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DNA Origami and Aptamer Assemblies
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DNA Origami and Aptamer Assemblies

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: closed (1 October 2018) | Viewed by 44662

Special Issue Editors

Dr. David E. Volk

E-Mail Website
Guest Editor
Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
Interests: chemistry; aptamers; thioaptamers; cancer; 3D printing
Special Issues, Collections and Topics in MDPI journals
Dr. Varatharasa Thiviyanathan

E-Mail Website
Guest Editor
School of Dentistry, University of Texas Health Science Center, Houston, TX 77030, USA
Interests: aptamers; nuclear magnetic resonance

Special Issue Information

Dear colleagues,

In the last decade, the field of DNA origami has gone from infancy to a field with a suite of building techniques for creating a wide variety of structures. Using DNA building blocks formed into wedges, bricks, and tubes, complex 3D objects can be created. Indeed, an object over a billion daltons has been made. Other methods using fractal assembly or bacteriophages can create complicated machines containing built-in DNAzymes to act as molecular scissors to create scaffolds with custom voids, hinges, designer apertures, or even nanorobots. Although creating shapes like a mini Mona Lisa or a rabbit is interesting, the next phase of DNA origami seeks to develop tools that are useful as diagnostic agents or drug delivery vehicles, at a large scale and at a reasonable cost. In this regard, the combination of DNA origami with aptamer assemblies or complimentary aptamer pairs may play a role, as could further developments in predictive software.

In this Special Issue, we welcome original research or review articles on any topic related to “DNA Origami and Aptamer Assemblies”. We look forward to your contributions.

Dr. David Volk
Dr. Varatharasa Thiviyanathan
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • DNA origami
  • aptamer
  • DNA cage
  • macromolecular structures
  • computational biology
  • diagnostic agents
  • drug delivery vehicles
  • DNAzymes

Published Papers (6 papers)

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Research

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7 pages, 1760 KiB  
Article
Tracking Biodistribution of Myeloid-Derived Cells in Murine Models of Breast Cancer
by Jun Li, Junhua Mai, Louis Hinkle, Daniel Lin, Jingxin Zhang, Xiaoling Liu, Maricela R. Ramirez, Youli Zu, Ganesh L. Lokesh, David E. Volk and Haifa Shen
Genes 2019, 10(4), 297; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10040297 - 12 Apr 2019
Cited by 2 | Viewed by 3639
Abstract
A growing tumor is constantly secreting inflammatory chemokines and cytokines that induce release of immature myeloid cells, including myeloid-derived suppressor cells (MDSCs) and macrophages, from the bone marrow. These cells not only promote tumor growth, but also prepare distant organs for tumor metastasis. [...] Read more.
A growing tumor is constantly secreting inflammatory chemokines and cytokines that induce release of immature myeloid cells, including myeloid-derived suppressor cells (MDSCs) and macrophages, from the bone marrow. These cells not only promote tumor growth, but also prepare distant organs for tumor metastasis. On the other hand, the myeloid-derived cells also have phagocytic potential, and can serve as vehicles for drug delivery. We have previously identified thioaptamers that bind a subset of MDSCs with high affinity and specificity. In the current study, we applied one of the thioaptamers as a probe to track myeloid cell distribution in the bone, liver, spleen and tumor in multiple murine models of breast cancer including the 4T1 syngeneic model and MDA-MB-231 and SUM159 xenograft models. Information generated from this study will facilitate further understanding of tumor growth and metastasis, and predict biodistribution patterns of cell-mediated drug delivery. Full article
(This article belongs to the Special Issue DNA Origami and Aptamer Assemblies)
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Review

