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Updated: Dec 31, 2025

Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry

Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry

Published on: January 17, 2025

Determining Functional Aptamer-Protein Interaction by Biolayer Interferometry.

Xinhui Lou¹, Martin Egli², Xianbin Yang³

¹Department of Chemistry, Capital Normal University, Beijing, China.

Current Protocols in Nucleic Acid Chemistry

|December 3, 2016

Summary

This summary is machine-generated.

Aptamers, short nucleic acid sequences, are effective for detecting proteins like thrombin. This study details protocols for analyzing aptamer-target interactions using biolayer interferometry and exploring modified aptamers for enhanced stability and activity.

Keywords:

affinity aptamer biolayer interferometry nucleic acid-protein interactions phosphorodithioate

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Bio-layer Interferometry for Measuring Kinetics of Protein-protein Interactions and Allosteric Ligand Effects

Bio-layer Interferometry for Measuring Kinetics of Protein-protein Interactions and Allosteric Ligand Effects

Published on: February 18, 2014

Area of Science:

Biochemistry
Molecular Biology
Biotechnology

Background:

Aptamers are short single-stranded nucleic acids with high affinity and specificity for target molecules, especially proteins.
Biolayer interferometry (BLI) offers a Dip-and-Read method for studying aptamer-protein interactions using aptamer-coated biosensors.
Phosphorodithioate (PS2) modification enhances RNA nuclease resistance and biological activity.

Purpose of the Study:

To describe a protocol for analyzing the interaction between an anti-thrombin RNA aptamer and thrombin using BLI.
To present a protocol for affinity screening of phosphorodithioate (PS2)-modified anti-thrombin RNA aptamers.
To investigate the impact of PS2 modification position on aptamer performance.

Main Methods:

Basic Protocol: Analysis of anti-thrombin RNA aptamer-thrombin interaction using BLI.
Support Protocol: Affinity screening of PS2-modified anti-thrombin RNA aptamers with systematic variation of modification position.
PS2 modification involves replacing non-bridging oxygen atoms with sulfur in the phosphodiester backbone.

Main Results:

Established a reliable protocol for aptamer-thrombin interaction analysis via BLI.
Developed and applied a method for screening PS2-modified aptamers.
Demonstrated that PS2-modified RNAs exhibit nuclease resistance and biological activity, with potential for enhanced gene silencing.

Conclusions:

The described BLI protocol enables efficient analysis of aptamer-protein binding.
PS2 modification is a valuable strategy for improving aptamer stability and efficacy.
Modified aptamers show promise for therapeutic applications, including enhanced antitumor activity.