Stability of the pH-Dependent Parallel-Stranded d(CGA) Motif.

Autor:	Luteran EM; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland., Kahn JD; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland., Paukstelis PJ; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland. Electronic address: paukstel@umd.edu.
Jazyk:	angličtina
Zdroj:	Biophysical journal [Biophys J] 2020 Oct 20; Vol. 119 (8), pp. 1580-1589. Date of Electronic Publication: 2020 Sep 11.
DOI:	10.1016/j.bpj.2020.09.002
Abstrakt:	Noncanonical DNA structures that retain programmability and structural predictability are increasingly being used in DNA nanotechnology applications, in which they offer versatility beyond traditional Watson-Crick interactions. The d(CGA) triplet repeat motif is structurally dynamic and can transition between parallel-stranded homo-base paired duplex and antiparallel unimolecular hairpin in a pH-dependent manner. Here, we evaluate the thermodynamic stability and nuclease sensitivity of oligonucleotides composed of the d(CGA) motif and several structurally related sequence variants. These results show that the structural transition resulting from decreasing the pH is accompanied by both a significant energetic stabilization and decreased nuclease sensitivity as unimolecular hairpin structures are converted to parallel-stranded homo-base paired duplexes. Furthermore, the stability of the parallel-stranded duplex form can be altered by changing the 5'-nucleobase of the d(CGA) triplet and the frequency and position of the altered triplets within long stretches of d(CGA) triplets. This work offers insight into the stability and versatility of the d(CGA) triplet repeat motif and provides constraints for using this pH-adaptive structural motif for creating DNA-based nanomaterials. (Copyright © 2020 Biophysical Society. Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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