Biointerfacial and Diagnostics Lab
We study how biomolecules organize and function at interfaces and how this behavior impacts applications, especially in biodiagnostics. Below are some examples from our work.
Nucleic Acid Diagnostics
Assemblies of nucleic acids on solid supports are integral to technologies that include biosensors, microarrays, and sequencing platforms. The functioning of these systems is strongly affected by the environment on the surface of the biochip or device. The plot at left illustrates one such example. The graph is a summary of microrray data revealing that base-pairing associations between immobilized strands, which increase from right to left side of plot due to partial  complementarity between immobilized strands (inset), correlate with deviations between surface (●) and solution (o) hybridization affinities. Adapted from Chiang et al, 2016, Langmuir.
Support: National Science Foundation

Optically Resonant Sensors
Sensors based on resonant microcavities are among the most sensitive detection devices known. These devices trap and concentrate light to very high intensities, allowing detection of   single particles like viruses or even proteins. We are collaborating with NYU Applied Physics Prof. Steve Arnold to adapt these sensors to multiplexed detection of viruses and immunology applications. The photograph at right shows a silica microcavity, around 80 microns in diameter. A waveguide feeds light from a laser to the sensor, allowing excitation of "whispering gallery mode" resonant modes. Detection occurs when analytes interact with the modal fields. The picture shows trapping of a nanosphere analyte by light gradient forces, causing scattering (appearing as the white streak) as the nanosphere orbits within a mode. 
Another area of interest is in integration of biosensor systems. Our group develops concepts based on both optical and electrochemical approaches, typically in collaboration with others. The images at right illustrate, clockwise from upper left, a total internal reflection fluorescence (TIRF) sample cell and array, gene expression readout for the pathogen Legionella pneumophila (collaboration with Dr. S. Kalachikov, Columbia Univ.), and an integrated microfluidic chip for concentrating sample nucleic acids through electrokinetic mechanisms (left) to accelerate  their simultaneous hybridization to an underlyling array (right) (collaboration with Prof. Yong-ak Song, NYU Abu Dhabi). Adapted from Qiao et al, 2013, Bioanalytical Chemistry; Martins et al, 2015, Biosensors Bioelectronics; Martins et al, 2016 Analytical Chemistry.
Support: National Science Foundation, National Institutes of Health

Sensing Applications of Morpholinos
The high backbone charge of nucleic acids can hinder use of DNA capture probes especially if detection or manipulation of hybridization is mediated through charge effects. These limitations can be suppressed by using synthetic DNA analogues that are charge neutral. Morpholino oligonucleotides (structure shown at left), which provide such an alternative, are being explored for their hybridization behavior as well as evaluated for new diagnostic concepts. The figures at left illustrate two morpholino-assisted capabilities: (i) electric field based hybridization tuning to distinguish matched () and mismatched (●) analyte (upper left) and (ii) capacitance-based sensing of nucleic acids hybridizing to morpholino-modified chips (lower right). Adapted from Ruffin et al, 2017, ACS Sensors; Tercero et al, 2010, Langmuir. 
Support: National Institutes of Health, National Science Foundation

Hao-Chun Chiang,* Rastislav Levicky, "Electrochemical Analysis of Ultrathin Polythiolsiloxane Films for Surface Biomodification," Int. J. Electrochem., art. 4705031, (2018). 
Ursula Koniges, Sade Ruffin, Rastislav Levicky, " DNA Brushes: Self-Assembly, Physicochemical Properties, and Applications," in Polymer and Biompolymer Brushes, eds. O. Azzaroni and I. Szleifer, John Wiley & Sons, Hoboken NJ, Chapter 21, (2018).  

Hai-Ling Liu, Jiao Cao, Sumaira Hanig, Chunge Yuan, Jie Pang, Rastislav Levicky, Xing-Hua Xia, Kang Wang,* "Size-Controllable Gold Nanopores with High SERS Activity," Analytical Chemistry, 89, 10407-10413, (2017). 
Sade Ruffin, Isabella A Hung, Ursula M Koniges, Rastislav Levicky*, "Electrostatic Cycling of Hybridization Using Nonionic DNA Mimics," ACS Sensors, 2, 892-896, (2017). 
Rastislav Levicky, Ursula M Koniges, Napoleon Tercero, "Diagnostic Applications of Morpholinos and Label-Free Electrochemical Detection of Nucleic Acids," in Morpholino Oligomers, Methods in Molecular Biology, eds. H. Moulton and J. Moulton, Humana Press, New York, Chapter 15, (2017). 

