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The Promise of Nanotechnology in Personalized Medicine. J Pers Med 2022; 12:jpm12050673. [PMID: 35629095 PMCID: PMC9142986 DOI: 10.3390/jpm12050673] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 02/04/2023] Open
Abstract
Both personalized medicine and nanomedicine are new to medical practice. Nanomedicine is an application of the advances of nanotechnology in medicine and is being integrated into diagnostic and therapeutic tools to manage an array of medical conditions. On the other hand, personalized medicine, which is also referred to as precision medicine, is a novel concept that aims to individualize/customize therapeutic management based on the personal attributes of the patient to overcome blanket treatment that is only efficient in a subset of patients, leaving others with either ineffective treatment or treatment that results in significant toxicity. Novel nanomedicines have been employed in the treatment of several diseases, which can be adapted to each patient-specific case according to their genetic profiles. In this review, we discuss both areas and the intersection between the two emerging scientific domains. The review focuses on the current situation in personalized medicine, the advantages that can be offered by nanomedicine to personalized medicine, and the application of nanoconstructs in the diagnosis of genetic variability that can identify the right drug for the right patient. Finally, we touch upon the challenges in both fields towards the translation of nano-personalized medicine.
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Choi W, Park E, Bae S, Choi KH, Han S, Son KH, Lee DY, Cho IJ, Seong H, Hwang KS, Nam JM, Choi J, Lee H, Choi N. Multiplex SNP Genotyping Using SWITCH: Sequence-Specific Nanoparticle with Interpretative Toehold-Mediated Sequence Decoding in Hydrogel. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105538. [PMID: 34923738 DOI: 10.1002/smll.202105538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Single nucleotide polymorphisms (SNPs) that can alter phenotypes of individuals play a pivotal role in disease development and, more importantly, responses to therapy. However, SNP genotyping has been challenging due to the similarity of SNP alleles and their low concentration in biological samples. Sequence-specific nanoparticle with interpretative toehold-mediated sequence decoding in hydrogel (SWITCH) for multiplex SNP genotyping is presented. The encoding with gold nanoparticle probes transduces each SNP target to ≈1000 invaders with prominently different sequences between wild and mutant types, featuring polymerase chain reaction (PCR)-free amplification. Subsequently, the toehold-mediated DNA replacement in hydrogel microparticles decodes the invaders via SNP-specific fluorescence signals. The 4-plex detection of the warfarin-associated SNP targets spiked in commercially validated human serum (S1-100ML, Merck) is successfully demonstrated with excellent specificity. This work is the first technology development presenting PCR-free, multiplex SNP genotyping with a single reporting fluorophore, to the best of knowledge.
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Affiliation(s)
- Woongsun Choi
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Korea
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | - Eunhye Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | - Seojin Bae
- OPTOLANE Technologies, Inc., Seongnam, 13494, Korea
| | | | - Sangeun Han
- OPTOLANE Technologies, Inc., Seongnam, 13494, Korea
| | - Kuk-Hui Son
- Department of Thoracic and Cardiovascular Surgery, Gachon University Gil Medical Center, Incheon, 21936, Korea
| | - Do Young Lee
- OPTOLANE Technologies, Inc., Seongnam, 13494, Korea
| | - Il-Joo Cho
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
- Yonsei-KIST Convergence Research Institute, Yonsei University, Seoul, 03722, Korea
- School of Electrical and Electronics Engineering, Yonsei University, Seoul, 03722, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Korea
| | - Hyejeong Seong
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | - Kyo Seon Hwang
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Jungkyu Choi
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Korea
| | - Hyojin Lee
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Korea
| | - Nakwon Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Korea
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Ortiz M, Jauset-Rubio M, Skouridou V, Machado D, Viveiros M, Clark TG, Simonova A, Kodr D, Hocek M, O’Sullivan CK. Electrochemical Detection of Single-Nucleotide Polymorphism Associated with Rifampicin Resistance in Mycobacterium tuberculosis Using Solid-Phase Primer Elongation with Ferrocene-Linked Redox-Labeled Nucleotides. ACS Sens 2021; 6:4398-4407. [PMID: 34797987 PMCID: PMC8715531 DOI: 10.1021/acssensors.1c01710] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Here, we report the
electrochemical detection of single-point mutations
using solid-phase isothermal primer elongation with redox-labeled
oligonucleotides. A single-base mutation associated with resistance
to rifampicin, an antibiotic commonly used for the treatment of Mycobacterium tuberculosis, was used as a model system
to demonstrate a proof-of-concept of the approach. Four 5′-thiolated
primers, designed to be complementary with the same fragment of the
target sequence and differing only in the last base, addressing the
polymorphic site, were self-assembled via chemisorption on individual
gold electrodes of an array. Following hybridization with single-stranded
DNA, Klenow (exo-) DNA polymerase-mediated primer extension with ferrocene-labeled
2′-deoxyribonucleoside triphosphates (dNFcTPs) was
only observed to proceed at the electrode where there was full complementarity
between the surface-tethered probe and the target DNA being interrogated.
