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Related Experiment Video

Updated: Jul 10, 2026

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

Exploring the sequence space of a DNA aptamer using microarrays.

Evaldas Katilius¹, Carole Flores, Neal W Woodbury

¹Center for BioOptical Nanotechnology, The Biodesign Institute and the Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-5201, USA. ekatilius@asu.edu

Nucleic Acids Research

|November 6, 2007

Summary

Investigating an immunoglobulin E (IgE) aptamer revealed that most sequence positions are critical for binding. Optimizing aptamer sequences through stepwise mutations is challenging due to a rugged sequence landscape.

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Last Updated: Jul 10, 2026

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

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Primer-Free Aptamer Selection Using A Random DNA Library

Primer-Free Aptamer Selection Using A Random DNA Library

Published on: July 26, 2010

Area of Science:

Biochemistry
Molecular Biology
Biotechnology

Background:

Aptamers are nucleic acid-based ligands with high specificity and affinity for target molecules.
Understanding the sequence-structure-function relationship is crucial for aptamer design and optimization.
Immunoglobulin E (IgE) is a key mediator of allergic reactions, making IgE-binding aptamers valuable diagnostic and therapeutic tools.

Purpose of the Study:

To investigate the relationship between the sequence and binding properties of an immunoglobulin E (IgE)-specific DNA aptamer.
To identify critical nucleotides and structural elements governing aptamer binding affinity.
To estimate the probability of discovering functional aptamer sequences from random libraries.

Main Methods:

Custom DNA microarray technology was employed to assess binding affinities of mutated aptamers.
Systematic single, double, and triple nucleotide mutations were introduced into the aptamer sequence.
Binding affinities were quantified by measuring changes in binding affinity across various mutations.

Main Results:

The majority of aptamer sequence positions were found to be immutable, with mutations causing >100-fold decrease in binding affinity.
Alterations in the aptamer's stem region led to improved binding affinity, highlighting its importance.
No compensatory mutations were observed within the tested mutation space, indicating a rugged functional landscape.

Conclusions:

The functional sequence space for this IgE aptamer is characterized by sharp peaks and highly constrained base compositions.
Rational optimization of aptamer sequences using stepwise mutagenesis is challenging due to the identified sequence landscape.
The probability of finding a functional IgE-binding aptamer by random selection is estimated to be between 10^-10 and 10^-9.