Yakai He, Jing Zhang, Sade Ruffin, Lina Ji, Kang Wang,* Rastislav Levicky, Xinghua Xia, "An Electrochemical Study of the Surface Hybridization Process of Morpholino-DNA: Thermodynamics and Kinetics," Electroanalysis, 28, 1647-1653, (2016).  
Diogo Martins, Xi Wei, Rastislav Levicky, Yong-Ak Song*, "Integration of Multiplexed Microfluidic Electrokinetic Concentrators with a Morpholino Microarray via Reversible Surface Bonding for Enhanced DNA Hybridization," Analytical Chemistry, 88, 3539-3547, (2016).  
Hao-Chun Chiang, Rastislav Levicky*, "Effects of Chain-Chain Associations on Hybridization in DNA Brushes," Langmuir, 32, 12603-12610, (2016). 
Wanqiong Qiao, Hao-Chun Chiang, Hui Xie, Rastislav Levicky,* "Surface vs Solution Hybridization: Effects of Salt, Temperature, and Probe Type, " Chem. Comm., 51, 17245-17248, (2015). 
Diogo Martins, Rastislav Levicky, Yong-Ak Song*, "Enhancing the Speed of Morpholino-DNA Biosensor by Electrokinetic Concentration of DNA in a Microfluidic Chip," Biosens. Bioelectron., 72, 87-94, (2015). 
Keeshan Williams, Chung-Sei Kim, Jin Ryoun Kim, Rastislav Levicky,* "Multimodal Electrochemical Sensing of Transcription Factor-Operator Complexes," Analyst, 139, 1463-1471 (2014). 
Peter M Levine, Ping Gong, Rastislav Levicky, Kenneth L Shepard, "Active CMOS biochip for electrochemical DNA assays," in Microfluidics and Nanotechnology for Biosensing to the Single Molecule Limit, eds. E. Lagally and K. Iniewski, Taylor & Francis, New York, Chapter 2, (2014). 

Kiejin Lee,* Arsen Babajanyan, Harutyun Melikyan, Chongchel Kim, Seungwan Kim, Jungho Kim, Jung-Ha Lee, Barry Friedman, Rastislav Levicky, Sergey Kalachikov, "Label-free DNA microarray bioassays using a near-field scanning microwave microscope," Biosens. Bioelectron., 42, 326-331, (2013). 
Wanqiong Qiao, Sergey Kalachikov, Yatao Liu, Rastislav Levicky*, "Charge-Neutral Morpholino Microarrays for Nucleic Acid Analysis," Analytical Biochemistry, 434, 207-214, (2013). 
Andrew Harrison, Hans Binder, Arnaud Buhot, Conrad Burden, Enrico Carlon, Cynthia Gibas, Lara Gamble, Avraham Halperin, Jef Hooyberghs, David Kreil, Rastislav Levicky, Peter Noble, Albrecht Ott, Montgomery Pettitt, Diethard Tautz, Alex Pozhitkov*, "Physico-Chemical Foundations Underpinning Microarray and Next Generation Sequencing Experiments," Nucleic Acids Research, 41, 2779-2796, (2013). 
Irina Belozerova, Dongbiao Ge, Rastislav Levicky, "Electrochemical Measurements of DNA Melting on Surfaces," in Nanomaterial Interfaces in Biology: Methods and Protocols, eds. Paolo Bergese and Kimberly Hamad-Schifferli, Springer Science + Business Media, New York, Chapter 10, (2013). 

