DNA Analysis in Nanostructured Devices

Mar 17, 2010, 10:15 AM
45m
Nordita Seminar Room 132:028 (Nordita)

Nordita Seminar Room 132:028

Nordita

Speaker

Jonas Tegenfeldt

Description

We use standard staining protocols and epifluorescence microscopy to gain information on the local AT/GC ratio along large DNA molecules stretched in nanoscale channels[1]. Our development opens up a novel route to mapping of large-scale genomic variations as well as fast identification of rare or single cells. With rising temperature, dark patches appear along the DNA corresponding to AT-rich regions that lose in intensity due to local melting of the double-stranded helix thereby resulting in a “barcode” pattern along the DNA (Figure 1) much like G-banding but with significantly improved resolution, currently on the order of 1-10kbp. Compared to standard techniques, such as paired-end sequencing and array comparative genomic hybridization (CGH), our technology may offer a simpler and quicker way to identify structural variations such as deletions, translocations, insertions and copy number variations on scales ranging from 1kbp and up[2] on the single-molecule level. Furthermore, the resulting "barcode" may be used for identification of organisms, such as difficult-to-grow fungi, bacteria and viruses. REFERENCES [1] Tegenfeldt, J.O., et al., The dynamics of genomic-­‐length DNA molecules in 100-­‐nm channels. Proceedings of the National Academy of Sciences of the United States of America, 2004. 101(30): p. 10979-­‐10983. [2] Stankiewicz, P. and J.R. Lupski, Genome architecture, rearrangements and genomic disorders. Trends in Genetics, 2002. 18(2): p. 74-­‐82.

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