of Antimicrobial Agents, 38(1), 27-34.
  13. Karig, D. K., Siuti, P., Dar, R. D., Retterer, S. T., Doktycz, M. J., Simpson, M. L., (2011) “Model for biological communication in a nanofabricated cell-mimic driven by stochastic resonance” Nano Communication Networks, 2, 39–49.
  14. Allison, D.P., Sullivan, C.J., Mortensen, N.P., Retterer, S. T., Doktycz, M.J. (2011) “Bacterial Immobilization for Imaging by Atomic Force Microscopy” J. Vis. Exp. (54), e2880.
  15. Suresh, A. K., Pelletier, D. A., Wang, W., Broich, M. L., Moon, J.-W., Gu, B., Allison, D. P., Joy, D. C., Phelps, T. J., and Doktycz, M. J. (2011) “Biofabrication of discrete spherical gold nanoparticles using the metal-reducing bacterium, Shewanella oneidensis” ActaBiomaterialia, 7(5), 2148-2152.
  16. Edwards, A. N., Siuti, P., Bible, A. N., Alexandre, G., Retterer, S. T., Doktycz, M. J., Morrell-Falvey, J. L. (2011) “Characterization of cell surface and EPS remodeling of Azospirillum brasilense chemotaxis-like 1 signal transduction pathway mutants by atomic force microscopy”, FEMS Microbiology Letters, 314 (2), 131-139.
  17. Srijanto, B., Retterer, S., Fowlkes, J. D., Doktycz, M.J. (2010) “Nanostructured silicon membranes for control of molecular transport” J. Vac. Sci. Technol. B, 28 (6), C6P48-C6P52.
  18. Pelletier, D. P., Suresh, A. K., Holton, G. A., McKeown, C., Wang, W., Gu, B., Mortensen, N. P., Allison, D. P., Joy, D. C., Allison, M. R., Brown, S. D., Phelps, T. J., Doktycz, M. J. (2010) “Engineered cerium oxide nanoparticles: Effects on bacterial growth and viability” Applied and Environmental Microbiology, 76(24), 7981-7989.
  19. Allison, D. P., Mortensen, N. P., Sullivan, C. J., Doktycz M. J. (2010) “Atomic Force Microscopy of Biological Samples” Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, 2(6), 618-634.
  20. Wang, W., Howe, J. Y., Li, Y., Qui, X., Joy, D. C., Paranthaman, M. P., Doktycz, M. J., Gu, B. (2010) “A Surfactant and Template-Free Route for Synthesizing Ceria Nanocrystals with Tunable Morphologies” J. Mater. Chem., 20(36), 7776-7781.
  21. Choi, C.K., Fowlkes, J.D., Retterer, S.T., Siuti, P., Iyer, S., Doktycz, M.J. (2010) “Surface Charge- and Space-Dependent Transport of Proteins in Crowded Environments of Nanotailored Posts”, ACS Nano, 4(6), 3345–3355.
  22. Suresh, A. K., Pelletier, D. A., Wang, W. Moon, J.-W., Gu, B., Mortensen, N. P., Allison, D. P., Joy, D. C., Phelps, T. J., Doktycz M. J. (2010) “Silver nanocrystallites: Biofabrication using Shewanella oneidensis, and an evaluation of their comparative toxicity on Gram-negative and Gram-positive bacteria” Environmental Science and Technology, 44, 5210–5215.
  23. Fowlkes, J. D., Doktycz, M. J., Rack, P. D. (2010) “An Optimized Nanoparticle Separator Enabled by Electron Beam Induced Deposition” Nanotechnology, 21, 165303.
  24. Retterer, S.T., Siuti, P., Choi, C.-K., Doktycz, M.J. (2010) “Development and Fabrication of Nanoporous Silicon Bioreactors within a Microfluidic Chip” Lab on a Chip, 10(9) 1174 - 1181.
  25. Edwards, A.N., Fowlkes, J.D., Standaert, R.F., Pelletier, D.A., Doktycz, M.J., and Morrell-Falvey, J.L. (2009) “An in vivo imaging-based protein interaction assay with high sensitivity for high-throughput applications” Analytical Biochemistry, 395, 166–177.
