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Wang H, Li M, Zhang H, Yang L. A Tunable Threshold Colorimetric DNA Logic Gate for Intuitive Assessment of Chemical Contaminant Exceedance. Anal Chem 2024; 96:11862-11868. [PMID: 38989925 DOI: 10.1021/acs.analchem.4c01529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Current molecular logic gates are predominantly focused on the qualitative assessment of target presence, which has certain limitations in scenarios requiring quantitative assessment, such as chemical contaminant monitoring. To bridge this gap, we have developed a novel DNA logic gate featuring a tunable threshold, specifically tailored to the limits of contaminants. At the core of this logic gate is a DNA-gold nanoparticle (AuNP) hybrid film that incorporates aptamer sequences to selectively bind to acetamiprid (ACE) and atrazine (ATR). Upon interaction with these contaminants, the film degrades, releasing AuNPs that, in the presence of Hg2+, catalyze the oxidation of TMB, resulting in a visible blue coloration on test paper. This aptamer-enabled process effectively establishes an OR logic gate, with ACE and ATR as inputs and the appearance of blue color as the output. A key innovation of our system is its tunable input threshold. By adjusting the concentration of Hg2+, we can fine-tune the color mutation points to match the input threshold to predefined limits, such as Maximum Residue Limits (MRLs). This alignment allows semiquantitative assessment of contaminant levels, providing intuitive visual feedback of contaminant exceedance. Validation experiments with spiked samples confirm its accuracy and reliability by closely matching HPLC results. Therefore, our colorimetric DNA logic gate is emerging as a promising tool for easy and semiquantitative monitoring of chemical contaminants across diverse applications.
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Affiliation(s)
- Hao Wang
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| | - Mingming Li
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| | - Hanyang Zhang
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| | - Limin Yang
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
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Yang U, Kang B, Yong MJ, Yang DH, Choi SY, Je JH, Oh SS. Type-Independent 3D Writing and Nano-Patterning of Confined Biopolymers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207403. [PMID: 36825681 PMCID: PMC10161081 DOI: 10.1002/advs.202207403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/07/2023] [Indexed: 05/06/2023]
Abstract
Biopolymers are essential building blocks that constitute cells and tissues with well-defined molecular structures and diverse biological functions. Their three-dimensional (3D) complex architectures are used to analyze, control, and mimic various cells and their ensembles. However, the free-form and high-resolution structuring of various biopolymers remain challenging because their structural and rheological control depend critically on their polymeric types at the submicron scale. Here, direct 3D writing of intact biopolymers is demonstrated using a systemic combination of nanoscale confinement, evaporation, and solidification of a biopolymer-containing solution. A femtoliter solution is confined in an ultra-shallow liquid interface between a fine-tuned nanopipette and a chosen substrate surface to achieve directional growth of biopolymer nanowires via solvent-exclusive evaporation and concurrent solution supply. The evaporation-dependent printing is biopolymer type-independent, therefore, the 3D motor-operated precise nanopipette positioning allows in situ printing of nucleic acids, polysaccharides, and proteins with submicron resolution. By controlling concentrations and molecular weights, several different biopolymers are reproducibly patterned with desired size and geometry, and their 3D architectures are biologically active in various solvents with no structural deformation. Notably, protein-based nanowire patterns exhibit pin-point localization of spatiotemporal biofunctions, including target recognition and catalytic peroxidation, indicating their application potential in organ-on-chips and micro-tissue engineering.
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Affiliation(s)
- Un Yang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Byunghwa Kang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Moon-Jung Yong
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Dong-Hwan Yang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Si-Young Choi
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Jung Ho Je
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
- Nanoblesse, 85-11 (4th fl.) Namwon-Ro, Pohang, Gyeongbuk, 37883, South Korea
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
- Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon, 21983, South Korea
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Yang Y, Liu Z, Ma H, Cao M. Application of Peptides in Construction of Nonviral Vectors for Gene Delivery. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12224076. [PMID: 36432361 PMCID: PMC9693978 DOI: 10.3390/nano12224076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 05/29/2023]
Abstract
Gene therapy, which aims to cure diseases by knocking out, editing, correcting or compensating abnormal genes, provides new strategies for the treatment of tumors, genetic diseases and other diseases that are closely related to human gene abnormalities. In order to deliver genes efficiently to abnormal sites in vivo to achieve therapeutic effects, a variety of gene vectors have been designed. Among them, peptide-based vectors show superior advantages because of their ease of design, perfect biocompatibility and safety. Rationally designed peptides can carry nucleic acids into cells to perform therapeutic effects by overcoming a series of biological barriers including cellular uptake, endosomal escape, nuclear entrance and so on. Moreover, peptides can also be incorporated into other delivery systems as functional segments. In this review, we referred to the biological barriers for gene delivery in vivo and discussed several kinds of peptide-based nonviral gene vectors developed for overcoming these barriers. These vectors can deliver different types of genetic materials into targeted cells/tissues individually or in combination by having specific structure-function relationships. Based on the general review of peptide-based gene delivery systems, the current challenges and future perspectives in development of peptidic nonviral vectors for clinical applications were also put forward, with the aim of providing guidance towards the rational design and development of such systems.
