Rational design of supramolecular hemin/G-quadruplex-dopamine aptamer nucleoapzyme systems with superior catalytic performance

Chemical Science
H Bauke AlbadaItamar Willner

Abstract

The rational design of a set of hemin/G-quadruplex (hGQ)-dopamine binding aptamer (DBA) conjugates, acting as nucleoapzymes, is described. The nucleoapzyme constructs consist of a hGQ DNAzyme as a catalytic unit and DBA as a substrate binding unit that are brought into spatial proximity by a duplex scaffold composed of complementary oligonucleotide strands. When the hGQ unit is linked to the duplex scaffold via a single-strand DNA tether of variable length, the resulting nucleoapzymes reveal a moderate catalytic enhancement toward the H2O2-mediated oxidation of dopamine to aminochrome as compared to the process stimulated by the separated hGQ and DBA units (5-7 fold enhancement). This limited enhancement is attributed to inappropriate spatial positioning of the hGQ in respect to the dopamine binding site, and/or to the flexibility of the tether that links the hGQ catalytic site to the double-stranded scaffold. To solve this, rigidification of the hGQ/DBA conjugates by triplex oligonucleotide structures that anchor the hGQ to a duplex domain associated with the DBA units was achieved. By the sequential, programmed, triplex-controlled rigidification of the hGQ/DBA structure, a nucleoapzyme with superior catalytic activity toward ...Continue Reading

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Citations

Jul 15, 2018·Chembiochem : a European Journal of Chemical Biology·Simon Chi-Chin ShiuJulian A Tanner
Apr 27, 2017·Angewandte Chemie·Yuwei HuItamar Willner
Nov 2, 2019·Organic & Biomolecular Chemistry·Ji Hye YumHiroshi Sugiyama
Jan 18, 2020·Chemical Communications : Chem Comm·Jiawei WangJun Zhou
Feb 8, 2020·Dalton Transactions : an International Journal of Inorganic Chemistry·Mannar R MauryaJoão Costa Pessoa
Mar 2, 2018·Chemical Communications : Chem Comm·Yu TokuraTanja Weil
Jul 3, 2020·Mikrochimica Acta·Yaqing LiuZhanhui Tao
Mar 30, 2016·Chemical Communications : Chem Comm·H Bauke AlbadaItamar Willner
Jan 30, 2020·Chemical Communications : Chem Comm·Yan LiuLiang Xu
Sep 7, 2019·Journal of Materials Chemistry. B, Materials for Biology and Medicine·Haiyang LinFeng Li
Mar 26, 2019·Chembiochem : a European Journal of Chemical Biology·Yonatan BiniuriItamar Willner
May 8, 2018·Chemical Science·Moira L FlanaganDavid J Gorin
Jan 23, 2020·Nature Communications·Valerie Vaissier WelbornTeresa Head-Gordon
Jun 20, 2017·Journal of the American Chemical Society·Shan WangItamar Willner
Sep 4, 2019·Journal of the American Chemical Society·Yonatan BiniuriItamar Willner
Jul 14, 2017·ACS Applied Materials & Interfaces·Xiaoqiang WangFang Huang
Apr 19, 2018·ACS Synthetic Biology·Manish DebnathJyotirmayee Dash
Nov 19, 2021·Chemical Communications : Chem Comm·Jordi F KeijzerBauke Albada

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Methods Mentioned

BETA
SELEX
circular dichroism

Software Mentioned

Fold
YASARA Structure
MC
Sym
POVRay
AMBER03
YASARA

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