  26. Kalyanaraman, M., Retterer, S. T., McKnight, T. E., Ericson, M. N., Allman, S. L., Elkins, J. G., Palumbo, A. V., Keller, M., Doktycz, M.J. (2009) “Controlled microfluidic production of alginate beads for in situ encapsulation of microbes” IEEE Proceedings Biomedical Science & Engineering Conference, 2009. BSEC 2009. First Annual ORNL 18-19 March 2009 Page(s):1 - 4.
  27. Siuti, P., Retterer, S. T., Choi, C. K., Fowlkes, J. D., Doktycz, M. J. (2009) “Cell Free Translation in Engineered Picoliter Volume Containers” IEEE Proceedings of the First Annual ORNL Biomedical Science and Engineering Conference, IEEE Proceedings Biomedical Science & Engineering Conference, 2009. BSEC 2009. First Annual ORNL 18-19 March 2009 Page(s):1 - 4.
  28. Fletcher, B.L., Fern, J.T., Rhodes, K., McKnight, T. E., Fowlkes, J.D., Retterer, S.T., Keffer, D.J., Simpson, M.L., Doktycz, M. J. (2009) “Effects of ultramicroelectrode dimensions on the electropolymerization of polypyrrole” Journal of Applied Physics, 105(12) Article Number: 124312.
  29. Pollas Mortensen, N. Fowlkes, J. D., Sullivan, C. J. Allison, D. P., Larsen, N. B. Molin, S. Doktycz, M. J. (2009) “The effects of the antimicrobial peptide colistin on surface ultrastructure and nanomechanics of Pseudomonas aeruginosa cells” Langmuir, 25(6) 3728-3733.
  30. Hildebrand, M., Holton, G., Joy, D.C., Doktycz, M. J., and Allison, D. P. (2008) “Diverse and conserved nano- and meso-scale structure of diatom silica revealed by atomic force microscopy” Journal of Microscopy, 235(2) 172-187.
  31. Fowlkes, J. D., Fletcher, B. L. Retterer, S. T., Melechko, A. V., Simpson, M. L., Doktycz, M. J., (2008) Size-selectivity and anomalous subdiffusion of nanoparticles through carbon nanofiber-based membranes, Nanotechnology, 19(41) Article Number: 415301.
  32. Lee CW, Kim MJ, Standaert R, Kim S, Owens E, Yan J, Choa YH, Doktycz M, Lee JS (2008) “Application of nanoparticles for materials recognition using peptide phage display technique - Part I: Preliminary study using LaPO4 and TiO2 nanoparticles” Journal of the Korean Institute of Metals and Materials, 46(1) 6-12.  
  33. Lee CW, Kim MJ, Standaert R, Kim S, Owens E, Yan J, Choa YH, Doktycz M, Lee JS (2008) “Application of nanoparticles for materials recognition using peptide phage display technique - Part II: Magnetic bio-panning using Fe3O4 nanoparticles” Journal of the Korean Institute of Metals and Materials, 46(3) 131-134.
  34. Retterer, S.T., Melechko, A., Hensley, D. K., Simpson, M. L., Doktycz, M. J., (2008) “Positional control of catalyst nanoparticles for synthesis of high density carbon nanofiber arrays” Carbon, 46, 1378-1383.
  35. Pelletier, D.P., Hurst, G.B., Foote, L.J., Lankford, P.K., McKeown, C.K., Lu, T.-Y., Schmoyer, D.D., Shah, M.B., Hervey IV, W.J., Hooker, B., Daly, D.S., Gilmore, J., Wiley, S., Auberry, D., Wang, Y., Larimer, F.W., Kennel, S.J., Doktycz, M.J., Morrell-Falvey, J.L., Owens, E.T., Buchanan, M.V. (2008) “A general system for studying protein-protein interactions in Gram-negative bacteria, Journal of Proteome Research, 7(8), 3319-3328.
  36. Fletcher, B. L., Retterer, S. T., McKnight, T. E., Melechko, A. V., Fowlkes, J. D., Simpson, M. L., Doktycz, M.J. (2008) “Actuatable membranes based on polypyrrole-coated vertically aligned carbon nanofibers” ACS NANO, 2(2) 247-254.
