DNA display of folded RNA libraries enabling RNA-SELEX without reverse transcription

I S MacPherson; J S Temme; I J Krauss

doi:10.1039/c6cc09991b

DNA display of folded RNA libraries enabling RNA-SELEX without reverse transcription

Chem Commun (Camb). 2017 Mar 2;53(19):2878-2881. doi: 10.1039/c6cc09991b.

Authors

I S MacPherson¹, J S Temme², I J Krauss²

Affiliations

¹ Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawai'i at Manoa, 651 Ilalo St., Biosciences Building, Suite 325, Honolulu, Hawaii 96813-5525, USA. iain.macpherson@hawaii.edu and Department of Chemistry, Brandeis University, 415 South St. MS 015, Waltham, MA 02454-9110, USA. kraussi@brandeis.edu.
² Department of Chemistry, Brandeis University, 415 South St. MS 015, Waltham, MA 02454-9110, USA. kraussi@brandeis.edu.

Abstract

A method for the physical attachment of folded RNA libraries to their encoding DNA is presented as a way to circumvent the reverse transcription step during systematic evolution of RNA ligands by exponential enrichment (RNA-SELEX). A DNA library is modified with one isodC base to stall T7 polymerase and a 5' "capture strand" which anneals to the nascent RNA transcript. This method is validated in a selection of RNA aptamers against human α-thrombin with dissociation constants in the low nanomolar range. This method will be useful in the discovery of RNA aptamers and ribozymes containing base modifications that make them resistant to accurate reverse transcription.

MeSH terms

Aptamers, Nucleotide / genetics
DNA / genetics*
Gene Library*
RNA / genetics*
RNA Folding*
RNA, Catalytic / genetics
RNA, Catalytic / metabolism
Reverse Transcription / genetics
SELEX Aptamer Technique*

Substances

Aptamers, Nucleotide
RNA, Catalytic
RNA
DNA

Abstract

MeSH terms

Substances

Grants and funding