DNA Origami-Enabled Plasmonic Sensing

Abstract

The reliable programmability of DNA origami makes it an extremely attractive tool for bottom-up self-assembly of complex nanostructures. Utilizing this property for the tuned arrangement of plasmonic nanoparticles holds great promise particularly in the field of biosensing. Plasmonic particles are beneficial for sensing in multiple ways, from enhancing fluorescence to enabling a visualization of the nanoscale dynamic actuation via chiral rearrangements. In this Perspective, we discuss the recent developments and possible future directions of DNA origami-enabled plasmonic sensing systems. We start by discussing recent advancements in the area of fluorescence-based plasmonic sensing using DNA origami. We then move on to surface-enhanced Raman spectroscopy sensors followed by chiral sensing, both utilizing DNA origami nanostructures. We conclude by providing our own views on the future prospects for plasmonic biosensors enabled using DNA origami.

Single antibody detection in a DNA origami nanoantenna

“…This unprecedented addressability of the DNA origami approach allows arranging different biosensing components, introducing new biorecognition elements and multiplexing strategies, as well as the implementation of signal transduction and amplification mechanisms. Using DNA origami, a number of biosensors have been developed capable of single-molecule detection of DNA and RNA (Ke et al, 2008;Zhang et al, 2010a;Kuzuya et al, 2011;Ochmann et al, 2017;Selnihhin et al, 2018;Funck et al, 2018;Trofymchuk et al, 2021), single nucleotide polymorphisms (Zhang et al, 2010b;Subramanian et al, 2011), specific metal ions (Ke et al, 2008;Marras et al, 2018), as well as various protein biomarkers (Rinker et al, 2008;Koirala et al, 2014;Godonoga et al, 2016;Raveendran et al, 2020) among many others (Wang et al, 2017a(Wang et al, , 2017b(Wang et al, , 2020Chandrasekaran, 2017;Ke et al, 2018;Loretan et al, 2020;Dass et al, 2021).…”

DNA Studies: Latest Spectroscopic and Structural Approaches

“…It is held in place with the help of hundreds of shorter complementary oligonucleotides, known as the “staple strands”. Through a precise software-based design (CaDNAno [ 46 , 47 ], SARSE [ 48 ], CanDO [ 49 , 50 ]) and the proper thermal treatments, it was possible to create planar objects (smiles, squares, triangles, circles, rectangles, stars [ 50 , 51 ]), as well as three-dimensional structures (cubes, cylinders, gears [ 33 , 34 , 52 ]). In all cases, the DNA objects are addressed.…”

“…DNA nanotechnology has shown increasing potential in its application in several areas, spanning from life sciences to plasmonic and biophysics. Recently, we have seen a rise in structures with programmed features devoted to the predesigned assembly of, e.g., nanoparticles [30] for different purposes, such as biosensing, imaging, and detection [31][32][33]. In recent years, various dynamic plasmonic DNA structures, based on the controlled structural reconfiguration after the exposure to the environment were realized, e.g., reversible and light-responsive DNA-locks [34], DNA-metamolecules to manipulate chirality [35], and plasmon rulers to monitor gold/silver nanoparticles distance and separation [36].…”

Emission Manipulation by DNA Origami‐Assisted Plasmonic Nanoantennas

“…DNA origami is a bottom-up fabrication method to create platforms that support the building of complex, hierarchical, and hybrid structures. [50][51][52][53][54][55][56][57][58][59][60] A DNA origami nanobreadboard is obtained by folding a long single-stranded DNA (scaffold) of a known sequence by hundreds of short oligonucleotides called staple strands, each one corresponding to a unique location in the scaffold. [50] DNA origami is a tremendously addressable platform due to the Watson-Crick base pairing nature of the DNA and the availability of the sequence information of scaffold and staple strands.…”

“…[97,98] There have been many reviews on origami design, synthesis, and functionalization [51,99,100] and how DNA origami is used to construct complex nanostructures. [53][54][55][56][57] During the preparation of this manuscript, reviews on DNA origami-assisted nanostructures for sensing [59] and spectroscopy [60] have also been just published.…”