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Affiliation(s)
- Yujie Yang
- State Key Laboratory of Heavy Oil Processing, Department of Biological and Energy Chemical Engineering, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Zhen Liu
- State Key Laboratory of Heavy Oil Processing, Department of Biological and Energy Chemical Engineering, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Hongchao Ma
- State Key Laboratory of Heavy Oil Processing, Department of Biological and Energy Chemical Engineering, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
| | - Meiwen Cao
- State Key Laboratory of Heavy Oil Processing, Department of Biological and Energy Chemical Engineering, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China
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Saikia J, Dharmalingam K, Anandalakshmi R, Redkar AS, Bhat VT, Ramakrishnan V. Electric field modulated peptide based hydrogel nanocatalysts. SOFT MATTER 2021; 17:9725-9735. [PMID: 34643203 DOI: 10.1039/d1sm00724f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The ability to modulate self-assembly is the key to manufacture application-oriented materials. In this study, we investigated the effect of three independent variables that can modulate the catalytic activity of self-assembling peptides. The first two variables, amino acid sequence and its stereochemistry, were examined for their specific roles in the epitaxial growth and hydrogelation properties of a series of catalytic tripeptides. We observed that aromatic π-π interactions that direct the self-assembly of designed peptides, and the catalytic properties of hydrogels, are governed by the position and chirality of the proline residue. Subsequently, the influence of the third variable, an external electric field, was also tested to confirm its catalytic efficiency for the asymmetric C-C bond-forming aldol reaction. In particular, the electric field treated pff and PFF gels showed 10 and 36% higher stereoselectivity, respectively, compared with the control. Structure-property analysis using CD and FTIR spectroscopy indicates the electric field-induced beta to non-beta conformational transition in the peptide secondary structure, which corroborates with its reduced cross-link density and fibril width, respectively. Amplitude sweep rheology of the gels suggests a decrease in the storage modulus, with increased field strength. The results showed that an electric field of optimal strength can modulate the physical characteristics of the hydrogel, which in turn is manifested in the observed difference in enantioselectivity.
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Affiliation(s)
- Jahnu Saikia
- Molecular Informatics and Design Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India.
| | - K Dharmalingam
- Advanced Energy & Materials Systems Laboratory, Department of Chemical Engineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | - R Anandalakshmi
- Advanced Energy & Materials Systems Laboratory, Department of Chemical Engineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Amay Sanjay Redkar
- Molecular Informatics and Design Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India.
| | - Venugopal T Bhat
- Organic Synthesis and Catalysis Laboratory SRM Research Institute and Department of Chemistry SRM Institute of Science and Technology, Tamil Nadu 603203, India.
| | - Vibin Ramakrishnan
- Molecular Informatics and Design Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India.
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Liu J, Ni R, Chau Y. A self-assembled peptidic nanomillipede to fabricate a tuneable hybrid hydrogel. Chem Commun (Camb) 2019; 55:7093-7096. [DOI: 10.1039/c9cc02967b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptidic ‘nanomillipede’, consisting of worm-like nanoscale ‘body’ and cysteine-terminated ‘legs’, was synthesized, tuned (with ultrasound) and utilized to crosslink the vinyl sulfone-modified dextran to form hybrid hydrogels with soft-tissue mimicking tuneable mechanical strength, self-healing property, and tuneable shear-thinning property, thereby indicating their potential use in tissue engineering and drug delivery.
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Affiliation(s)
- Jianhui Liu
- Department of Chemical and Biological Engineering
- the Hong Kong University of Science and Technology
- Clear Water Bay
- Hong Kong
| | - Rong Ni
- Department of Chemical and Biological Engineering
- the Hong Kong University of Science and Technology
- Clear Water Bay
- Hong Kong
- Institute for Advanced Study
| | - Ying Chau
- Department of Chemical and Biological Engineering
- the Hong Kong University of Science and Technology
- Clear Water Bay
- Hong Kong
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