Enzymatic synthesis of nucleobase-modified single-stranded DNA offers tunable resistance to nuclease degradation

TitleEnzymatic synthesis of nucleobase-modified single-stranded DNA offers tunable resistance to nuclease degradation
Publication TypeJournal Article
Year of Publication2018
AuthorsR Gu, T Oweida, YG Yingling, A Chilkoti, and S Zauscher
JournalBiomacromolecules
Volume19
Issue8
Start Page3525
Pagination3525 - 3535
Date Published07/2018
Abstract

We synthesized long, nucleobase-modified, single-stranded DNA (ssDNA) using terminal deoxynucleotidyl transferase (TdT) enzymatic polymerization. Specifically, we investigated the effect of unnatural nucleobase size and incorporation density on ssDNA resistance to exo- and endonuclease degradation. We discovered that increasing the size and density of unnatural nucleobases enhances ssDNA resistance to degradation in the presence of exonuclease I, DNase I, and human serum. We also studied the mechanism of this resistance enhancement using molecular dynamics simulations. Our results show that the presence of unnatural nucleobases in ssDNA decreases local chain flexibility and hampers nuclease access to the ssDNA backbone, which hinders nuclease binding to ssDNA and slows its degradation. Our discoveries suggest that incorporating nucleobase-modified nucleotides into ssDNA, using enzymatic polymerization, is an easy and efficient strategy to prolong and tune the half-life of DNA-based materials in nucleases-containing environments.

DOI10.1021/acs.biomac.8b00816
Short TitleBiomacromolecules