  37. Hildebrand, M., Doktycz, M.J., Allison, D. P. (2008) “Application of AFM to understanding biomineral formation in diatoms” Pflugers Archiv-European Journal of Physiology, 456(1), 127-137.
  38. Betanzos-Cabrera, G., Harker, B. W., Doktycz, M. J., Weber, J. L., Beattie, K. L., (2008) “Channel glass–based detection of human short insertion/deletion polymorphisms by tandem hybridization”, Molecular Biotechnology, 38(2) 145-153.
  39. Betanzos-Cabrera, G., Harker, B. W., Doktycz, M. J., Weber, J. L., Beattie, K. L., (2008) “A comparison of hybridization efficiency between flat glass and channel glass solid supports”, Molecular Biotechnology, 38(1) 71-80.
  40. Sullivan, C. J., S. Venkataraman, S., Retterer, S. T., Allison, D. P., Doktycz, M. J., (2007) “Comparison of the Indentation and Elasticity of E. coli and its Spheroplasts by AFM”, Ultramicroscopy, 107, 934–942.
  41. Doktycz, M. J. and M. L. Simpson (2007) “Nano-enabled synthetic biology” Molecular Systems Biology, 3:125.
  42. Liu, Y., Das, S., Olszewski, R. E., Carpenter, D., Culiat, C. T., Sundberg, J. P., Soteropoulos, P., Liu, X., Doktycz, M. J., Michaud, E. J., and B. H. Voy (2007) “The Near Naked Hairless (HrN) Mutation Disrupts Hair Formation but is not Due to a Mutation in the Hairless Coding Region” Journal of Investigative Dermatology, 127(7) 1605-14.
  43. Fletcher, B. L., McKnight, T. E., Fowlkes, J. D., Allison, D. P., Simpson, M. L., Doktycz, M. J. (2007) “Controlling the morphology of carbon nanofiber structures through the electropolymerization of pyrrole”, Synthetic Metal, 157, 282–289.
  44. Allison, D. P., Doktycz, M. J., (2006) “Cellular secretion studied by force microscopy” J. Cell. Mol. Med., 10(4) 847-856.
  45. Dhindsa, M. S., Smith, N. R., Heikenfeld, J., Rack, P. D., Fowlkes, J. D., Doktycz, M. J., Melechko, A. V., Simpson, M. L. (2006) “Reversible electrowetting of vertically aligned superhydrophobic carbon nanofibers”, Langmuir, 22, 9030-9034.
  46. Hildebrand, M., York, E., Kelz, J., Davis, A. K., Frigeri, L. G., Allison, D. P., Doktycz, M. J., (2006) “Nano-scale Control of Silica Morphology and Three-dimensional Structure during Diatom Cell Wall Formation”, J. Mater. Res., Vol. 21, No. 10, 2689-2698.
  47. Beckmann, M. A., Venkataraman, S., Doktycz, M. J., Nataro, J. P., Sullivan, C. J., Morrell-Falvey, J., Allison, D. P. (2006) “Measuring cell surface elasticity on enteroaggregative Escherichia coli wild type and dispersin mutant by AFM”, Ultramicroscopy, 106, 695–702.
  48. Chourey, K., Thompson, M. R., Morrell-Falvey, J., VerBerkmoes, N. C., Brown, S. D., Shah, M., Zhou, J. Z. Doktycz, M, Hettich, R. L., and Thompson, D. K. (2006) “Global molecular and morphological effects of 24-h chromium (VI) exposure on shewanella oneidensis MR-1” Applied and Environmental Microbiology, 72 (9): 6331-6344.
  49. McKnight T. E., Peeraphatdit C., Jones S. W., Fowlkes J. D., Fletcher B. L., Klein K. L., Melechko A. V., Doktycz M. J., Simpson M. L.  (2006) “Approaches for Site Specific Functionalization Along the Height of Vertically-Aligned Carbon Nanofiber Arrays” Chemistry of Materials, 18 (14): 3203-3211.
  50. Fowlkes, J. D., Hullander, E. D., Fletcher, B. L., Retterer, S. T., Melechko, A. V., Hensley, D. K., Simpson M. L. and Doktycz M. J. (2006) “Molecular Transport in a Crowded Volume Created from Vertically Aligned Carbon Nanofibers: A Fluorescence Recovery after Photobleaching Study”, Nanotechnology, 17, 5659-5668.
