Query: dye DNA origami

Candidate papers:

abstract: Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH induced, switchable assembly and dissociation of triplex DNA bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH responsive systems and materials are described. Examples include semiconductor loaded DNA stabilized microcapsules, DNA functionalized dye loaded metal organic frameworks (MOFs) and the pH induced release of the loads. Furthermore, the design of stimuli responsive DNA based hydrogels undergoing reversible pH induced hydrogel to solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.
author_names: Yuwei Hu

Alessandro Cecconello

Andrea Idili

Francesco Ricci

Itamar Willner
title: Triplex DNA Nanostructures: From Basic Properties to Applications.
venue: Angewandte Chemie
year: 2017

abstract: Antibiotics such as the quinolones and fluoroquinolones kill bacterial pathogens ultimately through DNA damage. They target the essential type IIA topoisomerases in bacteria by stabilising the normally transient double strand break state which is created to modify the supercoiling state of the DNA. Here we discuss the development of these antibiotics and their method of action. Existing methods for DNA damage visualisation, such as the comet assay and immunofluorescence imaging can often only be analysed qualitatively and this analysis is subjective. We describe a putative single molecule fluorescence technique for quantifying DNA damage via the total fluorescence intensity of a DNA origami tile fully saturated with an intercalating dye, along with the optical requirements for how to implement these into a light microscopy imaging system capable of single molecule millisecond timescale imaging. This system promises significant improvements in reproducibility of the quantification of DNA damage over traditional techniques.
author_names: Helen Miller

Adam J M Wollman

Mark C Leake
title: Designing a Single Molecule Biophysics Tool for Characterising DNA Damage for Techniques that Kill Infectious Pathogens Through DNA Damage Effects.
venue: Advances in experimental medicine and biology
year: 2016

abstract: DNA origami nanocarriers have emerged as a promising tool for many biomedical applications, such as biosensing, targeted drug delivery, and cancer immunotherapy. These highly programmable nanoarchitectures are assembled into any shape or size with nanoscale precision by folding a single stranded DNA scaffold with short complementary oligonucleotides. The standard scaffold strand used to fold DNA origami nanocarriers is usually the M13mp18 bacteriophage's circular single stranded DNA genome with limited design flexibility in terms of the sequence and size of the final objects. However, with the recent progress in automated DNA origami design allowing for increasing structural complexity and the growing number of applications, the need for scalable methods to produce custom scaffolds has become crucial to overcome the limitations of traditional methods for scaffold production. Improved scaffold synthesis strategies will help to broaden the use of DNA origami for more biomedical applications. To this end, several techniques have been developed in recent years for the scalable synthesis of single stranded DNA scaffolds with custom lengths and sequences. This review focuses on these methods and the progress that has been made to address the challenges confronting custom scaffold production for large scale DNA origami assembly.
author_names: Joshua Bush

Shrishti Singh

Merlyn Vargas

Esra Oktay

Chih-Hsiang Hu

Remi Veneziano
title: Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies
venue: Molecules
year: 2020

abstract: DNA nanotechnology is a powerful and promising tool for the development of nanoscale devices for numerous and diverse applications. One of the greatest potential fields of application for DNA nanotechnology is in biomedicine, in particular biosensing. Thanks to the control over their size, shape, and fabrication, DNA origami represents a unique opportunity to assemble dynamic and complex devices with precise and predictable structural characteristics. Combined with the addressability and flexibility of the chemistry for DNA functionalization, DNA origami allows the precise design of sensors capable of detecting a large range of different targets, encompassing RNA, DNA, proteins, small molecules, or changes in physico chemical parameters, that could serve as diagnostic tools. Here, we review some recent, salient developments in DNA origami based sensors centered on optical detection methods (readout) with a special emphasis on the sensitivity, the selectivity, and response time. We also discuss challenges that still need to be addressed before this approach can be translated into robust diagnostic devices for bio medical applications.
author_names: Morgane Loretan

