scholarly journals All-or-none switching of transcriptional activity on single DNA molecules caused by a discrete conformational transition

2005 ◽  
Vol 86 (22) ◽  
pp. 223901 ◽  
Author(s):  
Ayako Yamada ◽  
Koji Kubo ◽  
Tonau Nakai ◽  
Kenichi Yoshikawa ◽  
Kanta Tsumoto
Keyword(s):  
Transcriptional Activity ◽  
Conformational Transition ◽  
Dna Molecules ◽  
Single Dna Molecules

scholarly journals Marked Difference in the Conformational Transition of DNA Caused by Propanol Isomer

Polymers ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1607
Author(s):  
Yue Ma ◽  
Yuko Yoshikawa ◽  
Hidehiro Oana ◽  
Kenichi Yoshikawa
Keyword(s):  
Conformational Transition ◽  
Electrical Potential ◽  
Phase Segregation ◽  
Order Structure ◽  
Dna Molecules ◽  
Single Dna Molecules ◽  
Phage Dna ◽  
Unfolded State ◽  
Compact State ◽  
Characteristic Effect

We measured the changes in the higher-order structure of DNA molecules (λ phage DNA, 48 kbp) at different concentrations of 1- and 2-propanol through single-molecular observation. It is known that 2-propanol is usually adapted for the procedure to isolate genomic DNA from living cells/organs in contrast to 1-propanol. In the present study, it was found that with an increasing concentration of 1-propanol, DNA exhibits reentrant conformational transitions from an elongated coil to a folded globule, and then to an unfolded state. On the other hand, with 2-propanol, DNA exhibits monotonous shrinkage into a compact state. Stretching experiments under direct current (DC) electrical potential revealed that single DNA molecules intermediately shrunk by 1- and 2-propanol exhibit intrachain phase segregation, i.e., coexistence of elongated and compact parts. The characteristic effect of 1-propanol causing the reentrant transition is argued in terms of the generation of water-rich nanoclusters.

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 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.

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

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