scholarly journals Molecular conformations of DNA targets captured by model nanoarrays

Nanoscale ◽  
2017 ◽  
Vol 9 (36) ◽  
pp. 13419-13424 ◽  
Author(s):  
X. Hao ◽  
E. A. Josephs ◽  
Q. Gu ◽  
T. Ye
Keyword(s):  
Dna Molecules ◽  
Molecular Conformations ◽  
Single Dna Molecules

We generated nanoarrays with tailored surface functionalities and morphologies to probe how single DNA molecules interact with surface heterogeneities.

Thermoplastic Nanofluidic Devices for Identifying Abasic Sites in Single DNA Molecules

Lab on a Chip ◽  
2021 ◽  
Author(s):  
Steven A Soper ◽  
Swarnagowri Vaidyanathan ◽  
Franklin Uba ◽  
Bo Hu ◽  
David Kaufman ◽  
...  
Keyword(s):  
Dna Damage ◽  
Therapeutic Efficacy ◽  
Double Strand Breaks ◽  
Dna Molecules ◽  
Strand Breaks ◽  
Single Dna Molecules ◽  
Abasic Sites ◽  
Nanofluidic Devices ◽  
Ap Sites

DNA damage can take many forms such as double-strand breaks and/or the formation of abasic (apurinic/apyrimidinic; AP) sites. The presence of AP sites can be used to determine therapeutic efficacy...

scholarly journals Active Delivery of Single DNA Molecules into a Plasmonic Nanopore for Label-Free Optical Sensing

Nano Letters ◽  
2018 ◽  
Vol 18 (12) ◽  
pp. 8003-8010 ◽  
Author(s):  
Xin Shi ◽  
Daniel V. Verschueren ◽  
Cees Dekker
Keyword(s):  
Optical Sensing ◽  
Label Free ◽  
Dna Molecules ◽  
Single Dna Molecules

scholarly journals Somatic mutation landscapes at single-molecule resolution

2021 ◽  
Author(s):  
Stefanie V. Lensing ◽  
Peter Ellis ◽  
Federico Abascal ◽  
Iñigo Martincorena ◽  
Robert J. Osborne
Keyword(s):  
Single Molecule ◽  
Single Cells ◽  
Error Rates ◽  
Dna Molecules ◽  
Base Pairs ◽  
Single Dna Molecules ◽  
Sequencing Library ◽  
Somatic Mutagenesis ◽  
Qpcr Quantification ◽  
Duplex Sequencing

Abstract Somatic mutations drive cancer development and may contribute to ageing and other diseases. Yet, the difficulty of detecting mutations present only in single cells or small clones has limited our knowledge of somatic mutagenesis to a minority of tissues. To overcome these limitations, we introduce nanorate sequencing (NanoSeq), a new duplex sequencing protocol with error rates <5 errors per billion base pairs in single DNA molecules from cell populations. The version of the protocol described here uses clean genome fragmentation with a restriction enzyme to prevent end-repair-associated errors and ddBTPs/dATPs during A-tailing to prevent nick extension. Both changes reduce the error rate of standard duplex sequencing protocols by preventing the fixation of DNA damage into both strands of DNA molecules during library preparation. We also use qPCR quantification of the library prior to amplification to optimise the complexity of the sequencing library given the desired sequencing coverage, maximising duplex coverage. The sample preparation protocol takes between 1 and 2 days, depending on the number of samples processed. The bioinformatic protocol is described in:https://github.com/cancerit/NanoSeqhttps://github.com/fa8sanger/NanoSeq_Paper_Code

Direct observation of individual RecA filaments assembling on single DNA molecules

Nature ◽  
2006 ◽  
Vol 443 (7113) ◽  
pp. 875-878 ◽  
Author(s):  
Roberto Galletto ◽  
Ichiro Amitani ◽  
Ronald J. Baskin ◽  
Stephen C. Kowalczykowski
Keyword(s):  
Direct Observation ◽  
Dna Molecules ◽  
Single Dna Molecules

scholarly journals On-Demand Delivery of Single DNA Molecules Using Nanopipets

ACS Nano ◽  
2015 ◽  
Vol 9 (4) ◽  
pp. 3587-3595 ◽  
Author(s):  
Aleksandar P. Ivanov ◽  
Paolo Actis ◽  
Peter Jönsson ◽  
David Klenerman ◽  
Yuri Korchev ◽  
...  
Keyword(s):  
Dna Molecules ◽  
Single Dna Molecules ◽  
On Demand
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