Probing Y-shaped DNA structure with time-resolved FRETElectronic supplementary information (ESI) available: Time-resolved spectra of Alexa 488 showing the effect of heating on the emission dynamics of the fluorophore conjugated with three Y-DNA systems (Y1, Y2, Y3). See DOI: 10.1039/c2nr12039a

• Main Authors: Chatterjee, Subhasish, Lee, Jong Bum, Valappil, Nikesh V, Luo, Dan, Menon, Vinod M
• Format: Journal Article
• Language: English
• Published: 16.02.2012
• ISSN: 2040-3364; 2040-3372
• DOI: 10.1039/c2nr12039a

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 (Frster 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. Time-resolved FRET revealed the structural integrity of Y-shaped DNA as a potential building block for nanostructures.