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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

A genome-inspired, reverse selection approach to aptamer discovery.

Christina M Albanese¹, Suttipong Suttapitugsakul¹, Shruthi Perati¹

¹Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA.

|November 8, 2017

Summary

Researchers developed a novel aptamer discovery method using genomic sequences to capture proteins. This approach successfully identified nucleolin, RPL19, and RPL14, offering potential for new diagnostics and therapeutics.

Keywords:

Aptamer Cancer G-quadruplex Genomic DNA Oncogene promoter

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Area of Science:

Biochemistry
Molecular Biology
Genomics

Background:

Systematic Evolution of Ligands by Exponential Enrichment (SELEX) limitations hinder aptamer discovery.
A novel approach utilizes human genomic sequences for aptamer development.
G-quadruplex (G4) forming genomic sequences are explored for protein capture.

Purpose of the Study:

To investigate protein capture using G-quadruplex forming genomic sequences from human oncogene promoters.
To identify proteins interacting with G4 sequences from CMYC, RB, VEGF, and ERBB2 promoters in breast cancer cells.
To establish a foundation for developing new aptamers based on these genomic sequences.

Main Methods:

Utilized G-quadruplex forming genomic sequences from human oncogene promoters (CMYC, RB, VEGF, ERBB2).
Performed mass spectrometry and Western blot analysis on proteins captured by oligonucleotide-modified surfaces.
Conducted chromatin immunoprecipitation (ChIP) assays to confirm in vivo interactions.

Main Results:

Nucleolin was captured by all tested G4 sequences in BT474 and MCF7 cells.
Ribosomal protein L19 (RPL19) was captured in BT474 cells.
ChIP confirmed interactions of nucleolin, RPL19, and RPL14 with specific G4 sequences.

Conclusions:

Genomic G-quadruplex sequences from CMYC, RB, VEGF, and ERBB2 promoters can capture specific proteins.
Identified nucleolin, RPL19, and RPL14 as targets for G4-based aptamer development.
These findings suggest potential biological and therapeutic applications for G4 aptamers.