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A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay
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A system for in vitro selection of fully 2'-modified RNA aptamers
Emily D Ziperman1, Kate B Fitzpatrick1, Malavika A Nair1
1Department of Chemistry, Brandeis University, Waltham, Massachusetts, USA. kraussi@brandeis.edu.
Organic & Biomolecular Chemistry
|February 6, 2025
Summary
This study shows that specific polymerases are compatible with SELection with Modified Aptamers (SELMA) for discovering aptamers with large modifications. This enables novel aptamer development with enhanced functionalities.
Area of Science:
- Biochemistry
- Molecular Biology
- Synthetic Biology
Background:
- Aptamer discovery methods are crucial for developing novel molecular tools.
- SELection with Modified Aptamers (SELMA) allows for incorporating large nucleobase modifications, like glycans.
- Enzyme compatibility with modified nucleotides is a key challenge in aptamer engineering.
Purpose of the Study:
- To investigate the compatibility of SFM4-3, KOD DGLNK, and Therminator polymerases with the SELMA method.
- To enable the incorporation of large nucleobase modifications, including glycans, into aptamers using SELMA.
- To optimize primer design and protocols for enhanced SELMA performance.
Main Methods:
- Utilized SELection with Modified Aptamers (SELMA) for aptamer discovery.
- Tested SFM4-3, KOD DGLNK, and Therminator polymerases for their ability to incorporate modified nucleobases.
- Modified primer design and experimental protocols to facilitate enzyme compatibility.
Main Results:
- SFM4-3, KOD DGLNK, and Therminator polymerases were found to be compatible with SELMA.
- The method successfully enabled 2'-fluoro or 2'-methoxy ribose modifications at all positions.
- Therminator polymerase demonstrated superior incorporation of alkyne-modified nucleobases for click chemistry with 2'-fluoro modifications.
Conclusions:
- Optimized SELMA protocols and primer designs allow for the use of standard DNA polymerases with modified nucleotides.
- This advancement expands the scope of aptamer modifications achievable through SELMA.
- Therminator polymerase shows promise for click chemistry applications in aptamer development.
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