scholarly journals Structure and Thermodynamic Insights on Acetylaminofluorene-Modified Deletion DNA Duplexes as Models for Frameshift Mutagenesis

2013 ◽  
Vol 26 (6) ◽  
pp. 937-951 ◽  
Author(s):  
Anusha Sandineni ◽  
Bin Lin ◽  
Alexander D. MacKerell ◽  
Bongsup P. Cho
Keyword(s):  
Dna Duplexes ◽  
Frameshift Mutagenesis

scholarly journals Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy

2021 ◽  
Author(s):  
Robert J. Fick ◽  
Amy Y. Liu ◽  
Felix Nussbaumer ◽  
Christoph Kreutz ◽  
Atul Rangadurai ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Infrared Spectroscopy ◽  
Dna Duplexes

scholarly journals Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes

2021 ◽  
Vol 22 (2) ◽  
pp. 947
Author(s):  
Mitsuki Tsuruta ◽  
Yui Sugitani ◽  
Naoki Sugimoto ◽  
Daisuke Miyoshi
Keyword(s):  
Molecular Crowding ◽  
Dna Duplexes ◽  
Crowding Effect ◽  
Backbone Flexibility ◽  
Cpg Dinucleotides ◽  
Key Factor ◽  
Dna Backbone ◽  
A Cell ◽  
Stabilization Effect ◽  
And Function

Methylated cytosine within CpG dinucleotides is a key factor for epigenetic gene regulation. It has been revealed that methylated cytosine decreases DNA backbone flexibility and increases the thermal stability of DNA. Although the molecular environment is an important factor for the structure, thermodynamics, and function of biomolecules, there are few reports on the effects of methylated cytosine under a cell-mimicking molecular environment. Here, we systematically investigated the effects of methylated cytosine on the thermodynamics of DNA duplexes under molecular crowding conditions, which is a critical difference between the molecular environment in cells and test tubes. Thermodynamic parameters quantitatively demonstrated that the methylation effect and molecular crowding effect on DNA duplexes are independent and additive, in which the degree of the stabilization is the sum of the methylation effect and molecular crowding effect. Furthermore, the effects of methylation and molecular crowding correlate with the hydration states of DNA duplexes. The stabilization effect of methylation was due to the favorable enthalpic contribution, suggesting that direct interactions of the methyl group with adjacent bases and adjacent methyl groups play a role in determining the flexibility and thermodynamics of DNA duplexes. These results are useful to predict the properties of DNA duplexes with methylation in cell-mimicking conditions.

Structural studies of the 5′-phenazinium-tethered matched and G-A-mismatched DNA duplexes by NMR spectroscopy

1993 ◽  
Vol 26 (2-3) ◽  
pp. 173-236 ◽  
Author(s):  
T. Maltseva ◽  
A. Sandström ◽  
I.M. Ivanova ◽  
D.S. Sergeyev ◽  
V.F. Zarytova ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Structural Studies ◽  
Dna Duplexes ◽  
Mismatched Dna

Studies on the thymine–mercury–thymine base pairing in parallel and anti-parallel DNA duplexes

2015 ◽  
Vol 39 (11) ◽  
pp. 8752-8762 ◽  
Author(s):  
Gaofeng Liu ◽  
Zhiwen Li ◽  
Junfei Zhu ◽  
Yang Liu ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Dna Duplexes ◽  
Base Pairing ◽  
Dna Duplex ◽  
Base Pairs ◽  
Thermal Stabilities

Parallel and anti-parallel T–Hg–T base pairs have different thermal stabilities and conformational influences on DNA duplex structures.

scholarly journals Evaluation of Ion Binding to DNA Duplexes Using a Size-Modified Poisson-Boltzmann Theory

2007 ◽  
Vol 93 (9) ◽  
pp. 3202-3209 ◽  
Author(s):  
Vincent B. Chu ◽  
Yu Bai ◽  
Jan Lipfert ◽  
Daniel Herschlag ◽  
Sebastian Doniach
Keyword(s):  
Ion Binding ◽  
Dna Duplexes ◽  
Poisson Boltzmann
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