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

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.

Enhanced H-bonding and π-stacking in DNA: a potent duplex-stabilizing and mismatch sensing nucleobase analogue

2014 ◽  
Vol 5 (10) ◽  
pp. 3836-3844 ◽  
Author(s):  
Chenguang Lou ◽  
Andre Dallmann ◽  
Pietro Marafini ◽  
Rachel Gao ◽  
Tom Brown
Keyword(s):  
Electrostatic Attraction ◽  
Dna Duplex ◽  
Π Stacking ◽  
Duplex Stability

Combining enhanced π-stacking, H-bonding and electrostatic attraction in a single C-monomer greatly increases DNA duplex stability and massively destabilises mismatches.

Predicting DNA Duplex Stability on Oligonucleotide Arrays

2007 ◽  
pp. 393-403 ◽  
Author(s):  
Arnold Vainrub ◽  
Norha Deluge ◽  
Xiaolin Zhang ◽  
Xiaochuan Zhou ◽  
Xiaolian Gao
Keyword(s):  
Dna Duplex ◽  
Oligonucleotide Arrays ◽  
Duplex Stability

Effects of Polyethylene Glycol on DNA Duplex Stability at Different NaCl Concentrations

2007 ◽  
Vol 80 (10) ◽  
pp. 1987-1994 ◽  
Author(s):  
Hisae Karimata ◽  
Shu-ichi Nakano ◽  
Naoki Sugimoto
Keyword(s):  
Polyethylene Glycol ◽  
Dna Duplex ◽  
Duplex Stability

DNA duplex stability as discriminative characteristic for Escherichia coli σ54- and σ28- dependent promoter sequences

Biologicals ◽  
2014 ◽  
Vol 42 (1) ◽  
pp. 22-28 ◽  
Author(s):  
Scheila de Avila e Silva ◽  
Franciele Forte ◽  
Ivaine T.S. Sartor ◽  
Tahila Andrighetti ◽  
Günther J.L. Gerhardt ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Duplex ◽  
Promoter Sequences ◽  
Duplex Stability
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