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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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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High-Density DNA and RNA microarrays - Photolithographic Synthesis, Hybridization and Preparation of Large Nucleic Acid Libraries
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High-Density DNA and RNA microarrays - Photolithographic Synthesis, Hybridization and Preparation of Large Nucleic Acid Libraries

Published on: August 12, 2019

A microarray-based method to perform nucleic acid selections.

Olga Aminova1, Matthew D Disney

  • 1Department of Chemistry and The Center for Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)
|September 22, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a novel microarray platform for nucleic acid selections, offering a faster and more cost-effective alternative to traditional methods. This technique enables parallel selections and minimizes biases, making it ideal for discovering RNA binders.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Genomics

Background:

  • Systematic Evolution of Ligands by Exponential Enrichment (SELEX) is a common method for identifying nucleic acid binders.
  • Traditional SELEX methods often face challenges with parallel processing, kinetic biases, and high costs associated with resins and equipment.

Purpose of the Study:

  • To develop and present a microarray-based platform for nucleic acid selections.
  • To offer an improved alternative to traditional resin-based SELEX with enhanced efficiency and reduced costs.

Main Methods:

  • Immobilizing chemical ligands onto an agarose microarray surface.
  • Incubating the microarray with an RNA library to allow binding.
  • Harvesting bound RNA library members via gel excision from the array.
  • Amplifying harvested RNA using RT-PCR, followed by cloning and sequencing.

Main Results:

  • The microarray platform allows multiple selections to be performed in parallel on a single surface.
  • The gel excision method mitigates kinetic biases inherent in traditional SELEX.
  • The protocol significantly minimizes the required amount of chemical ligand and avoids expensive resins or equipment.
  • The selection matrix is inexpensive and simple to prepare.

Conclusions:

  • The developed microarray-based method provides an efficient, cost-effective, and versatile platform for nucleic acid selections.
  • This approach is applicable to various nucleic acid selection processes beyond RNA, including DNA selections.
  • The method overcomes limitations of traditional SELEX, offering advantages in speed, cost, and bias reduction.