Department: NanoEngineering
Research Institute Affiliation: Graduate Program in Materials Science and Engineering
Faculty Advisor(s): Michael J. Heller

Primary Student
Name: Taeseok Oh
Email: taoh@ucsd.edu
Phone: 858-837-2808
Grad Year: 2016

Student Collaborators
Jae-young Choi, jac125@ucsd.edu

Three surfactants (Triton X-100, CTAB and SDS), which induce less emission quenching by reducing dimerization of dyes, was investigated in order to enhance the antenna effect in FRET from three fluorescent donor dyes (TAMRA) to one fluorescent acceptor dye (TexasRed) attached at the middle of 21mer dsDNA. Even though the TexasRed acceptor was absent in the DNA, a strong hydrophobic interaction among the three TAMRAs conjugated on DNA strand caused emission quenching and absorbance shifting, which indicates the dimerization of the TAMRAs. When the inter-TAMRA distance was closer and the TAMRA dyes were on a flexible single strand, the dimerization occurred more seriously. When Triton X-100 was added to the solution, the dimerization did not change due to the neutral charged surfactant, which does not interact with the DNA strand. By increasing the CTAB concentration to 100 uM and above, the neutralized DNA backbone by cationic surfactant induced the aggregation, resulting enhacement of antenna effect due to CTAB molecules covering or sheathing the fluorescent dyes and suppressing the quenching by dimerization. Even though SDS alone did not affect the emission quenching due to repulsive forces between DNA and SDS micelles, with the addition of cations, such as sodium and magnesium, the dimerization and the emission quenching were reduced significantly. It is concluded that SDS micelle, which approached the DNA strand when the repulsive force was screened by the cations, sheathes/shields/insulates three TAMRA dyes conjugated on a DNA strand, reducing the dimerization and thus recovering the fluorescent emission. When the three TAMRA conjugated DNA strand and the TexasRed conjugated complementary strand were hybridized without surfactants, formation of dimers such as homodimer by donor-donor stacks and heterodimer by donor-acceptor stacks caused the emission quenching and low antenna effect in the DNA FRET structure. Similar results as three TAMRA conjugated DNA strand without acceptor dye, SDS micelles with magnesium reduced dimerization and enhanced the antenna effect between dyes conjugated on DNA. Overall, this study opens the door for using surfactants with cations to reduce the quenching by dimerization and to improve the antenna effect in DNA FRET structures containing multi-donor and acceptor fluorescent dye molecules.

Industry Application Area(s)
Life Sciences/Medical Devices & Instruments | Materials | Semiconductor

Related Links:

  1. http://onlinelibrary.wiley.com/doi/10.1002/jbio.201500221/abstract

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