Journal article
Effect of Internal and Bulge Loops on the Thermal Stability of Small DNA Duplexes
The journal of physical chemistry. B, Vol.128(42), pp.10339-10347
10/15/2024
DOI: 10.1021/acs.jpcb.4c03458
PMCID: PMC11514024
PMID: 39404757
Appears in UI Libraries Support Open Access
Abstract
The thermal stabilities of DNA duplexes analogous to the let-7 microRNA:lin-41 mRNA complex from Caenorhabditis elegans have been measured by free solution capillary electrophoresis. DNA duplexes with the same stems but different types of internal or bulge loops and a control with no loop have also been studied. The melting temperatures of the DNA derivatives increased linearly with the logarithm of the Na+ or K+ ion concentration in the solution. Peaks in the electropherograms corresponding to duplexes with internal or bulge loops exhibited extensive tailing at high temperatures, suggesting that denaturation occurred by slow exchange between the duplexes and their component single strands. The single strands did not separate completely from the duplexes in aqueous solutions; instead, they appeared as small subpeaks on the tails of the duplex peaks. However, complete separation of the duplexes from their component single strands was observed at 20 °C in solutions containing 300 mM tetrapropylammonium ions. In addition, counterion condensation appears to be significantly reduced in DNA duplexes containing internal or bulge loops.
Details
- Title: Subtitle
- Effect of Internal and Bulge Loops on the Thermal Stability of Small DNA Duplexes
- Creators
- Earle Stellwagen - University of Iowa, Biochemistry and Molecular BiologyPaul J Barnard - University of IowaNancy C Stellwagen - University of Iowa, Biochemistry and Molecular Biology
- Resource Type
- Journal article
- Publication Details
- The journal of physical chemistry. B, Vol.128(42), pp.10339-10347
- DOI
- 10.1021/acs.jpcb.4c03458
- PMID
- 39404757
- PMCID
- PMC11514024
- NLM abbreviation
- J Phys Chem B
- ISSN
- 1520-6106
- eISSN
- 1520-5207
- Publisher
- American Chemical Society
- Grant note
- Analytical and Surface Chemistry Program of the National Science Foundation: CHE0748271 National Institute of General Medical Sciences: GM061009
Partial support of this work (to N.C.S.) from the Analytical and Surface Chemistry Program of the National Science Foundation, Grant CHE0748271, and the National Institute of General Medical Sciences, Grant GM061009, is gratefully acknowledged.
- Language
- English
- Date published
- 10/15/2024
- Academic Unit
- Biochemistry and Molecular Biology
- Record Identifier
- 9984720636702771
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