We tested all four ferrocenylethynyl-linked dNTPs and optimized the
ratio of labeled/natural nucleotides to achieve maximum sensitivity.
Following a 20 min hybridization step, Klenow (exo-) DNA polymerase-mediated
primer elongation at 37 °C for 5 min was optimal for the enzymatic
incorporation of a ferrocene-labeled nucleotide, achieving unequivocal
electrochemical detection of a single-point mutation in 14 samples
of genomic DNA extracted from Mycobacterium tuberculosis strains. The approach is rapid, cost-effective, facile, and can
be extended to multiplexed electrochemical single-point mutation genotyping.
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Affiliation(s)
- Mayreli Ortiz
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Miriam Jauset-Rubio
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Vasso Skouridou
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Diana Machado
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisbon, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisbon, Portugal
| | - Taane G. Clark
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisbon, Portugal
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, U.K
| | - Anna Simonova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam.2, 16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843 Prague 2, Czech Republic
| | - David Kodr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam.2, 16610 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam.2, 16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843 Prague 2, Czech Republic
| | - Ciara K. O’Sullivan
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010 Barcelona, Spain
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Tang C, He Z, Liu H, Xu Y, Huang H, Yang G, Xiao Z, Li S, Liu H, Deng Y, Chen Z, Chen H, He N. Application of magnetic nanoparticles in nucleic acid detection. J Nanobiotechnology 2020; 18:62. [PMID: 32316985 PMCID: PMC7171821 DOI: 10.1186/s12951-020-00613-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid is the main material for storing, copying, and transmitting genetic information. Gene sequencing is of great significance in DNA damage research, gene therapy, mutation analysis, bacterial infection, drug development, and clinical diagnosis. Gene detection has a wide range of applications, such as environmental, biomedical, pharmaceutical, agriculture and forensic medicine to name a few. Compared with Sanger sequencing, high-throughput sequencing technology has the advantages of larger output, high resolution, and low cost which greatly promotes the application of sequencing technology in life science research. Magnetic nanoparticles, as an important part of nanomaterials, have been widely used in various applications because of their good dispersion, high surface area, low cost, easy separation in buffer systems and signal detection. Based on the above, the application of magnetic nanoparticles in nucleic acid detection was reviewed.
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Affiliation(s)
- Congli Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziyu He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yuyue Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hao Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Gaojian Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziqi Xiao
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
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Motaghi H, Mehrgardi MA. Spectrofluorometric genotyping of single nucleotide polymorphisms using carbon dots as fluorophores. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 206:154-159. [PMID: 30099312 DOI: 10.1016/j.saa.2018.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
In the present manuscript, a new spectrofluorometric method for the genotyping of various single nucleotide polymorphisms (SNPs) using carbon dots (CDs) is investigated. For the construction of the assay, thiolated probe DNA is self-assembled on a gold surface via sulfur‑gold chemistry and afterward, the probe is partially hybridized with a longer target DNA strand. Subsequently, the unhybridized section of the target DNA is hybridized with a capture DNA to form the DNA double-helix self-assembled monolayer on the gold surface. Finally, CDs surface amine groups are covalently attached to the 5' phosphate groups of various monobases (MB-CDs) using phosphoramidite chemistry. In this method, genotyping of SNPs is based on following the changes in fluorescence intensity of the MB-CDs suspensions before and after incubation with DNA modified gold surface. The assay is straightforward with no need for target labeling and is sensitive and low cost enough to genotype various SNPs independent of their position in a DNA double helix with an acceptable limit of detections in picomolar ranges.
