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Khajouei S, Ravan H, Ebrahimi A. DNA hydrogel-empowered biosensing. Adv Colloid Interface Sci 2020; 275:102060. [PMID: 31739981 PMCID: PMC7094116 DOI: 10.1016/j.cis.2019.102060] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 01/28/2023]
Abstract
DNA hydrogels as special members in the DNA nanotechnology have provided crucial prerequisites to create innovative gels owing to their sufficient stability, biocompatibility, biodegradability, and tunable multifunctionality. These properties have tailored DNA hydrogels for various applications in drug delivery, tissue engineering, sensors, and cancer therapy. Recently, DNA-based materials have attracted substantial consideration for the exploration of smart hydrogels, in which their properties can change in response to chemical or physical stimuli. In other words, these gels can undergo switchable gel-to-sol or sol-to-gel transitions upon application of different triggers. Moreover, various functional motifs like i-motif structures, antisense DNAs, DNAzymes, and aptamers can be inserted into the polymer network to offer a molecular recognition capability to the complex. In this manuscript, a comprehensive discussion will be endowed with the recognition capability of different kinds of DNA hydrogels and the alternation in physicochemical behaviors upon target introducing. Finally, we offer a vision into the future landscape of DNA based hydrogels in sensing applications.
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Affiliation(s)
- Sima Khajouei
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hadi Ravan
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Ali Ebrahimi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
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Detection of ciprofloxacin through surface plasmon resonance nanosensor with specific recognition sites. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2018; 29:1302-1318. [DOI: 10.1080/09205063.2018.1457417] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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HARA R, KAWAGUCHI H. Highly Sensitive Detection of Telomerase by Using G-Quartet DNA Binder Conjugated Polymeric Microspheres. KOBUNSHI RONBUNSHU 2012. [DOI: 10.1295/koron.69.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Barnett A, Goldys EM. Modeling of the SPR resolution enhancement for conventional and nanoparticle inclusive sensors by using statistical hypothesis testing. OPTICS EXPRESS 2010; 18:9384-97. [PMID: 20588785 DOI: 10.1364/oe.18.009384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
This paper describes a statistical approach that improves the detection accuracy in simulated experimental surface plasmon resonance (SPR) systems operated in a conventional angular readout scheme. Two SPR system have been investigated: a conventional one and a second one, containing absorbing metallic nanoparticles within the sensing layer. The modified Maxwell-Garnett model that optimally describes the experimental literature results was applied to modeling of the nanoparticle-inclusive sensor. Statistical hypothesis testing was then used to determine the limit of detection of the analyte and nanoparticles. Analyte concentrations as low as 1 pM, corresponding to the refractive index change of 4x10(-8) have been detected with optimized metal layers operated close to the nanoparticle absorption maximum. This is about one order of magnitude smaller than the values obtained in conventional SPR systems with nanoparticles and comparable to the phase-sensitive surface plasmon resonance detection.
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Affiliation(s)
- Anne Barnett
- MQ Photonics,Department of Physics and Engineering, Macquarie University,North Ryde 2109 NSW, Australia
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Homola J. Surface plasmon resonance sensors for detection of chemical and biological species. Chem Rev 2008; 108:462-93. [PMID: 18229953 DOI: 10.1021/cr068107d] [Citation(s) in RCA: 1756] [Impact Index Per Article: 109.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jirí Homola
- Institute of Photonics and Electronics ASCR, Chaberská 57, 182 51 Prague 8, Czech Republic.