  51. Beckmann, M. A., Venkataraman, S., Doktycz, M. J., Nataro, J. P., Sullivan, C. J., Morrell-Falvey, J., Allison, D. P. (2006) “Measuring cell surface elasticity on enteroaggregative Escherichia coli wild type and dispersin mutant by AFM”, Ultramicroscopy, 106, 695–702.
  52. Chourey, K., Thompson, M. R., Morrell-Falvey, J., VerBerkmoes, N. C., Brown, S. D., Shah, M., Zhou, J. Z. Doktycz, M, Hettich, R. L., and Thompson, D. K. (2006) “Global molecular and morphological effects of 24-h chromium (VI) exposure on shewanella oneidensis MR-1” Applied and Environmental Microbiology, 72 (9): 6331-6344.
  53. Fletcher, B. L., McKnight, T. E., Melechko, A. V., Simpson, M. L. and Doktycz, M. J. (2006) “Biochemical Functionalization of Vertically Aligned Carbon Nanofibres” Nanotechnology, 17, 1-8.
  54. Van Berkel, G. J., Ford, M. J., Doktycz, M. J., Kennel, S. J. (2006) “Evaluation of a Surface Sampling Probe Electrospray Mass Spectrometry System for the Analysis of Surface Deposited and Affinity Captured Proteins” Rapid Commun. Mass Spectrom. 20: 1–9.
  55. Fowlkes, J. D., Melechko, A. V., Klein, K. L., Rack, P. D., Smith, D. A., Hensley, D. K., Doktycz, M. J., Simpson M. L. (2006) “Control of catalyst particle crystallographic orientation in vertically aligned carbon nanofiber synthesis” Carbon, 44, 1503–1510.
  56. Fowlkes, J. D., Fletcher, B. L., Hullander, E. D., Klein, K. L., Hensley, D. K., Melechko, A. V., Simpson, M. L., and Doktycz, M. J., (2005) “Cell mimic structure with tailored membrane pore sizes; controlled synthesis, modeling, and passive diffusion experiments” Nanotechnology 16, 3101–3109.
  57. Chourey, K., Thompson, M. R., Morrell-Falvey, J., VerBerkmoes, N. C., Brown, S. D., Shah, M., Zhou, J. Z. Doktycz, M, Hettich, R. L., and Thompson, D. K. (2006) “Global molecular and morphological effects of 24-h chromium (VI) exposure on shewanella oneidensis MR-1” Applied and Environmental Microbiology, 72 (9): 6331-6344.
  58. Fletcher, B. L., Hullander, E. L., Melechko, A. V., McKnight, T. E., Klein, K. L., Hensley, D. K., Simpson, M. L., Doktycz, M. J. (2004) “Microarrays of biomimetic cells formed by the controlled synthesis of carbon nanofiber membranes” Nano Letters, 4(10), 1809-1814.
  59. Coffman, E. A., Melechko, A. V., Allison, D. P., Simpson, M. L., Doktycz, M. J. (2004) “Surface patterning of silica nanostructures using bio-inspired templates and directed synthesis” Langmuir, 20, 8431-8436.
  60. Hoyt, P. R. and M. J. Doktycz (2004) “Optimized beadmilling of tissues for high throughput RNA production and microarray-based analyses” Analytical Biochemistry, 332(1), 100-108.
  61. M. J. Doktycz, J. E. Johnson, M. J. Cornett (2004) “Hybrid valve structure for high throughput, low volume liquid handling applications” Journal of the Association for Laboratory Automation, 9(4), 250-256.
  62. McKnight, T. E., Melechko, A. V., Guillorn, M. A., Merkulov, V. I., Doktycz, M. J., Culbertson, C. T., Jacobson, S. C., Lowndes, D. H., Simpson, M. L. (2003) “Effects of microfabrication processing on the electrochemistry of carbon nanofiber electrodes” J. Phys. Chem. B, 107 (39): 10722-10728.