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Affiliation(s)
- Hasan Motaghi
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
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Feng N, Ma H, Ma C, Xu Z, Li S, Jiang W, Liu Y, Ma L. Characterization of 40 single nucleotide polymorphism (SNP) via Tm-shift assay in the mud crab (Scylla paramamosain). Mol Biol Rep 2014; 41:5467-71. [PMID: 24867081 DOI: 10.1007/s11033-014-3420-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 05/16/2014] [Indexed: 11/28/2022]
Abstract
In this study, single nucleotide polymorphism (SNP) were identified, confirmed and genotyped in the mud crab (Scylla paramamosain) using Tm-shift assay. High quality sequences (13, 311 bp long) were obtained by re-sequencing that contained 91 SNPs, with a density of one SNP every 146 bp. Of all 91 SNPs, 40 were successfully genotyped and characterized using 30 wild specimens by Tm-shift assay. The minor allele frequency per locus ranged from 0.017 to 0.500. The observed and expected heterozygosity, and polymorphism information content (PIC) ranged from 0.000 to 0.600, from 0.033 to 0.509, and from 0.033 to 0.375, respectively, with an average of 0.142, 0.239 and 0.198 per locus. Seventeen SNPs were significantly deviated from Hardy-Weinberg equilibrium. No significant linkage disequilibrium between pairs of loci was detected after sequential Bonferroni correction (P > 0.00125). Seventeen SNPs were related with known function genes. This study provided new molecular markers for investigation of population genetic diversity, construction of genetic linkage maps and molecular marker-assisted selection in this important crustacean species.
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Affiliation(s)
- Nana Feng
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
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Kuang H, Ma W, Xu L, Wang L, Xu C. Nanoscale superstructures assembled by polymerase chain reaction (PCR): programmable construction, structural diversity, and emerging applications. Acc Chem Res 2013; 46:2341-54. [PMID: 23742672 DOI: 10.1021/ar300206m] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Polymerase chain reaction (PCR) is an essential tool in biotechnology laboratories and is becoming increasingly important in other areas of research. Extensive data obtained over the last 12 years has shown that the combination of PCR with nanoscale dispersions can resolve issues in the preparation DNA-based materials that include both inorganic and organic nanoscale components. Unlike conventional DNA hybridization and antibody-antigen complexes, PCR provides a new, effective assembly platform that both increases the yield of DNA-based nanomaterials and allows researchers to program and control assembly with predesigned parameters including those assisted and automated by computers. As a result, this method allows researchers to optimize to the combinatorial selection of the DNA strands for their nanoparticle conjugates. We have developed a PCR approach for producing various nanoscale assemblies including organic motifs such as small molecules, macromolecules, and inorganic building blocks, such as nanorods (NRs), metal, semiconductor, and magnetic nanoparticles (NPs). We start with a nanoscale primer and then modify that building block using the automated steps of PCR-based assembly including initialization, denaturation, annealing, extension, final elongation, and final hold. The intermediate steps of denaturation, annealing, and extension are cyclic, and we use computer control so that the assembled superstructures reach their predetermined complexity. The structures assembled using a small number of PCR cycles show a lower polydispersity than similar discrete structures obtained by direct hybridization between the nanoscale building blocks. Using different building blocks, we assembled the following structural motifs by PCR: (1) discrete nanostructures (NP dimers, NP multimers including trimers, pyramids, tetramers or hexamers, etc.), (2) branched NP superstructures and heterochains, (3) NP satellite-like superstructures, (4) Y-shaped nanostructures and DNA networks, (5) protein-DNA co-assembly structures, and (6) DNA block copolymers including trimers and pentamers. These results affirm that this method can produce a variety of chemical structures and in yields that are tunable. Using PCR-based preparation of DNA-bridged nanostructures, we can program the assembly of the nanoscale blocks through the adjustment of the primer intensity on the assembled units, the number of PCR cycles, or both. The resulting structures are highly complex and diverse and have interesting dynamics and collective properties. Potential applications of these materials include chirooptical materials, probe fabrication, and environmental and biomedical sensors.