Irina Belozerova, Rastislav Levicky*, "Melting Thermodynamics of Reversible DNA/Ligand Complexes at Interfaces," J. Am. Chem. Soc., 134, 18667-18676, (2012). 
Dongbiao Ge, Xin Wang, Keeshan Williams, Rastislav Levicky*, "Thermostable DNA Immobilization and Temperature Effects on Surface Hybridization," Langmuir, 28, 8446-8455, (2012).  
Yatao Liu, Damion Irving, Wanqiong Qiao, Dongbiao Ge, Rastislav Levicky*, "Kinetic Mechanisms in Morpholino-DNA Surface Hybridization," J. Am. Chem. Soc., 133, 11588-11596, (2011).  
Robert O'Connor, Napoleon Tercero, Wanqiong Qiao, Rastislav Levicky*, "Electrochemical Studies of Morpholino-DNA Surface Hybridization," ECS Transactions, 35, 99-110, (2011).  

Ta-chien Huang, Sunirmal Paul, Ping Gong, Rastislav Levicky, John Kymissis, Sally Amundson, Kenneth L Shepard*, "Gene Expression Analysis With an Integrated CMOS Microarray by Time-Resolved Fluorescence Detection," Biosensors and Bioelectronics, 26, 2660-2665, (2011).  
Napoleon Tercero, Kang Wang, Rastislav Levicky,* "Capacitive Monitoring of Morpholino-DNA Surface Hybridization: Experimental and Theoretical Analysis," Langmuir, 26, 14351-14358, (2010). 
Damion Irving, Ping Gong, Rastislav Levicky*, "DNA Surface Hybridization: Comparison of Theory and Experiment," J. Phys. Chem. B, 114, 7631-7640, (2010). 
Ping Gong, Kang Wang, Yatao Liu, Kenneth L Shepard, Rastislav Levicky*, "Molecular Mechanisms in Morpholino-DNA Surface Hybridization," J. Am. Chem. Soc., 132, 9663-9671, (2010).  
Dongbiao Ge, Rastislav Levicky*,"A Comparison of Five Bioconjugatable Ferrocenes for Labeling of Biomolecules," Chemical Communications, 46, 7190-7192, (2010). 
Napoleon Tercero, Kang Wang, Ping Gong, Rastislav Levicky*, "Morpholino Monolayers: Preparation and Label-Free DNA Analysis by Surface Hybridization," J. Am. Chem. Soc., 131, 4953-4961, (2009).  
Sachin Khapli,* Jin Ryun Kim, Jin Kim Montclare, Rastislav Levicky, Maurizio Porfiri, Stavroula Sofou, "Frozen Cyclohexane-in-Water Emulsion as a Sacrificial Template for the Synthesis of Multilayered Polyelectrolyte Microcapsules," Langmuir, 25, 9728-9733, (2009).  
Ta-Chien Huang, Sebastian Sorgenfrei, Ping Gong, Rastislav Levicky, Kenneth L Shepard*, "A 0.18-m CMOS Array Sensor for Integrated Time-Resolved Fluorescence Detection," IEEE J. Solid State Circuits, 44, 1644-1654, (2009). 
Kang Wang, Rebecca A Zangmeister, Rastislav Levicky*, "Equilibrium Electrostatics of Responsive Polyelectrolyte Monolayers," J. Am. Chem. Soc., 131, 318-326, (2009).  
Peter M Levine*, Ping Gong, Rastislav Levicky, Kenneth L Shepard*, "Real Time, Multiplexed Electrochemical DNA Detection Using an Active Complementary Metal-Oxide-Semiconductor Biosensor Array with Integrated Sensor Electronics," Biosensors and Bioelectronics, 24, 1995-2001, (2008).  
Peter M Levine, Ping Gong, Rastislav Levicky, Kenneth L Shepard*, "Active CMOS Sensor Array for Electrochemical Biomolecular Detection," IEEE J. Solid State Circuits, 43, 1859-1871, (2008). 
Robert G Bozic, Alan C West*, Rastislav Levicky*, "Square Wave Voltammetric Detection of 2,4,6- Trinitrotoluene and 2,4-Dinitrotoluene on a Gold Electrode Modified With Self-Assembled Monolayers," Sensors & Actuators B: Chemical, 133, 509-515, (2008). 
Ping Gong, Rastislav Levicky*, "DNA Surface Hybridization Regimes," Proc. Natl. Acad. Sci. USA, 105, 5301-5306, (2008).  
Peter M Levine, Ping Gong, Kenneth L Shepard,* Rastislav Levicky, "Active CMOS array for electrochemical sensing of biomolecules," Proc. IEEE Custom Integrated Circuits Conference, 825-828, (2007). 

