Chemistries for DNA nanotechnology

M Madsen, KV Gothelf - Chemical reviews, 2019 - ACS Publications
The predictable nature of DNA interactions enables the programmable assembly of highly
advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger …

Aptamer–Protein Interactions: From Regulation to Biomolecular Detection

C Ji, J Wei, L Zhang, X Hou, J Tan, Q Yuan… - Chemical …, 2023 - ACS Publications
Serving as the basis of cell life, interactions between nucleic acids and proteins play
essential roles in fundamental cellular processes. Aptamers are unique single-stranded …

Rapid and efficient detection of the SARS-CoV-2 spike protein using an electrochemical aptamer-based sensor

A Idili, C Parolo, R Alvarez-Diduk, A Merkoçi - ACS sensors, 2021 - ACS Publications
The availability of sensors able to rapidly detect SARS-CoV-2 directly in biological fluids in a
single step would allow performing massive diagnostic testing to track in real time and …

Small‐Molecule Quenchers for Förster Resonance Energy Transfer: Structure, Mechanism, and Applications

B Fang, Y Shen, B Peng, H Bai, L Wang… - Angewandte …, 2022 - Wiley Online Library
For fluorogenic probes, Förster resonance energy transfer (FRET) is one of the most widely
used mechanisms to realize the detection of biochemical activities. Dark quenchers relax …

Duplexed aptamers: history, design, theory, and application to biosensing

JD Munzar, A Ng, D Juncker - Chemical Society Reviews, 2019 - pubs.rsc.org
Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a
cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents …

Comparison of aptamer signaling mechanisms reveals disparities in sensor response and strategies to eliminate false signals

O Alkhamis, J Canoura, C Willis, L Wang… - Journal of the …, 2023 - ACS Publications
Aptamers are nucleic acid-based affinity reagents that have been incorporated into a variety
of molecular sensor formats. However, many aptamer sensors exhibit insufficient sensitivity …

IDT SciTools: a suite for analysis and design of nucleic acid oligomers

R Owczarzy, AV Tataurov, Y Wu… - Nucleic acids …, 2008 - academic.oup.com
DNA and RNA oligomers are used in a myriad of diverse biological and biochemical
experiments. These oligonucleotides are designed to have unique biophysical, chemical …

Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments

M Levitus, S Ranjit - Quarterly reviews of biophysics, 2011 - cambridge.org
The breakthroughs in single molecule spectroscopy of the last decade and the recent
advances in super resolution microscopy have boosted the popularity of cyanine dyes in …

[HTML][HTML] Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement

NEC Haley, TE Ouldridge, I Mullor Ruiz… - Nature …, 2020 - nature.com
Recent years have seen great advances in the development of synthetic self-assembling
molecular systems. Designing out-of-equilibrium architectures, however, requires a more …

[HTML][HTML] Programmable energy landscapes for kinetic control of DNA strand displacement

RRF Machinek, TE Ouldridge, NEC Haley… - Nature …, 2014 - nature.com
DNA is used to construct synthetic systems that sense, actuate, move and compute. The
operation of many dynamic DNA devices depends on toehold-mediated strand …