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Your search keyword '"Nandivada, Santoshi"' showing total 12 results
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12 results on '"Nandivada, Santoshi"'

1. Real-time shape approximation and 5-D fingerprinting of single proteins

Author

Yusko, Erik C., Bruhn, Brandon R., Eggenberger, Olivia, Houghtaling, Jared, Rollings, Ryan C., Walsh, Nathan C., Nandivada, Santoshi, Pindrus, Mariya, Hall, Adam R., Sept, David, Li, Jiali, Kalonia, Devendra S., and Mayer, Michael

Subjects
Quantitative Biology - Biomolecules, Condensed Matter - Soft Condensed Matter, Physics - Biological Physics
Abstract

This work exploits the zeptoliter sensing volume of electrolyte-filled nanopores to determine, simultaneously and in real time, the approximate shape, volume, charge, rotational diffusion coefficient, and dipole moment of individual proteins. We have developed the theory for a quantitative understanding and analysis of modulations in ionic current that arise from rotational dynamics of single proteins as they move through the electric field inside a nanopore. The resulting multi-parametric information raises the possibility to characterize, identify, and quantify individual proteins and protein complexes in a mixture. This approach interrogates single proteins in solution and determines parameters such as the approximate shape and dipole moment, which are excellent protein descriptors and cannot be obtained otherwise from single protein molecules in solution. Taken together, this five-dimensional characterization of biomolecules at the single particle level has the potential for instantaneous protein identification, quantification, and possibly sorting with implications for structural biology, proteomics, biomarker detection, and routine protein analysis.

Published
2015
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4. Real-time shape approximation and fingerprinting of single proteins using a nanopore

Author

Yusko, Erik C., primary, Bruhn, Brandon R., additional, Eggenberger, Olivia M., additional, Houghtaling, Jared, additional, Rollings, Ryan C., additional, Walsh, Nathan C., additional, Nandivada, Santoshi, additional, Pindrus, Mariya, additional, Hall, Adam R., additional, Sept, David, additional, Li, Jiali, additional, Kalonia, Devendra S., additional, and Mayer, Michael, additional

Published
2016
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10. Real-time shape approximation and fingerprinting of single proteins using a nanopore

Author

Yusko, Erik C., Bruhn, Brandon R., Eggenberger, Olivia M., Houghtaling, Jared, Rollings, Ryan C., Walsh, Nathan C., Nandivada, Santoshi, Pindrus, Mariya, Hall, Adam R., Sept, David, Li, Jiali, Kalonia, Devendra S., and Mayer, Michael

Abstract

Established methods for characterizing proteins typically require physical or chemical modification steps or cannot be used to examine individual molecules in solution. Ionic current measurements through electrolyte-filled nanopores can characterize single native proteins in an aqueous environment, but currently offer only limited capabilities. Here we show that the zeptolitre sensing volume of bilayer-coated solid-state nanopores can be used to determine the approximate shape, volume, charge, rotational diffusion coefficient and dipole moment of individual proteins. To do this, we developed a theory for the quantitative understanding of modulations in ionic current that arise from the rotational dynamics of single proteins as they move through the electric field inside the nanopore. The approach allows us to measure the five parameters simultaneously, and we show that they can be used to identify, characterize and quantify proteins and protein complexes with potential implications for structural biology, proteomics, biomarker detection and routine protein analysis.

Published
2017
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11. Characterization of Nanoparticles Using Solid State Nanopores

Author

Nandivada, Santoshi

Subjects
Characterization, Solid State Nanopores, Spherical Nanoparticles, Engineering Physics, Nanoscience and Nanotechnology
Abstract

Solid state nanopores are widely used in detection of highly charged biomolecules like DNA and proteins. In this study, we use a solid state nanopore based device to characterize spherical nanoparticles to estimate their size and electrical charge using the principle of resistive pulse technique. The principle of resistive pulse technique is the method of counting and sizing particles suspended in a fluid medium, which are electrophoretically driven through a channel and produce current blockage signals due to giving rise to a change in its initial current. This change in current is denoted as a current blockage or as a resistive pulse. The information from these current blockage signals in case of nanopore devices and spherical nanoparticles helps us to look at the properties of each individual nanoparticles such as size, electrical charge and electrophoretic mobility. In this thesis, two spherical nanoparticles of different sizes and different surface charge groups are used: Negatively charged 25 nm iron oxide nanoparticle with – COOH surface group and positively charged 53 nm polystyrene nanoparticle with – NH2 surface group. Nanopores used in these studies are about twice the nanoparticle size. These nanopores were fabricated by various fabrication techniques such as, Focused ion beam milling and ion beam sculpting method. The current blockage events produced by these two nanoparticles were measured as a function of applied voltage. The parameters extracted from the current blockage events, such as the current drop amplitudes and event duration are analyzed to estimate the size and electrical charge of the nanoparticles. Estimation of drift velocity of the nanoparticle and diffusion coefficient are also discussed. The estimated size is then compared to the nanoparticle size obtained from dynamic light scattering technique. Stable nanoparticles are widely used in biological and pharmacological studies and understanding the behavior of these nanoparticles in a nanopore environment would make a significant contribution to the studies at the nanoscale.

Published
2017

12. Estimating RNA Polymerase Protein Binding Sites on λ DNA Using Solid-State Nanopores.

Author

Kaur H, Nandivada S, Acharjee MC, McNabb DS, and Li J

Subjects
Binding Sites, Formaldehyde chemistry, Protein Binding, DNA metabolism, DNA-Directed RNA Polymerases metabolism, Nanopores
Abstract

In this work, using a silicon nitride nanopore based device, we measure the binding locations of RNA Polymerase (RNAP) on 48.5 kbp (16.5 μm) long λ DNA. To prevent the separation of bound RNAPs from a λ DNA molecule in the high electric field inside a nanopore, we cross-linked RNAP proteins to λ DNA by formaldehyde. We compare the current blockage event data measured with a mixture of λ DNA and RNAP under cross-link conditions with our control samples: RNAP, λ DNA, RNAP, and λ DNA incubated in formaldehyde separately and in a mixture. By analyzing the time durations and amplitudes of current blockage signals of events and their subevents, as well as subevent starting times, we can estimate the binding efficiency and locations of RNAPs on a λ DNA. Our data analysis shows that under the conditions of our experiment with the ratio of 6 to 1 for RNAP to λ DNA molecules, the probability of an RNAP molecule to bind a λ DNA is ∼42%, and that RNAP binding has a main peak at 3.51 μm ± 0.53 μm, most likely corresponding to the two strong promoter regions at 3.48 and 4.43 μm of λ DNA. However, individual RNAP binding sites were not distinguished with this nanopore setup. This work brings out new perspectives and complications to study transcription factor RNAP binding at various positions on very long DNA molecules.

Published
2019
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