Systematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage T4 DNA Polymerase

TLDR

High‑affinity nucleic‑acid ligands for a protein are isolated by alternating cycles of selection from variant sequence pools and amplification of bound species, and these protocols can be minimally modified to yield high‑affinity ligands for any protein that binds nucleic acids, potentially enabling ligand development for any target molecule. Multiple rounds exponentially enrich the population for the highest‑affinity species, which can be clonally isolated and characterized, and in this study an eight‑base RNA region that interacts with T4 DNA polymerase was chosen and randomized. Two distinct eight‑base RNA sequences were selected from a pool of 65,536 variants—one matching the wild‑type sequence in bacteriophage mRNA and the other differing at four positions—and both bind T4 DNA polymerase with equivalent affinity.

Abstract

High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound species. Multiple rounds exponentially enrich the population for the highest affinity species that can be clonally isolated and characterized. In particular one eight-base region of an RNA that interacts with the T4 DNA polymerase was chosen and randomized. Two different sequences were selected by this procedure from the calculated pool of 65,536 species. One is the wild-type sequence found in the bacteriophage mRNA; one is varied from wild type at four positions. The binding constants of these two RNA's to T4 DNA polymerase are equivalent. These protocols with minimal modification can yield high-affinity ligands for any protein that binds nucleic acids as part of its function; high-affinity ligands could conceivably be developed for any target molecule.