Journal article
Single-molecule denaturation mapping of DNA in nanofluidic channels
Stochastic Systems and Signals Group, Theory Section, Department of Micro- and Nanotechnology, Technical University of Denmark1
Theory Section, Department of Micro- and Nanotechnology, Technical University of Denmark2
Department of Micro- and Nanotechnology, Technical University of Denmark3
Polymer Microsystems for Cell Processing Group, Polymer Micro and Nano Engineering Section, Department of Micro- and Nanotechnology, Technical University of Denmark4
Polymer Micro and Nano Engineering Section, Department of Micro- and Nanotechnology, Technical University of Denmark5
NSE-Optofluidics Group, NanoSystemsEngineering Section, Department of Micro- and Nanotechnology, Technical University of Denmark6
NanoSystemsEngineering Section, Department of Micro- and Nanotechnology, Technical University of Denmark7
Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO (R)-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips and peaks in the intensity trace along the extended molecule.
We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence. Consequently, the technique is sensitive to sequence variation without requiring enzymatic labeling or a restriction step.
This technique may serve as the basis for a new mapping technology ideally suited for investigating the long-range structure of entire genomes extracted from single cells.
| Language: | English |
|---|---|
| Publisher: | National Academy of Sciences |
| Year: | 2010 |
| Pages: | 13294-13299 |
| ISSN: | 10916490 and 00278424 |
| Types: | Journal article |
| DOI: | 10.1073/pnas.1007081107 |
| ORCIDs: | 0000-0001-6181-2705 , Larsen, Niels Bent , Kristensen, Anders and Flyvbjerg, Henrik |
1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium Algorithms Bacteriophages Benzoxazoles DNA Formamides Microfluidic Analytical Techniques Models, Chemical Nanotechnology Nucleic Acid Conformation Nucleic Acid Denaturation Quinolinium Compounds Transition Temperature formamide
