| 1. |
- Beech, Jason P., et al.
(författare)
-
Sample preparation for single-cell whole chromosome analysis
- 2012
-
Ingår i: Proceedings of the 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012. - 9780979806452 ; , s. 998-999
-
Konferensbidrag (refereegranskat)abstract
- In this work we present an integrated system for whole chromosome analysis of single bacterium. Using whole genome barcoding techniques, which offer direct and rapid microscopic visualization of the entire genome in one field-of-view, we aim to rapidly identify individual bacterium. We are developing our device to achieve the crucial, and difficult process of isolating a bacterium, removing the DNA in one piece and transferring it to a nano-channel for visualisation. In order to achieve control over the bacteria we encapsulate them in agarose, using flow focusing. The encapsulated bacteria can then be transported in microchannels to proximity with the nanochannels and then chemically lysis can be performed. Following lysis the intact genome can be extracted and transferred to the meandering nanochannel for analysis. We believe this device holds the potential to significantly decrease analysis times for single cell, whole genome analysis with the potential of opening up for automated, high-throughput genome analysis in microfluidic systems.
|
|
| 2. |
- Frykholm, Karolin, 1977, et al.
(författare)
-
Probing concentration-dependent behavior of DNA-binding proteins on a single-molecule level illustrated by Rad51
- 2013
-
Ingår i: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 443:2, s. 261-268
-
Tidskriftsartikel (refereegranskat)abstract
- Low throughput is an inherent problem associated with most single-molecule biophysical techniques. We have developed a versatile tool for high-throughput analysis of DNA and DNA-binding molecules by combining microfluidic and dense DNA arrays. We use an easy-to-process microfluidic flow channel system in which dense DNA arrays are prepared for simultaneous imaging of large amounts of DNA molecules with single-molecule resolution. The Y-shaped microfluidic design, where the two inlet channels can be controlled separately and precisely, enables the creation of a concentration gradient across the microfluidic channel as well as rapid and repeated addition and removal of substances from the measurement region. A DNA array stained with the fluorescent DNA-binding dye YOYO-1 in a gradient manner illustrates the method and serves as a proof of concept. We have applied the method to studies of the repair protein Rad51 and could directly probe the concentration-dependent DNA-binding behavior of human Rad51 (HsRad51). In the low-concentration regime used (100 nM HsRad51 and below), we detected binding to double-stranded DNA (dsDNA) without positive cooperativity. (C) 2013 Elsevier Inc. All rights reserved.
|
|
| 3. |
- McGinn, Steven, et al.
(författare)
-
New Technologies for DNA analysis-A review of the READNA Project.
- 2016
-
Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784.
-
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.
|
|
| 4. |
- Noble, Charleston, et al.
(författare)
-
A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings.
- 2015
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:4
-
Tidskriftsartikel (refereegranskat)abstract
- Optical mapping by direct visualization of individual DNA molecules, stretched in nanochannels with sequence-specific fluorescent labeling, represents a promising tool for disease diagnostics and genomics. An important challenge for this technique is thermal motion of the DNA as it undergoes imaging; this blurs fluorescent patterns along the DNA and results in information loss. Correcting for this effect (a process referred to as kymograph alignment) is a common preprocessing step in nanochannel-based optical mapping workflows, and we present here a highly efficient algorithm to accomplish this via pattern recognition. We compare our method with the one previous approach, and we find that our method is orders of magnitude faster while producing data of similar quality. We demonstrate proof of principle of our approach on experimental data consisting of melt mapped bacteriophage DNA.
|
|
