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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.
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

RAPID-SELEX for RNA aptamers.

Kylan Szeto¹, David R Latulippe¹, Abdullah Ozer²

¹School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America.

|December 31, 2013

Summary

This summary is machine-generated.

We developed RAPID-SELEX, a streamlined method for discovering RNA aptamers. This faster technique simplifies the selection process, significantly reducing the time needed to identify high-affinity aptamers for specific protein targets.

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Area of Science:

Biotechnology
Molecular Biology
Drug Discovery

Background:

Aptamers are high-affinity ligands selected from nucleic acid libraries using SELEX (Systematic Evolution of Ligands by Exponential Enrichment).
RNA SELEX is typically complex due to mandatory transcription and reverse transcription steps, increasing overall process time.
Conventional SELEX involves repetitive selection and amplification cycles, which can be time-consuming.

Purpose of the Study:

To introduce a simplified and accelerated RNA SELEX method, termed RAPID-SELEX (RNA Aptamer Isolation via Dual-cycles SELEX).
To demonstrate the efficiency and robustness of RAPID-SELEX in identifying high-affinity aptamers.
To reduce the overall time required for aptamer selection compared to conventional SELEX.

Main Methods:

Developed RAPID-SELEX, a novel selection scheme that streamlines RNA aptamer discovery by minimizing amplification steps.
Utilized affinity microcolumns for multiplex selection of aptamers against protein targets (CHK2 and UBLCP1).
Employed high-throughput sequencing to analyze enriched aptamer pools from both RAPID-SELEX and conventional SELEX.

Main Results:

RAPID-SELEX completed multiplex selections for protein targets in one-third the time of conventional SELEX.
High-throughput sequencing revealed numerous identical candidate aptamers between RAPID-SELEX and conventional SELEX pools.
The top candidate aptamer for CHK2 was preferentially enriched in both selection methods and demonstrated target binding.

Conclusions:

RAPID-SELEX is an efficient and robust method for accelerating aptamer discovery.
The streamlined process significantly reduces the time and complexity of RNA aptamer selection.
This generalized approach can be applied to various selection technologies to expedite aptamer identification without compromising performance.