Ivana Domljanovic

Mathias Lakatos

Curzio Ruegg

Guillermo P Acuna
title: DNA Origami as Emerging Technology for the Engineering of Fluorescent and Plasmonic Based Biosensors
venue: Materials
year: 2020

abstract: Fluorescent dyes used for single molecule spectroscopy can undergo millions of excitation emission cycles before photobleaching. Due to the upconcentration of light in a plasmonic hotspot, the conditions for fluorescent dyes are even more demanding in DNA origami nanoantennas. Here, we briefly review the current state of fluorophore stabilization for single molecule imaging and reveal additional factors relevant in the context of plasmonic fluorescence enhancement. We show that despite the improved photostability of single molecule fluorophores by DNA origami nanoantennas, their performance in the intense electric fields in plasmonic hotspots is still limited by the underlying photophysical processes, such as formation of dim states and photoisomerization. These photophysical processes limit the photon count rates, increase heterogeneity and aggravate quantification of fluorescence enhancement factors. These factors also reduce the time resolution that can be achieved in biophysical single molecule experiments. Finally, we show how the photophysics of a DNA hairpin assay with a fluorophore quencher pair can be influenced by plasmonic DNA origami nanoantennas leading to implications for their use in fluorescence based diagnostic assays. Especially, we show that such assays can produce false positive results by premature photobleaching of the dark quencher.
author_names: Lennart Grabenhorst

Kateryna Trofymchuk

Florian Steiner

Viktorija Glembockyte

Philip Tinnefeld
title: Fluorophore photostability and saturation in the hotspot of DNA origami nanoantennas.
venue: Methods and applications in fluorescence
year: 2020

abstract: The DNA origami technique itself is considered a milestone of DNA nanotechnology and DNA origami nanorulers represent the first widespread application of this technique. DNA origami nanorulers are used to demonstrate the capabilities of techniques and are valuable training samples. They have meanwhile been developed for a multitude of microscopy methods including optical microscopy, atomic force microscopy, and electron microscopy, and their unique properties are further exploited to develop point light sources, brightness references, nanophotonic test structures, and alignment tools for correlative microscopy. In this perspective, we provide an overview of the basics of DNA origami nanorulers and their increasing applications in fields of optical and especially super resolution fluorescence microscopy. In addition, emerging applications of reference structures based on DNA origami are discussed together with recent developments.
author_names: Michael Scheckenbach

J A Bauer

Jonas Zahringer

Florian Selbach

Philip Tinnefeld
title: DNA origami nanorulers and emerging reference structures
year: 2020

abstract: Biosensors are small but smart devices responding to the external stimulus, widely used in many fields including clinical diagnosis, healthcare and environment monitoring, etc. Moreover, there is still a pressing need to fabricate sensitive, stable, reliable sensors at present. DNA origami technology is able to not only construct arbitrary shapes in two/three dimension but also control the arrangement of molecules with different functionalities precisely. The functionalization of DNA origami nanostructure endows the sensing system potential of filling in weak spots in traditional DNA based biosensor. Herein, we mainly review the construction and sensing mechanisms of sensing platforms based on DNA origami nanostructure according to different signal output strategies. It will offer guidance for the application of DNA origami structures functionalized by other materials. We also point out some promising directions for improving performance of biosensors.
author_names: Shuang-Yue Wang

Zhaoyu Zhou

Ningning Ma

Sichang Yang

Kai Li

Chao Teng

Yonggang Ke

Ye Tian
title: DNA Origami Enabled Biosensors
venue: Sensors
year: 2020

abstract: DNA as a biomaterial has evoked great interest as a potential platform for therapeutics and diagnostics and as hydrogel scaffolds due to the relative ease of programming its robust and uniform shape, site specific functionality and controlled responsive behavior. However, for a stable self assembled product, a relatively high cation concentration is required to prevent denaturation. Physiological and cell culture conditions do not match these concentrations and present additional nucleases that cause a serious threat to the integrity of DNA based materials. For the translation of this promising technology towards bioengineering challenges, stability needs to be guaranteed. Over the past years, various methods have been developed addressing the stability related weaknesses of DNA origami. This mini review explains the common stability issues and compares the stabilization strategies recently developed. We present a detailed overview of each method in order to ease the selection process on which method to use for future users of DNA origami as a biomaterial.
author_names: Hale Bila

Eva E Kurisinkal

Maartje M C Bastings
title: Engineering a stable future for DNA origami as a biomaterial.
venue: Biomaterials science
year: 2019

abstract: Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami based protein networks are discussed, including protein DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.
author_names: Gezhi Kong

Mengyi Xiong

Lu Liu

Ling-wei Hu

Hongmin Meng

Guoliang Ke

Xiao-Bing Zhang

Weihong Tan
title: DNA origami based protein networks: from basic construction to emerging applications.
venue: Chemical Society reviews
year: 2020

abstract: The review article provides an overview of the DNA origami technique for fabricating nanomaterials with specific patterns and structures.
author_names: Raima M Larter
title: Using DNA origami to produce nanoscale patterns and structures
year: 2020