skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Nanoplasmonic molecular ruler for nuclease activity and DNAfootprinting

Abstract

We have constructed a nanoplasmonic molecular ruler, which can perform label-free and real-time monitoring of DNA length changes and perform DNA footprinting. The ruler was created by tethering double-stranded DNA to single Au nanoparticles. The scattering spectra of Au-DNA nanoconjugates showed red-shifted peak plasmon resonance wavelength dependent on DNA length, which can be measured with sub-nanometer axial resolution, averaging {approx}1.24 nm peak wavelength shift per DNA base pair. The spectra of individual Au-DNA nanoconjugates in the presence of nuclease showed a time-resolved dependence on the reaction dynamics, allowing quantitative, kinetic and real-time measurement of nuclease activity. The ruler was further developed into a new DNA footprinting platform. We showed the specific binding of a protein to DNA and the accurate mapping of its footprint. This work promises a very fast and convenient platform for mapping DNA-protein interactions, for nuclease activity monitoring, and for other DNA size-based methods.

Authors:
; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
Sponsoring Org.:
USDOE Director, Office of Science. Office of Biological andEnvironmental Research. Life Sciences Division
OSTI Identifier:
919256
Report Number(s):
LBNL-61485
R&D Project: L0350; BnR: 400403209; TRN: US0806334
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
Nature Nanotechnology
Additional Journal Information:
Journal Volume: 1; Journal Issue: 1; Related Information: Journal Publication Date: 10/2006
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; DNA; KINETICS; MONITORING; NUCLEASES; PLASMONS; PROTEINS; RESOLUTION; RESONANCE; SCATTERING; SPECTRA; WAVELENGTHS

Citation Formats

Chen, Fanqing Frank, Liu, Gang L, Yin, Yadong, Gerion, Daniele, Kunchakarra, Siri, Mukherjee, Bipasha, Jett, Stephen D, Bear, David G, Alivisatos, Paul, and Lee, Luke P. Nanoplasmonic molecular ruler for nuclease activity and DNAfootprinting. United States: N. p., 2006. Web.
Chen, Fanqing Frank, Liu, Gang L, Yin, Yadong, Gerion, Daniele, Kunchakarra, Siri, Mukherjee, Bipasha, Jett, Stephen D, Bear, David G, Alivisatos, Paul, & Lee, Luke P. Nanoplasmonic molecular ruler for nuclease activity and DNAfootprinting. United States.
Chen, Fanqing Frank, Liu, Gang L, Yin, Yadong, Gerion, Daniele, Kunchakarra, Siri, Mukherjee, Bipasha, Jett, Stephen D, Bear, David G, Alivisatos, Paul, and Lee, Luke P. Tue . "Nanoplasmonic molecular ruler for nuclease activity and DNAfootprinting". United States. https://www.osti.gov/servlets/purl/919256.
@article{osti_919256,
title = {Nanoplasmonic molecular ruler for nuclease activity and DNAfootprinting},
author = {Chen, Fanqing Frank and Liu, Gang L and Yin, Yadong and Gerion, Daniele and Kunchakarra, Siri and Mukherjee, Bipasha and Jett, Stephen D and Bear, David G and Alivisatos, Paul and Lee, Luke P},
abstractNote = {We have constructed a nanoplasmonic molecular ruler, which can perform label-free and real-time monitoring of DNA length changes and perform DNA footprinting. The ruler was created by tethering double-stranded DNA to single Au nanoparticles. The scattering spectra of Au-DNA nanoconjugates showed red-shifted peak plasmon resonance wavelength dependent on DNA length, which can be measured with sub-nanometer axial resolution, averaging {approx}1.24 nm peak wavelength shift per DNA base pair. The spectra of individual Au-DNA nanoconjugates in the presence of nuclease showed a time-resolved dependence on the reaction dynamics, allowing quantitative, kinetic and real-time measurement of nuclease activity. The ruler was further developed into a new DNA footprinting platform. We showed the specific binding of a protein to DNA and the accurate mapping of its footprint. This work promises a very fast and convenient platform for mapping DNA-protein interactions, for nuclease activity monitoring, and for other DNA size-based methods.},
doi = {},
journal = {Nature Nanotechnology},
number = 1,
volume = 1,
place = {United States},
year = {2006},
month = {8}
}