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20 pages, 2578 KiB  
Review
The Fusion of Lipid and DNA Nanotechnology
by Es Darley, Jasleen Kaur Daljit Singh, Natalie A. Surace, Shelley F. J. Wickham and Matthew A. B. Baker
Genes 2019, 10(12), 1001; https://0-doi-org.brum.beds.ac.uk/10.3390/genes10121001 - 03 Dec 2019
Cited by 14 | Viewed by 5848
Abstract
Lipid membranes form the boundary of many biological compartments, including organelles and cells. Consisting of two leaflets of amphipathic molecules, the bilayer membrane forms an impermeable barrier to ions and small molecules. Controlled transport of molecules across lipid membranes is a fundamental biological [...] Read more.
Lipid membranes form the boundary of many biological compartments, including organelles and cells. Consisting of two leaflets of amphipathic molecules, the bilayer membrane forms an impermeable barrier to ions and small molecules. Controlled transport of molecules across lipid membranes is a fundamental biological process that is facilitated by a diverse range of membrane proteins, including ion-channels and pores. However, biological membranes and their associated proteins are challenging to experimentally characterize. These challenges have motivated recent advances in nanotechnology towards building and manipulating synthetic lipid systems. Liposomes—aqueous droplets enclosed by a bilayer membrane—can be synthesised in vitro and used as a synthetic model for the cell membrane. In DNA nanotechnology, DNA is used as programmable building material for self-assembling biocompatible nanostructures. DNA nanostructures can be functionalised with hydrophobic chemical modifications, which bind to or bridge lipid membranes. Here, we review approaches that combine techniques from lipid and DNA nanotechnology to engineer the topography, permeability, and surface interactions of membranes, and to direct the fusion and formation of liposomes. These approaches have been used to study the properties of membrane proteins, to build biosensors, and as a pathway towards assembling synthetic multicellular systems. Full article
(This article belongs to the Special Issue DNA Origami and Aptamer Assemblies)
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14 pages, 4226 KiB  
Review
DNA-Based Super-Resolution Microscopy: DNA-PAINT
by Daniel J. Nieves, Katharina Gaus and Matthew A. B. Baker
Genes 2018, 9(12), 621; https://0-doi-org.brum.beds.ac.uk/10.3390/genes9120621 - 11 Dec 2018
Cited by 50 | Viewed by 16532
Abstract
Super-resolution microscopies, such as single molecule localization microscopy (SMLM), allow the visualization of biomolecules at the nanoscale. The requirement to observe molecules multiple times during an acquisition has pushed the field to explore methods that allow the binding of a fluorophore to a [...] Read more.
Super-resolution microscopies, such as single molecule localization microscopy (SMLM), allow the visualization of biomolecules at the nanoscale. The requirement to observe molecules multiple times during an acquisition has pushed the field to explore methods that allow the binding of a fluorophore to a target. This binding is then used to build an image via points accumulation for imaging nanoscale topography (PAINT), which relies on the stochastic binding of a fluorescent ligand instead of the stochastic photo-activation of a permanently bound fluorophore. Recently, systems that use DNA to achieve repeated, transient binding for PAINT imaging have become the cutting edge in SMLM. Here, we review the history of PAINT imaging, with a particular focus on the development of DNA-PAINT. We outline the different variations of DNA-PAINT and their applications for imaging of both DNA origamis and cellular proteins via SMLM. Finally, we reflect on the current challenges for DNA-PAINT imaging going forward. Full article
(This article belongs to the Special Issue DNA Origami and Aptamer Assemblies)
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15 pages, 958 KiB  
Review
Advances on Aptamers against Protozoan Parasites
by Juan David Ospina-Villa, César López-Camarillo, Carlos A. Castañón-Sánchez, Jacqueline Soto-Sánchez, Esther Ramírez-Moreno and Laurence A. Marchat
Genes 2018, 9(12), 584; https://0-doi-org.brum.beds.ac.uk/10.3390/genes9120584 - 28 Nov 2018
Cited by 26 | Viewed by 4452
Abstract
Aptamers are single-stranded DNA or RNA sequences with a unique three-dimensional structure that allows them to recognize a particular target with high affinity. Although their specific recognition activity could make them similar to monoclonal antibodies, their ability to bind to a large range [...] Read more.
