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Related Concept Videos

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. 
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Related Experiment Video

Updated: Jun 15, 2026

3' End Sequencing Library Preparation with A-seq2
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Published on: October 10, 2017

An extension-quenching-extension sequencing on a microarray.

Li Gao1, Hua Lu, Hong Zhao

  • 1State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. oga2001@163.com

Talanta
|March 2, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a novel DNA sequencing method using extension-quenching-extension on microarrays. Copper sulfate effectively quenches fluorescence, enabling cost-effective, high-throughput DNA sequencing.

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Area of Science:

  • Biotechnology
  • Genomics
  • Molecular Biology

Background:

  • Sequencing-by-synthesis (SBS) methods face challenges in cost reduction and fluorescence removal for continuous DNA sequencing.
  • Fluorescein-labeled nucleotides are commonly used in SBS, but their fluorescence can impede subsequent sequencing cycles.

Purpose of the Study:

  • To develop a cost-effective and high-throughput DNA sequencing strategy that overcomes limitations of current SBS methods.
  • To identify a method for efficient fluorescence quenching in DNA sequencing to enable repeated reading of the same template.

Main Methods:

  • A novel extension-quenching-extension sequencing strategy was developed on a microarray platform.
  • Hyperbranched rolling circle amplification (HRCA) was employed to prepare DNA templates on the microarray.
  • Copper sulfate (CuSO(4)) was investigated for its ability to quench fluorescein fluorescence via an energy-transfer mechanism.

Main Results:

  • Copper sulfate was found to effectively quench fluorescein fluorescence in DNA sequencing.
  • Optimization of CuSO(4) concentration, temperature, and duration successfully enabled fluorescence quenching.
  • The developed method demonstrated a strategy for sequencing using a known DNA template.

Conclusions:

  • The extension-quenching-extension strategy combined with HRCA and copper sulfate-mediated fluorescence quenching offers a viable solution for cost-effective DNA sequencing.
  • This approach addresses the challenge of fluorescence interference in repeated sequencing reads.
  • The study provides a foundational strategy for advancing high-throughput microarray-based sequencing technologies.