posted on 2020-06-05, 12:40authored byXiuhai Mao, Mengmeng Liu, Lei Yan, Mengying Deng, Fan Li, Min Li, Fei Wang, Jiang Li, Lihua Wang, Yang Tian, Chunhai Fan, Xiaolei Zuo
Active
sites of proteins are generally encapsulated within three-dimensional
peptide scaffolds that provide the molecular-scale confinement microenvironment.
Nevertheless, the ability to tune thermodynamic stability in biomimetic
molecular confinement relies on the macromolecular crowding effect
of lack of stoichiometry and reconfigurability. Here, we report a
framework nucleic acid (FNA)-based strategy to increase thermodynamic
stability of aptamers. We demonstrate that the molecular-scale confinement
increases the thermodynamic stability of aptamers via facilitated folding kinetics, which is confirmed by the single-molecule
FRET (smFRET). Unfavorable conformations of aptamers are restricted
as revealed by the Monte Carlo simulation. The binding affinity of
the DNA framework-confined aptamer is improved by ∼3-fold.
With a similar strategy we improve the catalytic activity of hemin-binding
aptamer. Our approach thus shows high potential for designing protein-mimicking
DNA nanostructures with enhanced binding affinity and catalytic activity
for biosensing and biomedical engineering.