Momčilo M. Gavrilov

Imaging the time course of DNA damage response at a nonrepetitive endogenous locus

Adam T Rybczynski, Wayne Taylor Cottle, Po-Ta Chen, Jiwoong Kwon et autres

DNA double-strand breaks (DSBs) are among the most genotoxic lesions. Investigating the cellular dynamics of repair factors during DSB repair requires methodologies that preserve both spatial and temporal information. Here, we describe a method for tracking repair progression over time at any …

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Free-energy measuring nanopore device

Momčilo M. Gavrilov, Jinghang Zhang, Olivia Yang, Taekjip Ha

Free energies (FEs) in molecular sciences can be used to quantify the stability of folded molecules. In this article, we introduce nanopores for measuring FEs. We pull DNA hairpin-forming molecules through a nanopore, measure work, and estimate the FE change in the …

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Imaging the Time Course of DNA Damage Response at a Nonrepetitive Endogenous Locus

Wayne Taylor Cottle, Adam Rybczynski, Yanbo Wang, Paul Meneses et autres

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Directing Uphill Strand Displacement with an Engineered Superhelicase

Helena Hall-Thomsen, Shavier Small, Momčilo M. Gavrilov, Taekjip Ha et autres

The ability to finely tune reaction rates and binding energies between components has made DNA strand displacement circuits promising candidates to replicate the complex regulatory functions of biological reaction networks. However, these circuits often lack crucial properties, such as signal turnover and …

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Information Engine in a Nonequilibrium Bath

Tushar K. Saha, Jannik Ehrich, Momčilo M. Gavrilov, Susanne Still et autres

Information engines can convert thermal fluctuations of a bath at temperature T into work at rates of order k_{B}T per relaxation time of the system. We show experimentally that such engines, when in contact with a bath that is out of equilibrium, …

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Achieving single nucleotide sensitivity in direct hybridization genome imaging

Yanbo Wang, Wayne Taylor Cottle, Haobo Wang, Momčilo M. Gavrilov et autres

Direct visualization of point mutations in situ can be informative for studying genetic diseases and nuclear biology. We describe a direct hybridization genome imaging method with single-nucleotide sensitivity, single guide genome oligopaint via local denaturation fluorescence in situ hybridization (sgGOLDFISH), which leverages …

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Engineered helicase replaces thermocycler in DNA amplification while retaining desired PCR characteristics

Momčilo M. Gavrilov, Joshua Yang, Roger S. Zou, Wen Ma et autres

Polymerase Chain Reaction (PCR) is an essential method in molecular diagnostics and life sciences. PCR requires thermal cycling for heating the DNA for strand separation and cooling it for replication. The process uses a specialized hardware and exposes biomolecules to temperatures above …

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Sequence-dependent mechanochemical coupling of helicase translocation and unwinding at single-nucleotide resolution

Andrew H. Laszlo, Jonathan M. Craig, Momčilo M. Gavrilov, Ramreddy Tippana et autres

We used single-molecule picometer-resolution nanopore tweezers (SPRNT) to resolve the millisecond single-nucleotide steps of superfamily 1 helicase PcrA as it translocates on, or unwinds, several kilobase-long DNA molecules. We recorded more than two million enzyme steps under various assisting and opposing forces …

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Information engine in a nonequilibrium bath

Tushar Kanti Saha, Jannik Ehrich, Momčilo M. Gavrilov, Susanne Still et autres

Information engines can convert thermal fluctuations of a bath at temperature $T$ into work at rates of order $k_\mathrm{B}T$ per relaxation time of the system. We show experimentally that such engines, when in contact with a bath that is out of equilibrium, …

Achieving single nucleotide sensitivity in direct hybridization genome imaging

Yanbo Wang, Wayne Taylor Cottle, Haobo Wang, Momčilo M. Gavrilov et autres

Abstract Direct visualization of point mutations in situ can be informative for studying genetic diseases and nuclear biology. We describe a direct hybridization genome imaging method with single-nucleotide sensitivity, sgGOLDFISH, which leverages the high cleavage specificity of enhanced Cas9 combined with a …

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Improving the specificity of nucleic acid detection with endonuclease-actuated degradation

Roger S. Zou, Momčilo M. Gavrilov, Yang Liu, Dominique Rasoloson et autres

Nucleic acid detection is essential for numerous biomedical applications, but often requires complex protocols and/or suffers false-positive readouts. Here, we describe SENTINEL, an approach that combines isothermal amplification with a sequence-specific degradation method to detect nucleic acids with high sensitivity and sequence-specificity. …

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Catalytic DNA Polymerization Can Be Expedited by Active Product Release**

Pepijn G. Moerman, Momčilo M. Gavrilov, Taekjip Ha, Rebecca Schulman

The sequence-specific hybridization of DNA facilitates its use as a building block for designer nanoscale structures and reaction networks that perform computations. However, the strong binding energy of Watson-Crick base pairing that underlies this specificity also causes the DNA dehybridization rate to …

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