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Rathinavelan T, Yathindra N. Molecular dynamics structures of peptide nucleic acid x DNA hybrid in the wild-type and mutated alleles of Ki-ras proto-oncogene--stereochemical rationale for the low affinity of PNA in the presence of an AC mismatch. FEBS J 2005; 272:4055-70. [PMID: 16098189 DOI: 10.1111/j.1742-4658.2005.04817.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The low affinity of peptide nucleic acid (PNA) to hybridize with DNA in the presence of a mismatch endows PNA with a high degree of discriminatory capacity that has been exploited in therapeutics for the selective inhibition of the expression of point-mutated genes. To obtain a structural basis for this intriguing property, molecular dynamics simulations are carried out on PNA x DNA duplexes formed at the Ki-ras proto-oncogene, comprising the point-mutated (GAT), and the corresponding wild-type (GGT) codon 12. The designed PNA forms an A...C mismatch with the wild-type sequence and a perfect A...T pair with the point mutated sequence. Results show that large movements in the pyrimidine base of the A...C mismatch cause loss of stacking, especially with its penultimate base, concomitant with a variable mismatch hydrogen bond, including its occasional absence. These, in turn, bring about dynamic water interactions in the vicinity of the mismatch. Enthalpy loss and the disproportionate entropy gain associated with these are implicated as the factors contributing to the increase in free energy and diminished stability of PNA x DNA duplex with the A...C mismatch. Absence of these in the isosequential DNA duplex, notwithstanding the A...C mismatch, is attributed to the differences in topology of PNA x DNA vis-à-vis DNA duplexes. It is speculated that similar effects might be responsible for the reduced stability observed in PNA x DNA duplexes containing other base pair mismatches, and also in mismatch containing PNA x DNA duplexes.
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Affiliation(s)
- Thenmalarchelvi Rathinavelan
- Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, India Institute of Bioinformatics and Applied Biotechnology, ITPB, Bangalore, India
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Oba S, Hatakeyama M, Handa H, Kawaguchi H. Development of Polymer Latex Particles for Selective Cleavage of Mismatched DNA and Their Application for DNA Diagnosis. Bioconjug Chem 2005; 16:551-8. [PMID: 15898721 DOI: 10.1021/bc049728l] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We developed functional polymer latex particles that can catch and cleave mismatched DNA selectively and propose a new mismatch detection system using the functional particles. The aimed particles possess two functional units composed of mismatch binding protein (MutS) and an anthraquinone derivative (AQ), a light-activated agent that photocleaves dsDNA. Use of the functional particles made it possible to discriminate complementary and mismatched DNAs and photocleave mismatched DNA selectively. The efficiency of photocleavage of mismatched DNA by the functional particles increased with UV irradiation time. It was also found that the functional particles were reusable and had dissociation constants (K(d)) of 1000 and 68.5 nM for G/C homoduplex and G/T heteroduplex, respectively. Using the functional particles and a dsDNA-binding fluorescent dye, SYBR-Gold, we could construct the system for detection of mismatched DNA that was 40 base pairs. The functional particles prepared in this study will be an absolutely new tool for mismatch detection in DNA diagnosis.
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Affiliation(s)
- Shinsuke Oba
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Kouhoku-ku, Yokohama 223-8522, Japan
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Okumura A, Sato Y, Kyo M, Kawaguchi H. Point mutation detection with the sandwich method employing hydrogel nanospheres by the surface plasmon resonance imaging technique. Anal Biochem 2005; 339:328-37. [PMID: 15797574 DOI: 10.1016/j.ab.2005.01.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Indexed: 11/27/2022]
Abstract
We propose a surface modification procedure to construct DNA arrays for use in surface plasmon resonance (SPR) imaging studies for the highly sensitive detection of a K-ras point mutation, enhanced with hydrogel nanospheres. A homobifunctional alkane dithiol was adsorbed on Au film to obtain the thiol surface, and ethyleneglycol diglycidylether (EGDE) was reacted to insert the ethyleneglycol moiety, which can suppress nonspecific adsorption during SPR analysis. Then streptavidin (SA) was immobilized on EGDE using tosyl chloride activation. Biotinylated DNA ligands were bound to the SA surface via biotin-SA interaction to fabricate DNA arrays. In SPR analysis, the DNA analyte was exposed on the DNA array and hybridized with the immobilized DNA probes. Subsequently, the hydrogel nanospheres conjugated with DNA probes were bound to the DNA analytes in a sandwich configuration. The DNA-carrying nanospheres led to SPR signal enhancement and enabled us to discriminate a K-ras point mutation in the SPR difference image. The application of DNA-carrying hydrogel nanospheres for SPR imaging assays was a promising technique for high throughput and precise detection of point mutations.