  63. McKnight, T. E, Melechko, A. V., Griffin, G. D., Guillorn, M. A., Merkulov, V. I., Serna, F., Hensley, D. K., Doktycz, M. J., Lowndes, D. H., Simpson, M. L. (2003) “Intracellular integration of synthetic nanostructures with viable cells for controlled biochemical manipulation” Nanotechnology, 14, 551-556.
  64. Hoyt, P. R., Doktycz, M. J., Beattie, K. L., and Greeley, Jr, M. S. (2003) “DNA microarrays detect 4-nonylphenol-induced alterations in gene expression during zebrafish early development”, Ecotoxicology, 12, 471- 476.
  65. Doktycz, M. J., Sullivan, C. J., Hoyt, P. R., Pelletier, D. A., Wu, S. Allison, D. P. (2003) “AFM imaging of bacteria in liquid media immobilized on gelatin coated mica surfaces” Ultramicroscopy, 97(1-4), 209-216.
  66. Reyes-López, M.-A., Méndez-Tenorio, A., Maldonado-Rodríguez, Doktycz, M. J., Fleming, J. T., Beattie, K. L. (2003) “Fingerprinting of prokaryotic 16S rRNA genes using oligonucleotide microarrays and virtual hybridization” Nucleic Acids Res., 31 (2): 779-789.
  67. Hoyt, P. R., Tack, L., Jones, B. L., Ahrweiller, P., Staat, S. and Doktycz, M. J. (2003) Automated high throughput probe production for DNA microarray analysis”, Biotechniques, 34(2), 402-407.
  68. Melechko, A. V., McKnight, T. E., Guillorn, M. A., Ilic, B., Merkulov, V. I., Doktycz, M. J., Lowndes, D. H. and M. L. Simpson (2003) “Vertically aligned carbon nanofibers as sacrificial templates for nanofluidic structures” Appl. Phys. Lett., 82 (6): 976-978.
  69. Buchanan, M. V. Larimer, F. W., Wiley, H. S., Kennel, S. J., Squier, T. J., Ramsey, J. M., Rodland K. D., Hurst, G. B., Smith, R. D., Xu, Y., Dixon, D., Doktycz, M. J., Colson, S., Gesteland, R., Giometti, C., Young, M., Giddings, M. (2002) “Genomes to Life "Center for Molecular and Cellular Systems": A Research Program for Identification and Characterization of Protein Complexes” Omics: A Journal of Integrative Biology 6(4), 287-303.
  70. Melechko, A. V., McKnight, T. E., Guillorn, M. A., Austin, D. W., Ilic, B., Merkulov, V. I., Doktycz, M. J., Lowndes, D. H.and M. L. Simpson (2002) “Nanopipe fabrication using vertically aligned carbon nanofiber templates” (2002), J Vac Sci Technol B, 20 (6): 2730-2733.
  71. Subramanium, A., Oden, P. I., Kennel, S.J., Jacobson, K. B., Warmack, R. J., Thundat, T., Doktycz, M. J., (2002) “Microcantilever based calorimetric biosensing”, Appl. Phys. Lett., 81(2), 385-387.
  72. Zhang, L, Melechko, A. V., Guillorn, M. A., Lowndes, D. H., Simpson, M. L., Doktycz, M. J. (2002) “Controlled particle transport across vertically aligned carbon nanofiber barriers”, Appl. Phys. Lett., 81(1), 135-137.
  73. Fredrickson, H. L., Perkins, E. J., Bridges, T. S., Tonucci, R. J., Fleming, J. K., Nagel, A., Diedrich, K., Mendez-Tenorio, A., Doktycz, M. J., Beattie, K. L. (2001) “Towards environmental toxicogenomics: development of a flow-through, high-density, DNA hybridization array and its application to ecotoxicity assessment” The Science of the Total Environment 274, 137-149.
  74. Hicks, J. S., Harker, B. W., Beattie, K. L., and Doktycz, M. J., (2001) “Modification of an automated liquid handling system for reagent-jet, nanoliter-level dispensing”, Biotechniques, 30 (4), 878-885.
  75. Kim, Y., Hurst, G. B., Doktycz, M. J., and M. V. Buchanan (2001) “Improving spot homogeneity by using polymer substrates in matrix-assisted laser desorption/ionization mass spectrometry of oligonucleotides”, Analytical Chemistry, 73(11), 2617-2624.