T.-C. Huang, Kenneth L Shepard,* Ping Gong, Rastislav Levicky, "A CMOS array sensor for sub-800-ps time-resolved fluorescence detection," Proc. IEEE Custom Integrated Circuits Conference, 829-832, (2007). 

Gang Shen, Napoleon Tercero, Mariafrancis Anand Gaspar, Bindhu Varughese, Kenneth Shepard, Rastislav Levicky*, "Charging Behavior of Single-Stranded DNA Polyelectrolyte Brushes," J. Am. Chem. Soc., 128, 8427-8433, (2006). 
George Patounakis, Kenneth Shepard*, Rastislav Levicky, "Active CMOS Array Sensor for Time-Resolved Fluorescence Detection," IEEE Journal of Solid-State Circuits, 41, 2521-2530, (2006). 
Barry Friedman, Mariafrancis Anand Gaspar, Sergey Kalachikov, Kiejin Lee*, Rastislav Levicky*, Gang Shen, Hyunjun Yoo, "Sensitive, Label-Free DNA Diagnostics Based on Near-Field Microwave Imaging," J. Am. Chem. Soc., 127, 9666-9667, (2005). 
George Patounakis, Kenneth Shepard,* Rastislav Levicky, "Active CMOS biochip for time resolved fluorescence detection," Symposium on VLSI Circuits, 68-71, (2005). 

