Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

The Label-Free Unambiguous Detection and Symbolic Display of Single Nucleotide Polymorphisms on DNA Origami

Single Nucleotide Polymorphisms (SNPs) are the most common genetic variation in the human genome. Kinetic methods based on branch migration have proved successful for detecting SNPs because a mispair will inhibit the progress of branch migration in the direction of the mispair. Biased single-stranded branch migration is used prominently for changing the shapes of DNA nanomachines, because it involves the isothermal removal of strands from a DNA machine frame, enabling a change in topology. Here, we have combined the effectiveness of this approach with atomic force microscopy (AFM) of DNA origami patterns to produce a direct visual readout of the target nucleotide contained in the probe sequence. The origami contains graphical representations of the four possible nucleotide alphabetic characters, A, T, G and C. Each of the components of the letters contains a nucleotide at the test site that is the complement of one of the nucleotides in the probe. Consequently, the symbol containing the test nucleotide identity vanishes in the presence of the probe. Computer processing of a statistically significant group of images produces a direct symbolic readout that directly identifies the nucleotide carried by the probe.

The figure above shows the schematic diagram of DNA Origami tile used (on the left) and the averaged AFM image of the origami tile (on right), showing the character readouts (the scale bar shows a distance of 50 nm). This method works not only with a single SNP, but also with two different probes, as would be found in the case of a heterozygous diploid organism.

This research has been supported by NIGMS, NSF, ARO, ONR and the W.M. Keck Foundation.

Hari K. K. Subramanian
Banani Chakraborty
Ruojie Sha
Nadrian C. Seeman

Department of Chemistry
New York University
New York, NY 10003, USA