Thermal stability of hydrophobic unnatural base pairs in DNA duplexes

2014 ◽  
Author(s):  
Michiko Kimoto ◽  
Ichiro Hirao
Keyword(s):  
Thermal Stability ◽  
Dna Duplexes ◽  
Base Pairs ◽  
Thermal Stability Of

The thermal stability of RNA duplexes containing modified base pairs placed at internal and terminal positions of the oligoribonucleotides

2002 ◽  
Vol 97 (2-3) ◽  
pp. 233-241 ◽  
Author(s):  
Krzysztof Ziomek ◽  
Elżbieta Kierzek ◽  
Ewa Biała ◽  
Ryszard Kierzek
Keyword(s):  
Thermal Stability ◽  
Base Pairs ◽  
Rna Duplexes ◽  
Thermal Stability Of

Calibration of the change in thermal stability of DNA duplexes and degree of base pair mismatch

1988 ◽  
Vol 27 (3) ◽  
pp. 212-216 ◽  
Author(s):  
Adalgisa Caccone ◽  
Rob DeSalle ◽  
Jeffrey R. Powell
Keyword(s):  
Thermal Stability ◽  
Base Pair ◽  
Dna Duplexes ◽  
Base Pair Mismatch ◽  
Thermal Stability Of

Effects of formamide on the thermal stability of DNA duplexes on biochips

2010 ◽  
Vol 397 (1) ◽  
pp. 132-134 ◽  
Author(s):  
Julia Fuchs ◽  
Daniela Dell’Atti ◽  
Arnaud Buhot ◽  
Roberto Calemczuk ◽  
Marco Mascini ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Dna Duplexes ◽  
Thermal Stability Of

scholarly journals Second generation silver(I)-mediated imidazole base pairs

2014 ◽  
Vol 10 ◽  
pp. 2139-2144 ◽  
Author(s):  
Susanne Hensel ◽  
Nicole Megger ◽  
Kristina Schweizer ◽  
Jens Müller
Keyword(s):  
Thermal Stability ◽  
Melting Temperature ◽  
Base Pair ◽  
Metal Ion ◽  
Second Generation ◽  
Dna Duplex ◽  
Base Pairs ◽  
Double Helices ◽  
Thermal Stability Of

The imidazole–Ag(I)–imidazole base pair is one of the best-investigated artificial metal-mediated base pairs. We show here that its stability can be further improved by formally replacing the imidazole moiety by a 2-methylimidazole or 4-methylimidazole moiety. A comparison of the thermal stability of several double helices shows that the addition of one equivalent of Ag(I) leads to a 50% larger increase in the melting temperature when a DNA duplex with methylated imidazole nucleosides is applied. This significant effect can likely be attributed to a better steric shielding of the metal ion within the metal-mediated base pair.

A Comparative Study of the Influence of Aquaous 2,2,2-Trifluoroethanol And Ethanol on the Structural Organization, the Kinetic and Thermodynamic Properties of Oligodeoxyribonucleotides Intermolecular Complex Formation

2013 ◽  
Vol 8 (1) ◽  
pp. 115-124
Author(s):  
Aleksandr Lomzov ◽  
Kseniya Ivanova ◽  
Inna Pyshnaya ◽  
Elena Dmitrienko ◽  
Dmitriy Pyshnyi
Keyword(s):  
Thermal Stability ◽  
Aqueous Solution ◽  
Comparative Study ◽  
Melting Temperature ◽  
Structural Organization ◽  
Volume Fraction ◽  
Dna Duplexes ◽  
Intermolecular Complex ◽  
Linear Decrease ◽  
Thermal Stability Of

A comparative study of the structural organization, thermodynamic and kinetic properties of the oligodeoxynucleotides complexes formation in the presence of 2,2,2-trifluoroethanol and ethanol in aqueous solution (volume fraction of alcohol 0 to 50 %) was performed. No significant changes in the circular dichroism spectra of oligonucleotides and their complexes at the adding of 50 % v/v alcohol into a solution, was observed, and they retain the profile typical for B-form DNA. The study of the thermal stability of DNA duplexes showed that the increase in the volume fraction of ethanol in the aqueous solution up to 50 % results in a linear decrease in the melting temperature of the intermolecular DNA complexes. In the case of the 2,2,2-trifluoroethanol we observed atypical dependence of thermal stability of DNA duplexes on the fraction of the fluorine-containing co-solvent. Increasing the alcohol fraction from 0 to 20% v/v led to a linear decrease of the melting point of the complex. A further increase in the volume fraction of alcohol (up to 50 %) did not change the thermal stability of the duplexes. It was shown, that the destabilizing effect of the two co-solvents is due to the increase of the dissociation rate constant of the complex and has mainly entropic nature. On the example of oligonucleotides complexes of 8, 12, 15 and 20 base pairs length the possibility of prediction DNA duplexes thermal stability was shown. A model taking into account the change of a number solvent molecules interacting with nucleic acids at the duplex formation in aqueous ethanol (50 % v/v) or trifluoroethanol (20 % v/v) was applied. An accuracy of melting temperature prediction was 1.3 and 0.6 degrees. Using this model, we found that the addition of alcohols in solution leads to an increase in the number of water molecules that bind to a complementary pair of nucleotides at the formation of intermolecular complex (in the presence of ethanol or trifluoroethanol 0.51 ± 0.09 and 1.33 ± 0.12, respectively). At the same time, alcohols interacted with single-stranded oligonucleotides and double-stranded in the same way

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