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Piantanida L, Liddle JA, Hughes WL, Majikes JM. DNA nanostructure decoration: a how-to tutorial. NANOTECHNOLOGY 2024; 35:273001. [PMID: 38373400 DOI: 10.1088/1361-6528/ad2ac5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/18/2024] [Indexed: 02/21/2024]
Abstract
DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and developing protocols for reliable attachment routinely requires extensive trial and error. Additionally, the granular nature of scientific communication makes it difficult to discern general principles in DNA nanostructure decoration. This tutorial is a guidebook designed to minimize experimental bottlenecks and avoid dead-ends for those wishing to decorate DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocols.
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Affiliation(s)
- Luca Piantanida
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
| | - William L Hughes
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - Jacob M Majikes
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
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Ma KY, Perera-Gonzalez M, Langlois NI, Alzubi OM, Guimond JD, Flask CA, Clark HA. pH-responsive i-motif-conjugated nanoparticles for MRI analysis. SENSORS & DIAGNOSTICS 2024; 3:623-630. [PMID: 38646186 PMCID: PMC11025034 DOI: 10.1039/d3sd00285c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/21/2024] [Indexed: 04/23/2024]
Abstract
Gadolinium (Gd)-based contrast agents (CAs) are widely used to enhance anatomical details in magnetic resonance imaging (MRI). Significant research has expanded the field of CAs into bioresponsive CAs by modulating the signal to image and monitor biochemical processes, such as pH. In this work, we introduce the modular, dynamic actuation mechanism of DNA-based nanostructures as a new way to modulate the MRI signal based on the rotational correlation time, τR. We combined a pH-responsive oligonucleotide (i-motif) and a clinical standard CA (Gd-DOTA) to develop a pH-responsive MRI CA. The i-motif folds into a quadruplex under acidic conditions and was incorporated onto gold nanoparticles (iM-GNP) to achieve increased relaxivity, r1, compared to the unbound i-motif. In vitro, iM-GNP resulted in a significant increase in r1 over a decreasing pH range (7.5-4.5) with a calculated pKa = 5.88 ± 0.01 and a 16.7% change per 0.1 pH unit. In comparison, a control CA with a non-responsive DNA strand (T33-GNP) did not show a significant change in r1 over the same pH range. The iM-GNP was further evaluated in 20% human serum and demonstrated a 28.14 ± 11.2% increase in signal from neutral pH to acidic pH. This approach paves a path for novel programmable, dynamic DNA-based complexes for τR-modulated bioresponsive MRI CAs.
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Affiliation(s)
- Kristine Y Ma
- School of Biological and Health Systems Engineering, Arizona State University Tempe AZ USA
- Dept. of Bioengineering, Northeastern University Boston MA USA
| | | | - Nicole I Langlois
- Dept. of Chemistry and Chemical Biology, Northeastern University Boston MA USA
| | - Owen M Alzubi
- School of Biological and Health Systems Engineering, Arizona State University Tempe AZ USA
| | - Joseph D Guimond
- School of Biological and Health Systems Engineering, Arizona State University Tempe AZ USA
| | - Chris A Flask
- Depts. of Radiology, Biomedical Engineering, and Pediatrics, Case Western Reserve University Cleveland OH USA
| | - Heather A Clark
- School of Biological and Health Systems Engineering, Arizona State University Tempe AZ USA
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Zhang Y, Liao J, Li Z, Hu M, Bian C, Lin S. All fabric and flexible wearable sensors for simultaneous sweat metabolite detection and high-efficiency collection. Talanta 2023; 260:124610. [PMID: 37146456 DOI: 10.1016/j.talanta.2023.124610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/22/2023] [Accepted: 04/26/2023] [Indexed: 05/07/2023]
Abstract
Wearable sweat electrochemical sensors have attracted wide attention due to their advantages of non-invasive, portable, real-time monitoring, etc. However, existing sensors still have some problems with efficient sweat collection. Microfluidic channel technology and electrospinning technology are commonly used to collect sweat efficiently, but there are some limitations such as complex channel design and multiple spinning parameters. Besides, existing sensors are mostly based on flexible polymers, such as, PET, PDMS, PI and PI, which have limited wearability and permeability. Based on the above, all fabric and dual-function flexible wearable sweat electrochemical sensor is proposed in this paper. This sensor uses fabric as the raw material to implement the directional transport of sweat and the multi-component integrated detection dual functions. Meanwhile, the high-efficiency collection of sweat is obtained by a Janus fabric, wherein one side of the selected silk is superhydrophobic graft treated and the other side is hydrophilic plasma treated. Therefore, the resulting Janus fabric can effectively transfer sweat from the skin side to the electrode, and the minimum sweat droplet can reach 0.2 μL to achieve micro-volume collection. Besides, the patterned sensor, made of silk-based carbon cloth, is fabricated using a simple laser engraving, which could detect Na+, pH, and glucose instantaneously. As a result, these proposed sensors can achieve good sensing performance and high-efficiency sweat collection dual functionality; moreover, it has good flexibility and comfortable wearability.
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Affiliation(s)
- Yingwen Zhang
- School of Materials Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Jianjun Liao
- School of Ecological and Environmental Sciences, Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, 570228, China.
| | - Zehao Li
- School of Materials Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Mingxu Hu
- School of Materials Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Chao Bian
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, 100190, China
| | - Shiwei Lin
- School of Materials Science and Engineering, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China.
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Li Y, Arce A, Lucci T, Rasmussen RA, Lucks JB. Dynamic RNA synthetic biology: new principles, practices and potential. RNA Biol 2023; 20:817-829. [PMID: 38044595 PMCID: PMC10730207 DOI: 10.1080/15476286.2023.2269508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 08/23/2023] [Indexed: 12/05/2023] Open
Abstract
An increased appreciation of the role of RNA dynamics in governing RNA function is ushering in a new wave of dynamic RNA synthetic biology. Here, we review recent advances in engineering dynamic RNA systems across the molecular, circuit and cellular scales for important societal-scale applications in environmental and human health, and bioproduction. For each scale, we introduce the core concepts of dynamic RNA folding and function at that scale, and then discuss technologies incorporating these concepts, covering new approaches to engineering riboswitches, ribozymes, RNA origami, RNA strand displacement circuits, biomaterials, biomolecular condensates, extracellular vesicles and synthetic cells. Considering the dynamic nature of RNA within the engineering design process promises to spark the next wave of innovation that will expand the scope and impact of RNA biotechnologies.
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Affiliation(s)
- Yueyi Li
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Anibal Arce
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Tyler Lucci
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Rebecca A. Rasmussen
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
- Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, IL, USA
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