Issue 5, 2012
From the journal:

Nanoscale

Probing Y-shaped DNA structure with time-resolved FRET†

Subhasish Chatterjee,a   Jong Bum Lee,bc   Nikesh V. Valappil,a   Dan Luob  and  Vinod M. Menon*a  

* Corresponding authors

a Department of Physics, Queens College, and the Graduate Center of CUNY, 65-30 Kissena Blvd., Flushing, NY, USA
E-mail: vmenon@qc.cuny.edu
Fax: +1-718-997-334
Tel: +1-718-997-3147

b Department Bio and Environmental Engineering, Cornell University, Ithaca, NY, USA

c Department of Chemical Engineering, University of Seoul, Seoul 130-743, Republic of Korea

Abstract

Self-assembly based on nucleic acid systems has become highly attractive for bottom-up fabrication of programmable matter due to the highly selective molecular recognition property of biomolecules. In this context, Y-shaped DNA (Y-DNA) provides an effective building block for forming unique self-assembled large-scale architectures. The dimension and growth of the nano- and microstructures depend significantly on the configurational stability of Y-DNA as a building block. Here we present structural studies of Y-DNA systems using a time-resolved FRET (Förster resonance energy transfer) technique. A fluorophore (Alexa 488) and an acceptor (DABCYL) were placed at two different ends of Y-DNA, and the lifetime of the fluorophore was measured to probe the relative distance between the donor and acceptor. Our results confirmed different distances between the arms of the Y-DNA and highlighted the overall structural integrity of the Y-DNA system as a leading building block for molecular self-assembly. Temperature dependent lifetime measurements indicated configurational changes in the overall Y-DNA nanoarchitecture above 40 °C.

Graphical abstract: Probing Y-shaped DNA structure with time-resolved FRET

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Article information

DOI
https://doi.org/10.1039/C2NR12039A
Article type
Communication
Submitted
20 Dec 2011
Accepted
03 Jan 2012
First published
10 Jan 2012

Nanoscale, 2012,4, 1568-1571

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Probing Y-shaped DNA structure with time-resolved FRET

S. Chatterjee, J. B. Lee, N. V. Valappil, D. Luo and V. M. Menon, Nanoscale, 2012, 4, 1568 DOI: 10.1039/C2NR12039A

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