Development of methods to study the conformational dynamics of quantum dot-oligonucleotide conjugates by single molecule spectroscopy

W. Russ Algar; Maxim B. Prigozhin; Baoxu Liu; Ulrich J. Krull; Claudiu C. Gradinaru

doi:10.1117/12.840545

4 August 2009 Development of methods to study the conformational dynamics of quantum dot-oligonucleotide conjugates by single molecule spectroscopy

W. Russ Algar, Maxim B. Prigozhin, Baoxu Liu, Ulrich J. Krull, Claudiu C. Gradinaru

Author Affiliations +

Proceedings Volume 7386, Photonics North 2009; 73860J (2009) https://doi.org/10.1117/12.840545
Event: Photonics North 2009, 2009, Quebec, Canada

Abstract

The optical properties and significant surface area of CdSe/ZnS QDs make such nanoparticles an interesting platform for the preparation of nucleic acid biosensors based on fluorescence resonance energy transfer (FRET). Interactions between QDs and oligonucleotides affect biosensor performance and are not fully understood. Ensemble data obtained via FRET experiments indicated that, on average, 4-5 added oligonucleotides saturated the surface of green emitting QDs. An increase in the number of oligonucleotides per QD appeared to cause the oligonucleotides to transition from collapsed to upright conformations. Since bulk averaging hides details of such processes, methods must be developed and materials identified for studying QD-oligonucleotide conjugates at the single molecule level. Single QDs have been immobilized and fluorescence intensity trajectories measured. High count rates and good photostability were achieved using carboxyl polymer-coated QDs. Modeling of FRET efficiency based on the dimensions of QDs and oligonucleotides indicated that transitions between collapsed and upright conformations can be accurately measured based on changes in QD fluorescence lifetime. The ultimate goal of this work is to elucidate QD-oligonucleotide dynamics for better design and optimization of nucleic acid biosensors based on QDs.

Citation Download Citation

W. Russ Algar, Maxim B. Prigozhin, Baoxu Liu, Ulrich J. Krull, and Claudiu C. Gradinaru "Development of methods to study the conformational dynamics of quantum dot-oligonucleotide conjugates by single molecule spectroscopy", Proc. SPIE 7386, Photonics North 2009, 73860J (4 August 2009); https://doi.org/10.1117/12.840545

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