Computational Approaches Toward the Design of Pools for the in Vitro Selection of Complex Aptamers

Overview

Journal RNA

Specialty Molecular Biology

Date 2010 Sep 28

PMID 20870801

Citations 31

Authors

Xuemei Luo

Maureen McKeague

Sylvain Pitre

Michel Dumontier

James Green

Ashkan Golshani

Maria C DeRosa

Frank Dehne

Affiliations

Soon will be listed here.

Abstract

It is well known that using random RNA/DNA sequences for SELEX experiments will generally yield low-complexity structures. Early experimental results suggest that having a structurally diverse library, which, for instance, includes high-order junctions, may prove useful in finding new functional motifs. Here, we develop two computational methods to generate sequences that exhibit higher structural complexity and can be used to increase the overall structural diversity of initial pools for in vitro selection experiments. Random Filtering selectively increases the number of five-way junctions in RNA/DNA pools, and Genetic Filtering designs RNA/DNA pools to a specified structure distribution, whether uniform or otherwise. We show that using our computationally designed DNA pool greatly improves access to highly complex sequence structures for SELEX experiments (without losing our ability to select for common one-way and two-way junction sequences).

Citing Articles

Research Progress in Small-Molecule Detection Using Aptamer-Based SERS Techniques.

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Selection of DNA aptamers that prevent the fibrillization of α-synuclein protein in cellular and mouse models.

McConnell E, Chan D, Ventura K, Callahan J, Harris K, Hunt V Mol Ther Nucleic Acids. 2024; 35(3):102251.

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In vitro selection of aptamers and their applications.

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Minimizing amplification bias during reverse transcription for in vitro selections.

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