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Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

RNA-seq

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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Related Experiment Video

Updated: May 12, 2026

Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis

Split Hybridization Probe Utilizing a DNA Fluorescent Light-up Aptamer as a Signal Reporter for Sequence-Specific Nucleic Acid Analysis

Published on: July 8, 2025

Fluorogenic Aptamer Optimization on a Massively Parallel Sequencing Platform.

Yu-An Kuo¹, Yuan-I Chen¹, Naseem Siraj²

¹Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, USA.

|May 11, 2026

Summary

This summary is machine-generated.

We developed a high-throughput method to optimize fluorogenic aptamers (FAPs) for cellular sensing. This approach significantly enhances FAP performance, leading to improved diagnostic tools.

Keywords:

C14T FAP optimization fluorogenic aptamers pathogen diagnostics

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Area of Science:

Biochemistry
Molecular Biology
Biotechnology

Background:

Fluorogenic aptamers (FAPs) are crucial for cellular sensing and pathogen diagnostics.
Enhancing FAP performance is essential for advancing these applications.
Current optimization methods face significant challenges.

Purpose of the Study:

To develop a massively parallel screening approach for optimizing DNA-based FAPs.
To improve the fluorescence properties and cellular sensing capabilities of FAPs.
To gain deeper insights into aptamer-fluorogen interactions.

Main Methods:

Utilized repurposed next-generation sequencing flow cells for high-throughput screening.
Screened 8821 variants of the DNA-based FAP Lettuce with a novel fluorogen, TO1-biotin.
Employed co-crystal structure analysis and molecular dynamics simulations.

Main Results:

Achieved a 4-fold ensemble fluorescence enhancement and broader fluorescence lifetime modulation.
Identified the C14T mutant with improved dissociation constant, quantum yield, and emission intensity.
Demonstrated enhanced fluorescence intensity in cellular environments for optimized FAPs.

Conclusions:

Massively parallel screening enables efficient FAP optimization, even without prior structural knowledge.
Optimized FAPs show superior performance for fluorescence sensing applications.
The study provides valuable insights into aptamer-fluorogen complex stability and interactions.