Kinetic Characterization of On-Chip DNA ligation on Dendron-coated surfaces with Nanoscaled lateral spacing
SCIE
SCOPUS
- Title
- Kinetic Characterization of On-Chip DNA ligation on Dendron-coated surfaces with Nanoscaled lateral spacing
- Authors
- Kim, ES; Namgyu Lee; Park, JW; Choi, KY
- Date Issued
- 2013-10-11
- Publisher
- IOP science
- Abstract
- We analyzed the enzymatic profiles of on-chip DNA ligation as we controlled the lateral spacing of surface-immobilized DNA substrates using dendron molecules with different sizes at the nanoscale. Enzymatic on-chip DNA ligation was performed on the dendron-coated surface within 20 min with no need for post-ligation gel electrophoresis. The enzymatic DNA repair was assessed by the fluorescence intensity at the repaired DNA duplex after thermally dissociating the unligated Cy3-labeled DNA from the DNA duplex, in which the Cy3-labeled DNA was hybridized prior to the on-chip DNA ligation. The rate of the nick-sealing reaction on the 27-acid dendron surface was 3-fold higher than that on the 9-acid dendron surface, suggesting that the wider lateral spacing determined by the larger dendron molecule could facilitate the access of DNA ligase to the nick site. The performance of on-chip DNA ligation was dropped to 10% and 3% when the nick was replaced by one-and two-nucleotide-long gaps, respectively. The 5 0 terminal phosphorylation of DNA strands by polynucleotide kinase and the on-chip DNA cleavage by endonucleases were also quantitatively monitored throughout the on-chip DNA ligation on the dendron-coated surface. A better understanding of the enzymatic kinetics of on-chip DNA ligation will contribute to a more reliable performance of various on-chip DNA ligation-based assays.
- URI
- https://oasis.postech.ac.kr/handle/2014.oak/15156
- DOI
- 10.1088/0957-4484/24/40/405703
- ISSN
- 0957-4484
- Article Type
- Article
- Citation
- Nanotechnology, vol. 24, no. 40, page. 1 - 10, 2013-10-11
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