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Affiliation(s)
- Hua Kuang
- State Key Lab of Food Science & Technology, School of Food Science & Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Ma
- State Key Lab of Food Science & Technology, School of Food Science & Technology, Jiangnan University, Wuxi 214122, China
| | - Liguang Xu
- State Key Lab of Food Science & Technology, School of Food Science & Technology, Jiangnan University, Wuxi 214122, China
| | - Libing Wang
- State Key Lab of Food Science & Technology, School of Food Science & Technology, Jiangnan University, Wuxi 214122, China
| | - Chuanlai Xu
- State Key Lab of Food Science & Technology, School of Food Science & Technology, Jiangnan University, Wuxi 214122, China
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Tang Y, Zou J, Ma C, Ali Z, Li Z, Li X, Ma N, Mou X, Deng Y, Zhang L, Li K, Lu G, Yang H, He N. Highly sensitive and rapid detection of Pseudomonas aeruginosa based on magnetic enrichment and magnetic separation. Am J Cancer Res 2013; 3:85-92. [PMID: 23424183 PMCID: PMC3575588 DOI: 10.7150/thno.5588] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 01/04/2013] [Indexed: 12/25/2022] Open
Abstract
A method for highly sensitive and rapid detection of Pseudomonas aeruginosa, based on magnetic enrichment and magnetic separation, is described in this paper. The magnetic nanoparticles (MNPs) were applied to adsorb genome DNA after the sample was lysed. The DNA binding MNPs were directly subjected to polymerase chain reaction (PCR) to amplify gyrB specific sequence of Pseudomonas aeruginosa. The biotin labeled PCR products were detected by chemiluminescence when they were successively incubated with the probes-modified MNPs and alkaline phosphatase (ALP) labeled streptavidin (SA). Agarose gel electrophoresis analyses approved the method of in situ PCR to be highly reliable. The factors which could affect the chemiluminiscence were studied in detail. The results showed that the MNPs of 400 nm in diameter are beneficial to the detection. The sequence length and the binding site of the probe with a target sequence have obvious effects on the detection. The optimal concentration of the probes, hybridization temperature and hybridization time were 10 μM, 60 ºC and 60 mins, respectively. The method of in situ PCR based on MNPs can greatly improve the utilization rate of the DNA template ultimately enhancing the detection sensitivity. Experiment results proved that the primer and probe had high specificity, and Pseudomonas aeruginosa was successfully detected with detection limits as low as 10 cfu/mL by this method, while the detection of a single Pseudomonas aeruginosa can also be achieved.
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LeBron C, Pal P, Brait M, Dasgupta S, Guerrero-Preston R, Looijenga LH, Kowalski J, Netto G, Hoque MO. Genome-wide analysis of genetic alterations in testicular primary seminoma using high resolution single nucleotide polymorphism arrays. Genomics 2011; 97:341-9. [DOI: 10.1016/j.ygeno.2011.02.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 01/11/2011] [Accepted: 02/25/2011] [Indexed: 11/26/2022]
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Jangpatarapongsa K, Polpanich D, Yamkamon V, Dittharot Y, Peng-On J, Thiramanas R, Hongeng S, Jootar S, Charoenmak L, Tangboriboonrat P. DNAdetection of chronic myelogenous leukemia by magnetic nanoparticles. Analyst 2011; 136:354-8. [DOI: 10.1039/c0an00374c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Liu H, Li S, Liu L, Tian L, He N. An integrated and sensitive detection platform for biosensing application based on Fe@Au magnetic nanoparticles as bead array carries. Biosens Bioelectron 2010; 26:1442-8. [PMID: 20728338 DOI: 10.1016/j.bios.2010.07.078] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 07/20/2010] [Accepted: 07/21/2010] [Indexed: 10/19/2022]
Abstract
A sensitive and selective biosensor platform suited for SNP type using Fe@Au magnetic nanoparticles (GMNPs) to fabricate bead array is described. This new platform integrates the rapid binding kinetics of magnetic nanoparticles carriers, the multiplexing and encoding capabilities of chips, and tagged array. As a DNA sensor, the biotinylated single-stranded DNA was obtained by asymmetry PCR amplification, and then captured by GMNPs modified with streptavidin to form GMNP-ssDNA complexes without further purification. The complexes were immobilized on the slide to fabricate bead array through magnetic field. The bead array was hybridized with the corresponding allele-specific tag probes for each locus, and a pair of given universal detectors were applied to these markers analysis. Using bead array, all samples can be analyzed in one hybridization chamber which lowers the cost of the assay. Using universal tags, only a pair of universal dual-color probes labeled fluorophores was used for multiplex genotyping. Without the need of laborious and time-consuming elution, the experiment process was simple, reproducible and easy to handle. Two SNPs loci from 12 individual samples were discriminated using this platform and the results demonstrated that the expected scores and good discrimination were obtained between the two alleles from the two SNP loci. In summary, the integrated sensitive platform is adaptable and versatile, while offering a high-throughput capability needed for genome research and clinical applications.
