Hydration Is an Important Factor to Regulate Thermodynamic Stability of a DNA Duplex under Molecular Crowding Conditions

2008 ◽  
Vol 37 (8) ◽  
pp. 864-865 ◽  
Author(s):  
Kazuya Koumoto ◽  
Hirofumi Ochiai ◽  
Naoki Sugimoto
Keyword(s):  
Thermodynamic Stability ◽  
Molecular Crowding ◽  
Dna Duplex

scholarly journals Effects of cosolutes on the thermodynamic stability of parallel DNA duplex and triplex

2007 ◽  
Vol 51 (1) ◽  
pp. 167-168 ◽  
Author(s):  
K. Nakamura ◽  
H. Karimata ◽  
T. Ohmichi ◽  
D. Miyoshi ◽  
N. Sugimoto
Keyword(s):  
Thermodynamic Stability ◽  
Dna Duplex

The Effect of Molecular Crowding with Nucleotide Length and Cosolute Structure on DNA Duplex Stability

2004 ◽  
Vol 126 (44) ◽  
pp. 14330-14331 ◽  
Author(s):  
Shu-ichi Nakano ◽  
Hisae Karimata ◽  
Tatsuo Ohmichi ◽  
Junji Kawakami ◽  
Naoki Sugimoto
Keyword(s):  
Molecular Crowding ◽  
Dna Duplex ◽  
Duplex Stability

Influence of the Oxidatively Damaged Adduct 8-Oxodeoxyguanosine on the Conformation, Energetics, and Thermodynamic Stability of a DNA Duplex

Biochemistry ◽  
1995 ◽  
Vol 34 (49) ◽  
pp. 16148-16160 ◽  
Author(s):  
G. Eric Plum ◽  
Arthur P. Grollman ◽  
Francis Johnson ◽  
Kenneth J. Breslauer
Keyword(s):  
Thermodynamic Stability ◽  
Dna Duplex

Factors regulating thermodynamic stability of DNA structures under molecular crowding conditions

2006 ◽  
Vol 50 (1) ◽  
pp. 203-204 ◽  
Author(s):  
Daisuke Miyoshi ◽  
Hisae Karimata ◽  
Naoki Sugimoto
Keyword(s):  
Thermodynamic Stability ◽  
Molecular Crowding ◽  
Dna Structures

scholarly journals Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions

2020 ◽  
Vol 117 (25) ◽  
pp. 14194-14201 ◽  
Author(s):  
Saptarshi Ghosh ◽  
Shuntaro Takahashi ◽  
Tatsuya Ohyama ◽  
Tamaki Endoh ◽  
Hisae Tateishi-Karimata ◽  
...  
Keyword(s):  
Nearest Neighbor ◽  
Average Molecular Weight ◽  
Molecular Crowding ◽  
Dna Duplexes ◽  
Dna Duplex ◽  
Intracellular Environment ◽  
Duplex Stability ◽  
Key Factor ◽  
The Stability ◽  
Duplex Formation

The intracellular environment is crowded and heterogeneous. Although the thermodynamic stability of nucleic acid duplexes is predictable in dilute solutions, methods of predicting such stability under specific intracellular conditions are not yet available. We recently showed that the nearest-neighbor model for self-complementary DNA is valid under molecular crowding condition of 40% polyethylene glycol with an average molecular weight of 200 (PEG 200) in 100 mM NaCl. Here, we determined nearest-neighbor parameters for DNA duplex formation under the same crowding condition to predict the thermodynamics of DNA duplexes in the intracellular environment. Preferential hydration of the nucleotides was found to be the key factor for nearest-neighbor parameters in the crowding condition. The determined parameters were shown to predict the thermodynamic parameters (∆H°, ∆S°, and ∆G°37) and melting temperatures (Tm) of the DNA duplexes in the crowding condition with significant accuracy. Moreover, we proposed a general method for predicting the stability of short DNA duplexes in different cosolutes based on the relationship between duplex stability and the water activity of the cosolute solution. The method described herein would be valuable for investigating biological processes that occur under specific intracellular crowded conditions and for the application of DNA-based biotechnologies in crowded environments.

Using a Software Application to Evaluation Thermodynamic Stability on the Example of Iron

2019 ◽  
Vol 24 (3) ◽  
pp. 309-312
Author(s):  
Aleksandr S. Gulyaev ◽  
◽  
Vladimir B. Koltsov ◽  
Elena A. Sevryukova ◽  
◽  
...  
Keyword(s):  
Thermodynamic Stability ◽  
Software Application
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