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.

scholarly journals Monotonous behavior with 2-propanol converts into reentrant transition with 1-propanol: Higher-order structure of DNA

2019 ◽  
Author(s):  
Y. Ma ◽  
Y. Yoshikawa ◽  
K. Yoshikawa
Keyword(s):  
Secondary Structure ◽  
Genomic Dna ◽  
Conformational Transitions ◽  
Higher Order ◽  
Point Of View ◽  
Order Structure ◽  
Chemical Physics ◽  
Dna Molecules ◽  
Unfolded State ◽  
Compact State

ABSTRACTIn the present study, we measured the changes in the higher-order structure of genomic DNA molecules in the presence of alcohols through single-DNA observation by use of fluorescence microscopy, with particular focus on the different effects of 1-propanol and 2-propanol. The results showed 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. Thus, DNA molecules are more effectively condensed/precipitated with 2-propanol than with 1-propanol. The propanol isomers also had different effects on the changes in the secondary structure of DNA, as revealed by circular dichroism (CD) measurements. With 1-propanol, DNA maintains a B-form secondary structure. An A-like conformation appears with the addition of 2-propanol.STATEMENT OF SIGNIFICANCECurrently, 2-propanol has most often been used as the solvent to extract and purify genomic DNA molecules from living cells, according the protocols in molecular biology and biochemistry. Unfortunately, the reason why usage of 2-propanol is recommended instead of ethanol and 1-propanol has never been explained in a clear manner. We believe that the new insight based on chemical physics point of view would play an important role for the development of current chemical procedures/treatments adapted on an empirical basis.

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

Replication of Bacteriophage 186 DNA

1972 ◽  
Vol 30 ◽  
pp. 194-195
Author(s):  
Dhruba K. Chattoraj ◽  
Ross B. Inman
Keyword(s):  
Electron Microscopy ◽  
Dna Replication ◽  
Frame Of Reference ◽  
Dna Molecules ◽  
E Coli ◽  
Phage Dna ◽  
Partial Denaturation

Electron microscopy of replicating intermediates has been quite useful in understanding the mechanism of DNA replication in DNA molecules of bacteriophage, mitochondria and plasmids. The use of partial denaturation mapping has made the tool more powerful by providing a frame of reference by which the position of the replicating forks in bacteriophage DNA can be determined on the circular replicating molecules. This provided an easy means to find the origin and direction of replication in λ and P2 phage DNA molecules. DNA of temperate E. coli phage 186 was found to have an unique denaturation map and encouraged us to look into its mode of replication.

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.

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