  76. Hoyt, P. R., Doktycz, M. J., Warmack, R. J., Allison, D. P., (2001) “Spin-column isolation of DNA-protein interactions from complex protein mixtures for AFM imaging”, Ultramicroscopy, 86, 139-141.
  77. P. R. Hoyt, M. J. Doktycz, P. Modrich, R. J. Warmack, and D. P. Allison, (2000) “Identifying Sequence Similarities Between DNA Molecules”, Ultramicroscopy, 82, 237-244.
  78. Subramanian, A., Kennel, S. J., Oden, P. I., Jacobson, K. B. Woodward, J., and Doktycz, M. J. (1999) “Comparison of Techniques for Enzyme Immobilization on Silicon Supports”, Enzyme and Microbial Technology, 24, 26-34.
  79. Doktycz, M. J., Larimer, F. W., Pastrnak, M., and Stevens, A. (1998) “Comparative Analyses of the Secondary Structures of Synthetic and Intracellular Yeast MFA2 mRNAs”, Proc. Natl. Acad. Sci. (USA), 95, 14014-14022.
  80. Hurst, G. B., Weaver, K., Doktycz, M. J., Buchanan, M. V., Costello, A. M., and Lidstrom, M. E. (1998) “MALDI-TOF analysis of polymerase chain reaction products from methanotrophic bacteria”, Analytical Chemistry, 70(13), 2693-2698.
  81. Allison, D.  P., Kerper, P.  S., Doktycz, M.  J., Thundat, T., Modrich, P., Larimer, F.  W., Johnson, D.  K., Hoyt, P.  R., Mucenski, M.  L. and Warmack, R.  J. (1997)  “Mapping individual cosmid DNAs by direct AFM imaging”, Genomics, 41, 379-384.
  82. Allen R. C., Doktycz, M. J. (1996) “Discontinuous electrophoresis revisited: A review of the process”, Appl. Theor. Electroph., 6(1), 1-9.
  83. Allison, D.  P., Kerper, P.  S., Doktycz, M.  J., Spain, J.  A., Modrich, P., Larimer, F.  W., Thundat, T.  And Warmack, R.  J.  (1996) “Direct AFM imaging of EcoRI endonuclease site specifically bound to plasmid DNA molecules”, Proc.  Natl.  Acad.  Sci.  (USA), 96, 8826-8829.
  84. Hurst, G.  B., Doktycz, M.  J., Vass, A.  A., Buchanan, M.  V.  (1996) “Detection of bacterial DNA polymerase chain reaction products by matrix-assisted laser desorption/ionization mass spectrometry”, Rapid Commun. Mass Spectrom., 10, 377-382
  85. Doktycz, M. J., Hurst, G. B., Habibi-Goudarzi, S., McLuckey, S. A., Tang, K., Chen, C. H., Uziel, M., Jacobson, K. B., Woychik, R. P. and Buchanan, M. V. (1995) “Analysis of PCR-amplified DNA products by mass spectrometry using matrix-assisted laser desorption and electrospray: current capabilities and limitations”, Analytical Biochemistry, 230, 205-214.
  86. Doktycz, M. J., Morris, M. D., Dormady, S. J., Beattie, K. L. and Jacobson, K. B. (1995) “Optical melting of 128 octamer DNA duplexes:  effects of base pair location and nearest neighbors on thermal stability”, Journal of Biological Chemistry, 270, No. 15, 8439-8445.
  87. Doktycz, M. J., Habibi-Goudarzi, S., and McLuckey, S. A. (1994) “Accumulation and storage of ionized duplex DNA molecules in a quadrupole ion trap”, Analytical Chemistry, 66, 3416-3422.
  88. Lumetta, V. J. and Doktycz, M. J. (1994) “Electrophoresis for under five dollars”, Journal of College Science Teachers, March/April, 314-316.  Republished in “Favorite Demonstrations for College Science” B. R. Shmaefsky, Ed., NTSA Press, Arlington VA, 2004.
