Self-assembling DNA nanostructures as platforms for placement of fluorophores on
silicon [100]
Kyoung Nan Kim, Vladmir V. Protasenko, Jay P. Giblin, M. Kuno, Marya
Lieberman
Department of Chemistry and Biochemistry,University of Notre Dame, IN 46556, USA
Hierarchically assembled DNA nanostructures with dimensions of 2 × 8 × 37nm were
prepared as platforms for 6-carboxy-tetramethyl-rhodamine (Tamra) dyes. Each DNA
nanostructure was composed of 16 DNA oligomers and included Tamra dyes on zero,
one, two, or three specific thymines. The oligomers were designed to intertwine into a
rigid structure that links two double helices together. A 3D model was used to identify
the best locations for the Tamra-dT nucleotides. DNA nanostructures were immobilized
on mica and (3-aminopropyl)-triethoxysilane (APTES)-treated silicon wafers, and the
width and height of single DNA nanostructures were determined from AFM images.
Statistical results showed that the width of the DNA nanostructures increased as the
number of Tamra-dT nucleotides increased. Structural stabilities of four sub assemblies
of the DNA nanostructure with different number of Tamra-dT units were compared by
variable-temperature gel electrophoresis and UV-vis melting curves. UV-melting curves
showed several transition states and close Tm values for DNA nanostructures with
different number of Tamra-dT nucleotides. Fluorescence properties of Tamra-dT labeled
DNA rafts were studied by single-molecule fluorescence measurements. The Tamralabeled DNA rafts had blinking behavior and their bleaching behavior depended on the
number of Tamra-dT nucleotides.
Tamra labeled DNA nanostructure
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* ; Tamra-dT nucleotides
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