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Acousto-microfluidics for screening of ssDNA aptamer

Park, Jeewoong LU ; Lee, Sujin LU ; Ren, Shuo; Lee, Sangwook; Kim, Soyoun and Laurell, Thomas LU (2016) In Scientific Reports 6.
Abstract

We demonstrate a new screening method for obtaining a prostate-specific antigen (PSA) binding aptamer based on an acoustofluidic separation (acoustophoreis) technique. Since acoustophoresis provides simultaneous washing and separation in a continuous flow mode, we efficiently obtained a PSA binding aptamer that shows high affinity without any additional washing step, which is necessary in other screening methods. In addition, next-generation sequencing (NGS) was applied to accelerate the identification of the screened ssDNA pool, improving the selecting process of the aptamer candidate based on the frequency ranking of the sequences. After the 8 th round of the acoustophoretic systematic evolution of ligands by exponential enrichment... (More)

We demonstrate a new screening method for obtaining a prostate-specific antigen (PSA) binding aptamer based on an acoustofluidic separation (acoustophoreis) technique. Since acoustophoresis provides simultaneous washing and separation in a continuous flow mode, we efficiently obtained a PSA binding aptamer that shows high affinity without any additional washing step, which is necessary in other screening methods. In addition, next-generation sequencing (NGS) was applied to accelerate the identification of the screened ssDNA pool, improving the selecting process of the aptamer candidate based on the frequency ranking of the sequences. After the 8 th round of the acoustophoretic systematic evolution of ligands by exponential enrichment (SELEX) and following sequence analysis with NGS, 7 PSA binding ssDNA aptamer-candidates were obtained and characterized with surface plasmon resonance (SPR) for affinity and specificity. As a result of the new SELEX method with PSA as the model target protein, the best PSA binding aptamer showed specific binding to PSA with a dissociation constant (K d) of 0.7 nM.

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author
organization
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type
Contribution to journal
publication status
published
subject
in
Scientific Reports
volume
6
publisher
Nature Publishing Group
external identifiers
  • scopus:84976448852
  • wos:000377333900002
ISSN
2045-2322
DOI
10.1038/srep27121
language
English
LU publication?
yes
id
922e99bc-672c-4f13-94a7-0d2dacfc4be5
date added to LUP
2017-01-24 10:44:58
date last changed
2017-11-05 05:12:40
@article{922e99bc-672c-4f13-94a7-0d2dacfc4be5,
  abstract     = {<p>We demonstrate a new screening method for obtaining a prostate-specific antigen (PSA) binding aptamer based on an acoustofluidic separation (acoustophoreis) technique. Since acoustophoresis provides simultaneous washing and separation in a continuous flow mode, we efficiently obtained a PSA binding aptamer that shows high affinity without any additional washing step, which is necessary in other screening methods. In addition, next-generation sequencing (NGS) was applied to accelerate the identification of the screened ssDNA pool, improving the selecting process of the aptamer candidate based on the frequency ranking of the sequences. After the 8 th round of the acoustophoretic systematic evolution of ligands by exponential enrichment (SELEX) and following sequence analysis with NGS, 7 PSA binding ssDNA aptamer-candidates were obtained and characterized with surface plasmon resonance (SPR) for affinity and specificity. As a result of the new SELEX method with PSA as the model target protein, the best PSA binding aptamer showed specific binding to PSA with a dissociation constant (K d) of 0.7 nM.</p>},
  articleno    = {27121},
  author       = {Park, Jeewoong and Lee, Sujin and Ren, Shuo and Lee, Sangwook and Kim, Soyoun and Laurell, Thomas},
  issn         = {2045-2322},
  language     = {eng},
  month        = {06},
  publisher    = {Nature Publishing Group},
  series       = {Scientific Reports},
  title        = {Acousto-microfluidics for screening of ssDNA aptamer},
  url          = {http://dx.doi.org/10.1038/srep27121},
  volume       = {6},
  year         = {2016},
}