Aptamers are single-stranded DNA or RNA sequences with a unique three-dimensional structure that allows them to recognize a particular target with high affinity. Although their specific recognition activity could make them similar to monoclonal antibodies, their ability to bind to a large range of non-immunogenic targets greatly expands their potential as tools for diagnosis, therapeutic agents, detection of food risks, biosensors, detection of toxins, drug carriers, and nanoparticle markers, among others. One aptamer named Pegaptanib is currently used for treating macular degeneration associated with age, and many other aptamers are in different clinical stages of development of evaluation for various human diseases. In the area of parasitology, research on aptamers has been growing rapidly in the past few years. Here we describe the development of aptamers raised against the main protozoan parasites that affect hundreds of millions of people in underdeveloped and developing countries, remaining a major health concern worldwide, i.e. Trypanosoma spp., Plasmodium spp., Leishmania spp., Entamoeba histolytica, and Cryptosporidium parvuum. The latest progress made in this area confirmed that DNA and RNA aptamers represent attractive alternative molecules in the search for new tools to detect and treat these parasitic infections that affect human health worldwide. Full article
(This article belongs to the Special Issue DNA Origami and Aptamer Assemblies)
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20 pages, 3277 KiB  
Review
DNA Aptamers for the Functionalisation of DNA Origami Nanostructures
by Yusuke Sakai, Md. Sirajul Islam, Martyna Adamiak, Simon Chi-Chin Shiu, Julian Alexander Tanner and Jonathan Gardiner Heddle
Genes 2018, 9(12), 571; https://0-doi-org.brum.beds.ac.uk/10.3390/genes9120571 - 23 Nov 2018
Cited by 31 | Viewed by 8772
Abstract
DNA origami has emerged in recent years as a powerful technique for designing and building 2D and 3D nanostructures. While the breadth of structures that have been produced is impressive, one of the remaining challenges, especially for DNA origami structures that are intended [...] Read more.
DNA origami has emerged in recent years as a powerful technique for designing and building 2D and 3D nanostructures. While the breadth of structures that have been produced is impressive, one of the remaining challenges, especially for DNA origami structures that are intended to carry out useful biomedical tasks in vivo, is to endow them with the ability to detect and respond to molecules of interest. Target molecules may be disease indicators or cell surface receptors, and the responses may include conformational changes leading to the release of therapeutically relevant cargo. Nucleic acid aptamers are ideally suited to this task and are beginning to be used in DNA origami designs. In this review, we consider examples of uses of DNA aptamers in DNA origami structures and summarise what is currently understood regarding aptamer-origami integration. We review three major roles for aptamers in such applications: protein immobilisation, triggering of structural transformation, and cell targeting. Finally, we consider future perspectives for DNA aptamer integration with DNA origami. Full article
(This article belongs to the Special Issue DNA Origami and Aptamer Assemblies)
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20 pages, 957 KiB  
Review
Aptamer Chimeras for Therapeutic Delivery: The Challenging Perspectives
by Carla Lucia Esposito, Silvia Catuogno, Gerolama Condorelli, Paola Ungaro and Vittorio De Franciscis
Genes 2018, 9(11), 529; https://0-doi-org.brum.beds.ac.uk/10.3390/genes9110529 - 31 Oct 2018
Cited by 32 | Viewed by 4779
Abstract
Nucleic acid-based aptamers have emerged as efficient delivery carriers of therapeutics. Thanks to their unique features, they can be, to date, considered one of the best targeting moieties, allowing the specific recognition of diseased cells and avoiding unwanted off-target effects on healthy tissues. [...] Read more.
Nucleic acid-based aptamers have emerged as efficient delivery carriers of therapeutics. Thanks to their unique features, they can be, to date, considered one of the best targeting moieties, allowing the specific recognition of diseased cells and avoiding unwanted off-target effects on healthy tissues. In this review, we revise the most recent contributes on bispecific and multifunctional aptamer therapeutic chimeras. We will discuss key examples of aptamer-mediated delivery of nucleic acid and peptide-based therapeutics underlying their great potentiality and versatility. Achieved objectives and challenges will be highlighted as well. Full article
(This article belongs to the Special Issue DNA Origami and Aptamer Assemblies)
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