Probing Y-shaped DNA structure with time-resolved FRET.
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.
Department of Physics, Queens College, and the Graduate Center of CUNY, 65-30 Kissena Blvd., Flushing, NY 13367, USA.
Subhasish
S
Chatterjee
Jong Bum
JB
Lee
Nikesh V
NV
Valappil
Dan
D
Luo
Vinod M
VM
Menon
D004247:DNA / Q000737:chemistry*; D015342:DNA Probes / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer; D006834:Hydrazines / Q000737:chemistry; D049329:Nanostructures / Q000737:chemistry; D009693:Nucleic Acid Hybridization; D013696:Temperature; D013997:Time Factors; D004124:p-Dimethylaminoazobenzene / Q000031:analogs & derivatives / Q000737:chemistry
C417561:Alexa 488 hydrazide; D015342:DNA Probes; D006834:Hydrazines; C063127:4-(4-dimethylaminophenylazo)benzoic acid; D004247:DNA; D004124:p-Dimethylaminoazobenzene