  89. Paner, T. M., Gallo, F. J., Doktycz, M. J., and Benight A. S.  (1993) "Studies of DNA dumbbells V:  melting of a DNA triplex formed between a 28 base-pair DNA dumbbell substrate and a 16 base linear single strand", Biopolymers, 33, 1779-1789.
  90. Doktycz, M. J., Paner, T. M., and Benight A. S.  (1993) "Studies of DNA dumbbells IV:  preparation and melting of a DNA dumbbell with the sixteen base-pair sequence: 5’GTATCCCTCTGGATAC3’ linked on the ends by dodecyl chains", Biopolymers, 33, 1765-1777.
  91. Doktycz, M. J. (1993) “Discontinuous electrophoresis of DNA:  adjusting DNA mobility by trailing ion net mobility”, Analytical Biochemistry, 213, 400-406.
  92. Sheardy, R. D., Suh, D., Kurzinsky, R., Doktycz, M. J., Benight, A. S., and Chaires, J. B. (1993)  “Sequence dependence of the free energy of B-Z junction formation in deoxyribonucleotides”, J. Mol. Biol., 231, 475-488.
  93. T. Thundat, Allison, D. P., Warmack, R. J., Doktycz, M. J., Jacobson K. B., and Brown, G. M. (1993) “Atomic force microscopy of double and single stranded DNA on chemically treated mica”, J. Vac. Sci. Technol. A, 11(4), 824-828.
  94. Doktycz, M. J., Gibson, W. A., Arlinghaus, H. F., Allen, R. C., and Jacobson, K.B. (1993)  “Use of resonance ionization spectroscopy to detect DNA bands on ultra-thin spin-coated gels”, Applied and Theoretical Electrophoresis, 3, 157-162.
  95. Doktycz, M. J., Arlinghaus, H. F., Allen, R. C. and Jacobson, K. B. (1992) "Electrophoresis and detection of tin-labelled DNAs on open-faced gels", Electrophoresis, 13, 521-528.
  96. Doktycz, M. J., Goldstein, R. F., Paner, T. M., Gallo, F. J. and Benight A. S. (1992) "Studies of DNA dumbbells I: melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops  evaluation of the nearest-neighbor stacking interactions in DNA", Biopolymers, 32, 849-864.
  97. Doktycz, M. J., Benight, A. S. and Sheardy, R. D. (1990)  "Energetics of B-Z junction formation in a sixteen base-pair duplex DNA", J. Mol. Biol. 212, 3-6.
  98. Doktycz, M. J., Paner, T. M., Amaratunga, M. and Benight A. S.  (1990) "Thermodynamic stability of the 5' dangling-ended DNA hairpins formed from the sequences 5'-(XY)2GGATAC(T)4GTATCC-3', where X,Y= A,T,G,C", Biopolymers, 30, 829-845.
  99. Paner, T. M., Amaratunga, M., Doktycz, M. J. and Benight A. S. (1990) "Analysis of melting transitions of the DNA hairpins formed from the oligomer sequences d[GGATAC(X)4GTATCC] (X=A,T,G,C)", Biopolymers, 29, 1715-1734.

Book Chapters and Other Articles

  1. Neethirajan, S., Karig, D., Kumar, A., Mukherjee, P. P., Retterer, S. T., Doktycz, M. J. “Biofilms in microfluidic devices”, in Encyclopedia of Nanotechnology, Ed: B. Bhushan, Springer, New York (In Press)
  2. Doktycz, M.J., Sullivan, C.J., Mortensen, N., Allison, D.P. “Microbial Cell Imaging” in Life at the Nanoscale: Atomic Force Microscopy of Live Cells, Pan Stanford Publishing, (Y.F Dufrêne ed.) 2011.
  3. Allison, D.P. Dufrêne, Y.F., Doktycz, M.J. and Hildebrand, M. “Biomineralization at the Nanoscale: Learning from Diatoms” Methods in Cell Biology: Methods in Nano Cell Biology, B.P. Jena (Editor) Elsevier (2008)
  4. McKnight, T. E., Melechko, A. V., Griffin, G. D., Guillorn, M. A., Merkulov, V. I., Doktycz, M. J., Ericson, M. N., Simpson, M. L. “Cellular Interfacing with Arrays of Vertically Aligned Carbon Nanofibers and Nanofiber-Templated Materials” in Nanotechnology in Biology and Medicine, Tuan Vo-Dinh, ed. CRC Press, (2006) 329-350.
