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RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses
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Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing.

Minseon Cho1, Yi Xiao, Jeff Nie

  • 1Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106, USA.

Proceedings of the National Academy of Sciences of the United States of America
|August 14, 2010
PubMed
Summary

We developed a new method combining microfluidics and DNA sequencing for fast aptamer discovery. This technique efficiently identifies high-affinity aptamers, improving specificity and binding compared to traditional methods.

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Last Updated: Jun 10, 2026

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Published on: July 26, 2010

Area of Science:

  • Biotechnology
  • Molecular Biology
  • Genomics

Background:

  • Aptamer discovery is crucial for molecular diagnostics and therapeutics.
  • Traditional methods for aptamer selection can be time-consuming and may suffer from biases.

Purpose of the Study:

  • To develop a rapid and efficient method for discovering high-affinity nucleic acid aptamers.
  • To overcome limitations of conventional aptamer selection techniques.

Main Methods:

  • Integration of microfluidic selection with high-throughput DNA sequencing.
  • Quantitative Selection of Aptamers through Sequencing (QSAS) method to track sequence enrichment.
  • Analysis of over 10 million sequences across multiple selection rounds.

Main Results:

  • Identified aptamers binding to PDGF-BB protein with dissociation constants (K(d)) < 3 nM in just 3 rounds.
  • QSAS-aptamers demonstrated 3-8 fold higher affinity and 2-4 fold higher specificity than those from conventional methods.
  • Successfully discriminated true high-affinity binders from experimental biases.

Conclusions:

  • The developed method enables efficient and specific aptamer discovery.
  • QSAS offers a significant improvement over traditional aptamer selection approaches.
  • The method's potential extension to other molecular libraries and functions.