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Issue 5, 2012
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Probing Y-shaped DNA structure with time-resolved FRET

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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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The article was received on 20 Dec 2011, accepted on 03 Jan 2012 and first published on 10 Jan 2012

Article type: Communication
DOI: 10.1039/C2NR12039A
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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