Arnold Vainrub, MS, PhD Associate Professor of Biophysics, joined the College of Veterinary Medicine in 2004 . He received his M.S. degree in Physics from Leningrad University in 1973 and Ph.D. in Physics from Ioffe Physico-Technical Institute, St.-Petersburg, Russia in 1980. Dr. Vainrub worked on the faculty of the Institute of Chemical Physics and Biophysics, Estonia from 1980-92, Ecole Polytechnique, France from 1992-98, and Department of Chemistry, University of Houston from 1998-2004.
334-844-7092 vainrar@vetmed.auburn.edu
Research Interests Single strand DNA probes immobilized on the surfaces are a common element of DNA-based biosensors including microarrays and biochips. Dr. Vainrub’s research concerns the hybridization of nucleic acids with surface tethered oligonucleotides. The theoretical studies focus on understanding the hybridization thermodynamics. Role of surface charge, effect of the probe surface density, and large sensitivity enhancement by the linker oligomer between the probe and surface are investigated. Experimental studies’ goal is to verify theoretical predictions and find ways for technical advancement of DNA sensors. The projects under current development include 1) electrostatic control of hybridization on the surface, 2) hybridization isotherms and melting curves of DNA arrays, and 3) real time detection of hybridization using optical waveguide.  Selected Publications Vainrub A, Deluge N, Zhang X, Zhou X, and Gao X. (2007) Predicting DNA duplex stability on oligonucleotide arrays. In: Methods in Molecular Biology, vol. 382: Microarrays, editor J.B. Rampal, vol. 2, pp. 393-403, Humana Press, Totowa, NJ. Vodyanoy V, Pustovyy O, and Vainrub A. (2007) High resolution light microscopy of nanoforms. Proc SPIE 6694: 669413/1-669413/12. Vainrub A, Pustovyy O, and Vodyanoy V. (2006)  Resolution of 90 nm (lambda/5) in an optical transmission microscope with an annular condenser. Optics Lett 31:2855-2857. Pettitt BM, Vainrub A, and Wong KY.  (2005)  DNA saline solutions near surfaces: a few ideas towards design parameters of DNA arrays. In: Ionic Soft Matter: Modern Trends in Theory and Applications, eds. D. Henderson, M. Holovko, and Trokhymchuk, pp. 381–393, Springer. Vainrub A and Pettitt BM.  (2004)  Theoretical aspects of genomic variation screening using DNA microarrays. Biopolymers 73:614–620. Vainrub A, Li Tong-Bin, Fofanov Y, and Pettitt BM.  (2004) Theoretical considerations for the efficient design of DNA arrays. In: Biomedical Technology and Devices Handbook, editor J.E.Moore, Chapter 14, pp. 14-1 – 14-14, CRC Press, Boca Raton, FL. Wong K, Vainrub A, Powdrill T, Hogan M, and Pettitt BM  (2004)  A non-Watson-Krick motif of base-pairing on surfaces for untethered oligonucleotides. Molecular Simulation 30:121-129. Vainrub A and Pettitt BM.  (2003)  Sensitive quantitative nucleic acid detection using oligonucleotide microarrays. J Am Chem Soc 125:7798-7799. Vainrub A and Pettitt BM.  (2003)  Surface electrostatic effects in oligonucleotide microarrays: Control and optimization of binding thermodynamics. Biopolymers 68:265-270. Vainrub A and Pettitt BM.  (2002)  Coulomb blockage of hybridization in two-dimensional DNA arrays.  Phys Rev E 66:41951-41954. Vainrub A and Pettitt BM.  (2000)  Thermodynamics of association to a molecule immobilized in an electric double layer. Chem Phys Lett 323:160-166.