Nano-mechanical measurements of protein-DNA interactions with a silicon nitride pulley

Nucleic Acids Research
Min Ju Shon, Adam E Cohen

Abstract

Proteins adhere to DNA at locations and with strengths that depend on the protein conformation, the underlying DNA sequence and the ionic content of the solution. A facile technique to probe the positions and strengths of protein-DNA binding would aid in understanding these important interactions. Here, we describe a 'DNA pulley' for position-resolved nano-mechanical measurements of protein-DNA interactions. A molecule of λ DNA is tethered by one end to a glass surface, and by the other end to a magnetic bead. The DNA is stretched horizontally by a magnet, and a nanoscale knife made of silicon nitride is manipulated to contact, bend and scan along the DNA. The mechanical profile of the DNA at the contact with the knife is probed via nanometer-precision optical tracking of the magnetic bead. This system enables detection of protein bumps on the DNA and localization of their binding sites. We study theoretically the technical requirements to detect mechanical heterogeneities in the DNA itself.

References

Mar 14, 1970·Journal of Molecular Biology·J B Hays, B H Zimm
Nov 15, 1983·Journal of Molecular Biology·D Shore, R L Baldwin
Nov 15, 1983·Journal of Molecular Biology·D Shore, R L Baldwin
Apr 1, 1997·Biophysical Journal·E Evans, K Ritchie
Apr 3, 2002·Chemistry & Biology·Liwei ChenGregory L Verdine
Mar 30, 2007·Nucleic Acids Research·Loïc HamonOlivier Piétrement
Dec 22, 2007·Nucleic Acids Research·Quan DuAlexander Vologodskii
Jul 26, 2008·Nature Nanotechnology·Paul A WigginsPhilip C Nelson
Aug 6, 2008·Nature Structural & Molecular Biology·Jason Gorman, Eric C Greene
Oct 7, 2008·Methods : a Companion to Methods in Enzymology·Yuri L Lyubchenko, Luda S Shlyakhtenko
Sep 9, 2009·Nature Reviews. Genetics·Peter J Park
Nov 12, 2009·Nano Letters·Stefan W KowalczykCees Dekker
Nov 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·C DanilowiczM Prentiss
May 19, 2010·Quarterly Reviews of Biophysics·Justin P Peters, L James Maher
Jul 16, 2010·Methods in Enzymology·Ruobo ZhouTaekjip Ha
Aug 13, 2010·Proceedings of the National Academy of Sciences of the United States of America·Stephanie Geggier, Alexander Vologodskii
Aug 18, 2010·Biophysical Journal·Aartjan J W te VelthuisNynke H Dekker
Jun 15, 2011·Nano Letters·Andre SpieringDario Anselmetti
May 9, 2012·Molecular Cell·Iwijn De VlaminckCees Dekker
Jun 13, 2012·Nature Methods·Raghuveer Parthasarathy
May 17, 2013·Nucleic Acids Research·Alexander Vologodskii, Maxim D Frank-Kamenetskii
Jun 12, 2013·PloS One·Marijn T J van LoenhoutCees Dekker
Aug 21, 2013·Nucleic Acids Research·Alexander P FieldsAdam E Cohen
Jun 30, 2014·Methods in Cell Biology·Bridget E CollinsEric C Greene

❮ Previous
Next ❯

Citations

May 27, 2016·Evolutionary Bioinformatics Online·Alejandro Jiménez-Sánchez
Jul 26, 2018·Journal of Biomolecular Structure & Dynamics·Neeraj KumarAbhinav Grover

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Methods in Enzymology
V Dötsch
Trends in Biochemical Sciences
N Allewell
Nucleic Acids Research
Noëlle PougetLaurence Salomé
© 2021 Meta ULC. All rights reserved