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SELMA: Selection with Modified Aptamers.

J Sebastian Temme1, Isaac J Krauss1

  • 1Department of Chemistry, Brandeis University, Waltham, Massachusetts.

Current Protocols in Chemical Biology
|September 8, 2015
PubMed
Summary
This summary is machine-generated.

Selection with Modified Aptamers (SELMA) enables the discovery of novel DNA aptamers with optimized carbohydrate clustering for high-affinity binding. This method was applied to develop glycoDNA binders for the HIV antibody 2G12.

Keywords:
HIVSELEXSELMAin vitro aptamer selectionprotein-carbohydrate interaction

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Drug Discovery

Background:

  • Systematic Evolution of Ligands by Exponential Enrichment (SELEX) is a powerful method for discovering nucleic acid aptamers.
  • SELEX has limitations with modified bases that hinder PCR amplification, restricting the types of aptamers that can be discovered.
  • Carbohydrate-binding proteins often require clustered carbohydrate moieties for high-affinity recognition, posing a challenge for rational design.

Purpose of the Study:

  • To introduce and detail the application of Selection with Modified Aptamers (SELMA) for discovering aptamers with complex modifications.
  • To demonstrate SELMA's capability in evolving aptamers with optimized glycan clustering for enhanced target recognition.
  • To present a specific protocol for using SELMA to discover glycoDNA aptamers that bind to the HIV broadly neutralizing antibody 2G12.

Main Methods:

  • Selection with Modified Aptamers (SELMA) was employed to select DNA aptamers containing large base modifications.
  • The SELMA protocol was adapted for the evolution of aptamers featuring carbohydrate modifications (glycoaptamers).
  • The developed glycoaptamers were tested for their binding affinity to the HIV antibody 2G12.

Main Results:

  • SELMA successfully enabled the selection of DNA aptamers with non-PCR-compatible modifications.
  • The SELMA method yielded glycoaptamers with highly optimized glycan clustering.
  • The resulting glycoaptamers demonstrated low-nanomolar recognition of the HIV antibody 2G12.

Conclusions:

  • SELMA is a versatile method for discovering aptamers with complex and large base modifications, including carbohydrates.
  • SELMA facilitates the evolution of glycoaptamers with superior binding affinities due to optimized glycan presentation.
  • This study showcases SELMA's potential for discovering targeted glycoDNA binders, exemplified by the HIV 2G12 antibody binders.