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Affiliation(s)
- Aya Okumura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama 223-8522, Japan
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Abstract
In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Sato Y, Sato Y, Okumura A, Suzuki K, Kawaguchi H. Flow-stress-induced discrimination of a K-ras point mutation by sandwiched polymer microsphere-enhanced surface plasmon resonance. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2004; 15:297-310. [PMID: 15147163 DOI: 10.1163/156856204322977193] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The highly sensitive detection of a K-ras point mutation with the aid of DNA-carrying microspheres as a flow-stress receptor is proposed at the surface of a surface plasmon resonance (SPR) biosensor. Single-stranded DNAs were immobilized onto epoxy-group-derivatized gold surfaces and the hybridization of DNA targets was monitored. The subsequent interaction with DNA-carrying micospheres enhanced the SPR response. The increase of flow rate during the event of dissociation changed the amount of detachment of the DNA-carrying microspheres for the mismatched pair. In addition, the viscosity was changed by addition of glycerol to the buffer. The increase of shear stress from the flow resulted in detachment of DNA-carrying microspheres hybridized with the mismatched sequence and increased the ability to discriminate a point mutation. This is a new method which not only increases the lower detection limit of evanescent wave-based biosensors, but also the ability to discriminate a point mutation which is a critical factor for ultrasensitive DNA detection in flow devices.
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Affiliation(s)
- Yasunobu Sato
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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Pieper-Fürst U, Kleuser U, Stöcklein WFM, Warsinke A, Scheller FW. Detection of subpicomolar concentrations of human matrix metalloproteinase-2 by an optical biosensor. Anal Biochem 2004; 332:160-7. [PMID: 15301961 DOI: 10.1016/j.ab.2004.05.047] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2004] [Indexed: 10/26/2022]
Abstract
We describe in this paper the development of a one-step sandwich assay for the highly sensitive and fast detection of human matrix metalloproteinase (MMP)-2 (EC 3.4.24.24), using surface plasmon resonance (SPR). For the assay, two ligands were selected: monoclonal anti-MMP-2 antibody Ab-2 and the tissue inhibitor of metalloproteinases (TIMP)-2. They were chosen on the basis of (1) their affinities to MMP-2, (2) the efficiency of immobilization to the sensor chip, (3) the efficiency of adsorption to colloidal gold, and (4) the stability of these protein-coated gold particles. The assay included mixing of MMP-2 with antibody Ab-2 adsorbed to colloidal gold with a diameter of about 20nm and injection into the flowcell of the SPR instrument containing immobilized TIMP-2. By using colloidal gold particles an amplification factor of 114 and a detection limit of 0.5pM for MMP-2 were obtained. The precision of the assay was high even at low analyte concentrations, the standard deviation being 8.3% for five determinations of 1pM MMP-2. No significant binding was observed with the structurally related MMP-9. The assay is far more sensitive and faster than commonly used methods for MMP-2 detection. As TIMP-bound MMP-2 is not detected by this method, the assay can be applied for measuring free MMP-2, reflecting the imbalance of free and inhibitor-bound enzyme in various pathological situations.
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Affiliation(s)
- Ursula Pieper-Fürst
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Haus 25, D-14476, Golm, Germany.
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He L, Smith EA, Natan MJ, Keating CD. The Distance-Dependence of Colloidal Au-Amplified Surface Plasmon Resonance. J Phys Chem B 2004. [DOI: 10.1021/jp048536k] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lin He
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802-6300
| | - Emily A. Smith
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802-6300
| | - Michael J. Natan
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802-6300
| | - Christine D. Keating
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802-6300
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Literature Alerts. J Microencapsul 2004; 21:359-67. [PMID: 15204601 DOI: 10.1080/02652040410001662263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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