| 1. |
- McGinn, Steven, et al.
(författare)
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New Technologies for DNA analysis-A review of the READNA Project.
- 2016
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Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784.
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Forskningsöversikt (refereegranskat)abstract
- The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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| 2. |
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| 3. |
- Reisner, Walter, et al.
(författare)
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Directed self-organization of single DNA molecules in a nanoslit via embedded nanopit arrays
- 2009
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 106:1, s. 79-84
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Tidskriftsartikel (refereegranskat)abstract
- We show that arrays of nanopit structures etched in a nanoslit can control the positioning and conformation of single DNA molecules in nanofluidic devices. By adjusting the spacing, organization and placement of the nanopits it is possible to immobilize DNA at predetermined regions of a device without additional chemical modification and achieve a high degree of control over local DNA conformation. DNA can be extended between two nanopits and in closely spaced arrays will self-assemble into "connect-the-dots" conformations consisting of locally pinned segments joined by fluctuating linkers. These results have broad implications for nanotechnology fields that require methods for the nanoscale positioning and manipulation of DNA.
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| 4. |
- Reisner, Walter, et al.
(författare)
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Nanoconfinement-enhanced conformational response of single DNA molecules to changes in ionic environment
- 2007
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Ingår i: Physical Review Letters. - 1079-7114. ; 99:5
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Tidskriftsartikel (refereegranskat)abstract
- We show that the ionic environment plays a critical role in determining the configurational properties of DNA confined in silica nanochannels. The extension of DNA in the nanochannels increases as the ionic strength is reduced, almost tripling over two decades in ionic strength for channels around 100x100 nm in dimension. Surprisingly, we find that the variation of the persistence length alone with ionic strength is not enough to explain our results. The effect is due mainly to increasing self-avoidance created by the reduced screening of electrostatic interactions at low ionic strength. To quantify the increase in self-avoidance, we introduce a new parameter into the de Gennes theory: an effective DNA width that gives the increase in the excluded volume due to electrostatic repulsion.
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| 5. |
- Reisner, Walter, et al.
(författare)
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Single-molecule denaturation mapping of DNA in nanofluidic channels
- 2010
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 107:30, s. 13294-13299
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 6. |
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| 7. |
- Reisner, Walter W., et al.
(författare)
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Melting mapping in nanochannels
- 2008
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Ingår i: ; , s. 1516-1518
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Konferensbidrag (refereegranskat)abstract
- We demonstrate direct visualization of melting mapping of DNA stretched in nanoscale channels[1] using standard staining methods and epifluorescence microscopy to gain information on the local AT/GC ratio along large DNA molecules. Our development opens up a novel route to mapping of large-scale genomic variations.
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