| 1. |
- Beech, J. P., et al.
(författare)
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What do photons do to fluorescently stained DNA in confinement?
- 2013
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Ingår i: 17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013; Freiburg; Germany; 27 October 2013 through 31 October 2013. ; 1, s. 5-7
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Konferensbidrag (refereegranskat)abstract
- We have studied a selection of factors influencing the damage of DNA in nanochannels during fluorescence imaging. For cutting and nicking of DNA we show that the DNA is shortened during imaging. To avoid photodamage over the course of several hours of a typical experiment, we demonstrate the importance of an oxygen free gas to propel the buffer solution through the device. Finally, by varying the size of the channels, we show indications that higher DNA concentrations lead to higher rates of photodamage necessitating a balance between needs for highly stretched DNA and needs for long measurement times.
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| 2. |
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| 3. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
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Nanoconfined circular DNA
- 2014
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Ingår i: 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. - 9780979806476 ; , s. 1353-1355
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Konferensbidrag (refereegranskat)abstract
- Studies of nanoconfined circular DNA are of interest both from a biological as well as a fundamental polymer physics perspective. We here present the use of nanofluidic channels as a tool for comparing statics and dynamics of the linear and circular configuration of the same DNA molecule.
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| 4. |
- Nyberg, Lena, 1979, et al.
(författare)
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A single-step competitive binding assay for mapping of single DNA molecules
- 2012
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 417:1, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.
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