AI Article Synopsis
- SMFRET was used to study how a 25-nucleotide DNA aptamer interacts with vascular endothelial growth factor (VEGF) and to observe its structural changes in the absence of the target.
- The aptamer primarily adopts a base-paired conformation but frequently shifts to higher energy states, and these shifts are influenced by the concentration of Mg2+ ions.
- When VEGF is introduced, the aptamer shows a notable increase in lower SMFRET efficiencies, suggesting that binding to VEGF encourages the aptamer to adopt a more open structure.
Article Abstract
Single-molecule fluorescence resonance energy transfer (SMFRET) was used to study the interaction of a 25-nucleotide (nt) DNA aptamer with its binding target, vascular endothelial growth factor (VEGF). Conformational dynamics of the aptamer were studied in the absence of VEGF in order to characterize fluctuations in the unbound nucleic acid. SMFRET efficiency distributions showed that, while the aptamer favors a base-paired conformation, there are frequent conversions to higher energy conformations. Conversions to higher energy structures were also demonstrated to be dependent on the concentration of Mg2+-counterion by an overall broadening of the SMFRET efficiency distribution at lower Mg2+ concentration. Introduction of VEGF caused a distinct increase in the frequency of lower SMFRET efficiencies, indicating that favorable interaction of the DNA aptamer with its VEGF target directs aptamer structure towards a more open conformation.
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| http://dx.doi.org/10.1016/j.bbrc.2008.05.191 | DOI Listing |
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