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 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.

Isolation of genomic DNA molecule from a single cell and control its higher order structure using optical tweezers

2005 ◽  
Author(s):  
Hidehiro Oana ◽  
Isao Hagiya ◽  
Masao Washizu ◽  
Koji Kubo ◽  
Kenichi Yoshikawa ◽  
...  
Keyword(s):  
Single Cell ◽  
Optical Tweezers ◽  
Genomic Dna ◽  
Higher Order ◽  
Order Structure ◽  
Dna Molecule ◽  
And Control

scholarly journals 2P302 Control of higher order structure of single genomic DNA using optical tweezers

2004 ◽  
Vol 44 (supplement) ◽  
pp. S185
Author(s):  
H. Oana ◽  
K. Kubo ◽  
H. Atomi ◽  
T. Imanaka ◽  
K. Yoshikawa
Keyword(s):  
Optical Tweezers ◽  
Genomic Dna ◽  
Higher Order ◽  
Order Structure

Macrocycles of Higher Ortho-Phenylenes: Assembly and Folding

2019 ◽  
Author(s):  
Zacharias Kinney ◽  
Viraj Kirinda ◽  
Scott Hartley
Keyword(s):  
Chemical Shift ◽  
Higher Order ◽  
Order Structure ◽  
Complex Geometries ◽  
Spatial Relationships ◽  
Predominant Species ◽  
Bite Angle ◽  
Direct Assembly

<p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p>

Macrocycles of Higher ortho-Phenylenes: Assembly and Folding

2019 ◽  
Author(s):  
Zacharias Kinney ◽  
Viraj Kirinda ◽  
Scott Hartley
Keyword(s):  
Chemical Shift ◽  
Higher Order ◽  
Order Structure ◽  
Complex Geometries ◽  
Spatial Relationships ◽  
Predominant Species ◽  
Bite Angle ◽  
Direct Assembly

<p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p>

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