  5. Hoyt, P. R., Doktycz, M. J., and L. Tack, Chapter 5. Preparation of cDNA Probes for DNA Microarrays in DNA Sequencing II: Isolation and Preparation, Edited by Jan Kieleczawa, Jones and Bartlett Publishers (2006).
  6. Doktycz, M. J. (2005) “Reagent jetting based deposition technologies for array construction” in Microarray Technology and its Applications, eds: D. Nicolau and U. R. Muller, Springer-Verlag Berlin Heidelberg
  7. M. J. Doktycz (2002) “Nucleic acids: thermal stability and denaturation” in Encyclopedia of the Life Sciences, Macmillan Publishers Ltd., Nature Publishing Group www.els.net.
  8. M. J. Doktycz  (2000) “Discontinuous Electrophoresis” in Encyclopedia of Separation Science, edited by I. D. Wilson, T. R. Adlard, C. F. Poole and M. Cook, Academic Press, 1245-1250.
  9. T. J. Whitaker, K. B. Jacobson, and M. J. Doktycz, (2000) “Preparation and Application of DNA Arrays” in Encyclopedia of Analytical Chemistry: Instrumentation and Applications, edited by R. A. Meyers, John A. Wiley & Sons, Ltd., 1219-1238.
  10. Doktycz, M. J. (1998) “DNA Array Technology”, Advance for Administrators of the Laboratory, 7(11), 53-55.
  11. Allison, D.  P., Doktycz, M.  J., Hoyt, P. R., Thundat, T. and Warmack, R.  J. (1997) “The analysis of genomes by atomic force microscopy”, Scanning, 1997, 19, 136-137.
  12. Doktycz, M. J. and Beattie, K. L. (1997) “Genosensors and Model Hybridization Studies” in Automation Technologies for Genome Characterization, edited by T.  J.  Beugelsdijk, John Wiley & Sons, Inc., p. 205-225.
  13. G.B. Hurst, M.J. Doktycz, P.F. Britt, A.A. Vass and M.V. Buchanan, (1997) "Detection and analysis of polymerase chain reaction products by mass spectrometry."  Proceedings of SPIE, Vol. 1985, 120.
  14. Doktycz, M. J., Jacobson, K. B., Beattie, K. L., and Foote, R. S., (1995) “Optical melting as a tool for optimizing sequencing by hybridization analysis of DNA” in Ultrasensitive Instrumentation for DNA Sequencing and Biochemical Diagnostics, G. E. Cohn, J. M. Lerner, K. J. Liddane, A. Scheeline, S. A. Soper, Editors, Proc. SPIE 2386, 30-34.
  15. Allison, D. P., Thundat, T. G., Modrich, P., Isfort, R. J., Doktycz, M. J., Kerper, P. S., Warmack, R. J. (1995) “Mapping site-specific endonuclease binding to DNA by direct imaging with atomic force microscopy” in Ultrasensitive Instrumentation for DNA Sequencing and Biochemical Diagnostics, G. E. Cohn, J. M. Lerner, K. J. Liddane, A. Scheeline, S. A. Soper, Editors, Proc. SPIE 2386, 24-29.
  16. Allison, D. P., Doktycz, M. J., Thundat, T., Jacobson, K. B., Brown, G. M., and Warmack, R. J. (1993) “Scanning probe microscopy of immobilized DNA”, Polymer Preprints, 34(2), 332-333.
  17. Doktycz, M. J. (1993) “Nucleic acid separation” in Gel Electrophoresis of Proteins Nucleic Acids and Selected Techniques, eds. R. C. Allen and B. Budowle, Walter de Gruyter, Berlin.
  18. Jacobson, K. B., Arlinghaus, H. F., Doktycz, M. J., Sachleben, R. A., Brown, G. M., and Larimer, F. W.  (1993) “Development of resonance ionization spectroscopy for genome mapping and DNA sequencing using stable isotopes as DNA labels” In Advances in DNA Sequencing Technology, R. A. Keller, ed. SPIE vol. 1891, 27-65.