Electrophoretic mobility is a reporter of hairpin structure in single-stranded DNA oligomers.

Electrophoretic mobility is a reporter of hairpin structure in single-stranded DNA oligomers. Research Abstract Details 

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Electrophoretic mobility is a reporter of hairpin structure in single-stranded DNA oligomers. Abstract Text:

Earle Stellwagen,Arian Abdulla,Qian Dong,Nancy C Stellwagen,

The electrophoretic mobilities of 24 single-stranded DNA oligomers, each containing 26 nucleotide residues, have been measured in polyacrylamide gels and in free solution. The mobilities observed at 20 degrees C differed by approximately 20% in polyacrylamide gels and by approximately 10% in free solution, even though the oligomers contained the same number of bases. Increasing the temperature or adding urea to the solution equalized the mobilities of the oligomers, suggesting that the variable mobilities observed at 20 degrees C are due to the formation of stable secondary structures, most likely hairpins. Thermal melting profiles were measured for eight oligomers in 40 mM Tris acetate buffer. The observed melting temperatures of most oligomers correlated roughly with the mobilities observed at 20 degrees C; however, one oligomer was much more stable than the others. The melting temperatures of four of the oligomers were close to the values predicted by DINAMelt [Markham, N. R., and Zuker, M. (2005) Nucleic Acids Res. 33, W577-W581]; melting temperatures of the other oligomers differed significantly from the predicted values. Thermal melting profiles were also measured for two oligomers as a function of the Tris acetate buffer concentration. The salt concentration dependence of the melting temperatures suggests that 0.15 Tris+ ion per phosphate is released upon denaturation. Because the apparent number of Tris+ ions released is greater than that observed by others for the release of Na+ ions from similar hairpins, the results suggest that DNA hairpins (and, presumably, duplexes) bind more Tris+ ions than Na+ ions in solution.

Electrophoretic mobility is a reporter of hairpin structure in single-stranded DNA oligomers. Publishing Authors By Initials

E Stellwagen,A Abdulla,Q Dong,NC Stellwagen,

For similar organic chemicals: urea research abstracts see: organic chemicals: urea research

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Electrophoretic mobility is a reporter of hairpin structure in single-stranded DNA oligomers. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: Biochemistry

VOLUME: 46

Page Numbers: 10931-41

Journal Abbreviation: Biochemistry

ISSN: 0006-2960

DAY: 1

MONTH: 09

YEAR: 2007

Electrophoretic mobility is a reporter of hairpin structure in single-stranded DNA oligomers. Information

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LANGUAGE: eng

NlmUniqueID: 370623

Electrophoretic mobility is a reporter of hairpin structure in single-stranded DNA oligomers. Keywords Mesh Terms:

KEYWORDS: Urea

MESH TERMS: chemistry

Chemical & Substance for Abstract: Electrophoretic mobility is a reporter of hairpin structure in single-stranded DNA oligomers. Information

Substance Name: Urea

Registry Number: 57-13-6

Grant and Affiliation Information for Electrophoretic mobility is a reporter of hairpin structure in single-stranded DNA oligomers.

AFFILIATION: Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: GM061009

ACRONYM: GM

MEDLINETA: Biochemistry

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