Aptamers as Functional Modules for DNA Nanostructures

Simon Chi-Chin Shiu; Andrew B Kinghorn; Wei Guo; Liane S Slaughter; Danyang Ji; Xiaoyong Mo; Lin Wang; Ngoc Chau Tran; Chun Kit Kwok; Anderson Ho Cheung Shum; Edmund Chun Ming Tse; Julian A Tanner

doi:10.1007/978-1-0716-3028-0_17

Aptamers as Functional Modules for DNA Nanostructures

Methods Mol Biol. 2023:2639:301-337. doi: 10.1007/978-1-0716-3028-0_17.

Authors

Simon Chi-Chin Shiu¹, Andrew B Kinghorn¹, Wei Guo², Liane S Slaughter³, Danyang Ji^{4

5}, Xiaoyong Mo⁶, Lin Wang¹, Ngoc Chau Tran¹, Chun Kit Kwok^{4

5}, Anderson Ho Cheung Shum², Edmund Chun Ming Tse^{6

7}, Julian A Tanner⁸

Affiliations

¹ School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
² Microfluidics and Soft Matter Group, Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
³ Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China.
⁴ Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
⁵ Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
⁶ Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
⁷ HKU Zhejiang Institute of Research and Innovation, Zhejiang, China.
⁸ School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China. jatanner@hku.hk.

PMID: 37166724
DOI: 10.1007/978-1-0716-3028-0_17

Abstract

Watson-Crick base-pairing of DNA allows the nanoscale fabrication of biocompatible synthetic nanostructures for diagnostic and therapeutic biomedical purposes. DNA nanostructure design elicits exquisite control of shape and conformation compared to other nanoparticles. Furthermore, nucleic acid aptamers can be coupled to DNA nanostructures to allow interaction and response to a plethora of biomolecules beyond nucleic acids. When compared to the better-known approach of using protein antibodies for molecular recognition, nucleic acid aptamers are bespoke with the underlying DNA nanostructure backbone and have various other stability, synthesis, and cost advantages. Here, we provide detailed methodologies to synthesize and characterize aptamer-enabled DNA nanostructures. The methods described can be generally applied to various designs of aptamer-enabled DNA nanostructures with a wide range of applications both within and beyond biomedical nanotechnology.

Keywords: Aptamers; Atomic force microscopy; Bioanalytical sensors; Biophysical assays; Circular dichroism; DNA nanostructures; Droplet microfluidic SELEX; Transmission electron microscopy.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Aptamers, Nucleotide* / chemistry
DNA / chemistry
Nanostructures* / chemistry
Nanotechnology / methods
Nucleic Acid Conformation
Nucleic Acids* / chemistry

Substances

Aptamers, Nucleotide
DNA
Nucleic Acids