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Visualizing the entire DNA from a chromosome in a single frame

Camilla Freitag ; C. Noble ; Joachim Fritzsche (Institutionen för teknisk fysik, Kemisk fysik ; Institutionen för fysik (GU)) ; Fredrik Persson ; M. Reiter-Schad ; A. N. Nilsson ; Annette Graneli ; T. Ambjornsson ; K. U. Mir ; Jonas O. Tegenfeldt
Biomicrofluidics (1932-1058). Vol. 9 (2015), 4, p. 044114.
[Artikel, refereegranskad vetenskaplig]

The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field of view enabled us to directly visualize a repeat motif, count the repeat unit number, and chart its location in the genome by reference to unique barcode motifs found at measurable distances from the repeat. Meandering nanochannel dimensions can easily be tailored to human chromosome scales, which would enable the whole genome to be visualized in seconds.



Denna post skapades 2015-09-18. Senast ändrad 2015-10-08.
CPL Pubid: 222738

 

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Institutioner (Chalmers)

Institutionen för fysik (GU) (GU)
Institutionen för teknisk fysik, Kemisk fysik (1900-2015)

Ämnesområden

Cell- och molekylärbiologi

Chalmers infrastruktur