Songhui Kim, Hyunjun Yoo, Kiejin Lee*, Barry Friedman, Mariafrancis Anand Gaspar, Rastislav Levicky, "Distance Control for a Near-Field Scanning Microwave Microscope in Liquid Using a Quartz Tuning Fork," Applied Physics Letters, 86, art. no. 153506, (2005). 
Rastislav Levicky*, Adrian Horgan, "Physicochemical Perspectives on DNA Microarray and Biosensor Technologies," Trends in Biotechnology, 23, 143-149, (2005). 
Gang Shen, Maria Francis Anand Gaspar, Rastislav Levicky*, "X-ray Photoelectron Spectroscopy and Infrared Spectroscopy Study of Maleimide-Activated Supports for Immobilization of Oligodeoxyribonucleotides," Nucleic Acids Research, 32, 5973-5980 (2004).  
Patrick Johnson, Rastislav Levicky*, "X-ray Photoelectron Spectroscopy and Differential Capacitance Study of Thiol-functional Polysiloxane Films on Gold Supports," Langmuir, 20, 9621-9627 (2004). 
Patrick Johnson, Maria Francis Anand Gaspar, Rastislav Levicky*, "Polymer-Anchored DNA Gene Monolayers," J. Am. Chem. Soc., 126, 9910-9911 (2004).  
Zhen Liu, Rastislav Levicky*, "Formation of Nanoparticle Rings on Heterogeneous Soft Surfaces," Nanotechnology, 15, 1483-1488 (2004). 
Gang Shen, Adrian Horgan, Rastislav Levicky*, "Reaction of N-phenyl Maleimide with Aminosilane Monolayers," Colloids and Surfaces B - Biointerfaces, 35, 59-65 (2004). 
Zhen Liu, Rastislav Levicky, "Ring Structures from Nanoparticles and Other Nanoscale Building Blocks," in Dekker Encyclopedia of Nanoscience and Nanotechnology, eds. James A. Schwarz, Cristian I Contescu, and Karol Putyera; Marcel Dekker Inc, New York, 2004, vol 5. 3281-3288. 
Mohammad Islam, Stephen O'Brien, Michael Steigerwald, Zhen Liu, Rastislav Levicky, Irving Herman*, "Addition, Suppression, and Inhibition in the Electrophoretic Deposition of Nanocrystal Mixture Films for CdSe Nanocrystals with Fe2O3 and Au Nanocrystals," Nano Letters, 3, 1603-1606 (2003).  
Patrick Johnson, Rastislav Levicky*, "Polymercaptosiloxane Anchor Films for Robust Immobilization of Biomolecules to Gold Supports," Langmuir, 19, 10288-10294 (2003). 
Lei Jin, Adrian Horgan, Rastislav Levicky*, "Preparation of End-Tethered DNA Monolayers on Siliceous Surfaces Using Heterobifunctional Crosslinkers," Langmuir, 19, 6968-6975 (2003). 
Zhen Liu, Kristen Pappacena, Jane Cerise, Jaeup Kim, Christopher J. Durning, Ben O'Shaughnessy and Rastislav Levicky*, "Organization of Nanoparticles On Soft Polymer Surfaces," Nano Letters, 2, 219-224, (2002).  
Adam B. Steel*, Rastislav Levicky, Tonya M. Herne and Michael J Tarlov, "Immobilization of Nucleic Acids at Solid Surfaces: Effect of Oligonucleotide Length on Layer Assembly," Biophysical Journal, 79, 975-981, (2000). 
Rastislav Levicky, Tonya M. Herne, Michael J. Tarlov* and Sushil K. Satija, "Using Self-Assembly to Control the Structure of DNA Monolayers on Gold: A Neutron Reflectivity Study," J. Am. Chem. Soc., 120, 9787-9792, (1998). 
Rastislav Levicky, Nagraj Koneripalli, Matthew Tirrell*, John F. Ankner, Helmut Kaiser and Sushil K. Satija, "Selectively Swollen Films of Triblock/Diblock Copolymer Blends: Dependence of Swollen Film Structure on Blend Composition," Macromolecules, 31, 4908-4914, (1998). 
Rastislav Levicky, Nagraj Koneripalli, Matthew Tirrell* and Sushil K. Satija, "Stratification in Bidisperse Polymer Brushes from Neutron Reflectivity," Macromolecules, 31, 2616-2621, (1998). 
Rastislav Levicky, Nagraj Koneripalli, Matthew Tirrell* and Sushil K. Satija, "Concentration Profiles in Densely Tethered Polymer Brushes," Macromolecules, 31, 3731-3734 (1998). 
Nagraj Koneripalli*, Rastislav Levicky, Frank S. Bates*, Mark W. Matsen, Sushil K. Satija, John Ankner and Helmut Kaiser, "Ordering in Blends of Diblock Copolymers," Macromolecules, 31, 3498-3508 (1998). 
Matthew Tirrell* and Rastislav Levicky, "End-Tethered Chains at Liquid Interfaces," Curr. Opin. Solid State Mat. Sci., 2, 668-672 (1997). 
Nagraj Koneripalli, Rastislav Levicky, Frank S. Bates*, John Ankner, Helmut Kaiser and Sushil K. Satija, "Confinement-Induced Morphological Changes in Diblock Copolymer Films," Langmuir, 12, 6681-6690 (1996). 
Nagraj Koneripalli, Navjot Singh, Rastislav Levicky, Frank S. Bates*, Patrick D. Gallagher and Sushil K. Satija, "Confined Block Copolymer Thin Films," Macromolecules, 28, 2897-2904 (1995). 

Rastislav Levicky, Napoleon Tercero, Kang Wang, Ping Gong, Kenneth Shepard, "Capacitive Morpholino Diagnostics for Analysis of Nucleic Acids," U.S. Patent 8,263,411 (September 2012). 
Rastislav Levicky, Napoleon Tercero, Kang Wang, Ping Gong, Kenneth Shepard, "Capacitive Morpholino Diagnostics for Analysis of Nucleic Acids (divisional)," U.S. Patent 8,273,578 (September 2012). 
Kenneth Shepard, Rastislav Levicky, George Patounakis, "Active CMOS Biosensor Chip for Fluorescent-Based Detection," U.S. Patent 7,738,086 (June 2010). 
Peter M Levine, Kenneth L Shepard, Ping Gong, Rastislav Levicky, "Active CMOS sensor array for electrochemical biomolecular detection," International Patent Application No. PCT/US08/87773 (December 2008).