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Affiliation(s)
- Hongna Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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12
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DaRe JT, Kouri DP, Zimmerman PA, Thomas PJ. Differentiating Plasmodium falciparum alleles by transforming Cartesian X,Y data to polar coordinates. BMC Genet 2010; 11:57. [PMID: 20587031 PMCID: PMC2912781 DOI: 10.1186/1471-2156-11-57] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 06/29/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Diagnosis of infectious diseases now benefits from advancing technology to perform multiplex analysis of a growing number of variables. These advances enable simultaneous surveillance of markers characterizing species and strain complexity, mutations associated with drug susceptibility, and antigen-based polymorphisms in relation to evaluation of vaccine effectiveness. We have recently developed assays detecting single nucleotide polymorphisms (SNPs) in the P. falciparum genome that take advantage of post-PCR ligation detection reaction and fluorescent microsphere labeling strategies. Data from these assays produce a spectrum of outcomes showing that infections result from single to multiple strains. Traditional methods for distinguishing true positive signal from background can cause false positive diagnoses leading to incorrect interpretation of outcomes associated with disease treatment. RESULTS Following analysis of Plasmodium falciparum dihydrofolate reductase SNPs associated with resistance to a commonly used antimalarial drug, Fansidar (Sulfadoxine/pyrimethamine), and presumably neutral SNPs for parasite strain differentiation, we first evaluated our data after setting a background signal based on the mean plus three standard deviations for known negative control samples. Our analysis of single allelic controls suggested that background for the absent allele increased as the concentration of the target allele increased. To address this problem, we introduced a simple change of variables from customary (X,Y) (Cartesian) coordinates to planar polar coordinates (X = rcos(theta), Y = rsin(theta)). Classification of multidimensional fluorescence signals based on histograms of angular and radial data distributions proved more effective than classification based on Cartesian thresholds. Comparison with known diallelic dilution controls suggests that histogram-based classification is effective for major:minor allele concentration ratios as high as 10:1. CONCLUSION We have observed that the diallelic SNP data resulting from analysis of P. falciparum mutations is more accurately diagnosed when a simple polar transform of the (X,Y) data into (r,theta) is used. The development of high through-put methods for genotyping P. falciparum SNPs and the refinement of analytical approaches for evaluating these molecular diagnostic results significantly advance the evaluation of parasite population diversity and antimalarial drug resistance.
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Affiliation(s)
- Jeana T DaRe
- Center for Global Health and Disease, Case Western Reserve University School of Medicine, Wolstein Research Building, 4-125, Cleveland, Ohio 44106-7286, USA
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Li S, Liu H, Liu L, Tian L, He N. A novel automated assay with dual-color hybridization for single-nucleotide polymorphisms genotyping on gold magnetic nanoparticle array. Anal Biochem 2010; 405:141-3. [PMID: 20507822 DOI: 10.1016/j.ab.2010.05.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2010] [Accepted: 05/20/2010] [Indexed: 11/29/2022]
Abstract
A high-throughput and cost-effective single-nucleotide polymorphism (SNP) genotyping method based on a gold magnetic nanoparticle (GMNP) array with dual-color hybridization has been designed. Biotinylated single-strand polymerase chain reaction (PCR) products containing the SNP locus were captured by the GMNPs that were coated with streptavidin. The GMNP array was fabricated by immobilizing single-stranded DNA (ssDNA)-GMNP complexes onto a glass slide using a magnetic field, and SNPs were identified with dual-color fluorescence hybridization. Three different SNP loci from 24 samples were genotyped successfully using this platform. This procedure allows the user to directly analyze the bead fluorescence to determine the SNP genotype, and it eliminates the need for background subtraction for signal determination. This method also bypasses tedious PCR purification and concentration procedures, and it facilitates large-scale SNP studies by using a method that is highly sensitive, simple, labor-saving, and potentially automatable.
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Affiliation(s)
- Song Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering. Southeast University, Nanjing 210096, China
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14
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He N, Li S, Liu H. High-throughput SNP detection based on PCR amplification on magnetic nanoparticles using dual-color hybridization. Methods Mol Biol 2009; 578:393-402. [PMID: 19768607 DOI: 10.1007/978-1-60327-411-1_24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A microarray-based method for detecting single nucleotide polymorphisms (SNPs) using solid-phase polymerase chain reaction (PCR) on magnetic nanoparticles (MNPs) was developed. In this method one primer with a biotin label is captured by streptavidin-coated MNPs (SA-MNPs), and the PCR products are directly amplified on the surface of SA-MNPs in a 96-well plate. The samples are further probed by hybridization with a pair of dual-color probes to determine SNP. The genotype of each sample can be simultaneously identified by scanning the microarray printed with the denatured fluorescent probes. All the reactions can be performed in the same reaction volume without the necessity of purification of intermediates. This approach represents a novel, simple, and labor-saving method for SNP genotyping and can be applied in automation system(s) to achieve high-throughput SNP detection.
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Affiliation(s)
- Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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Furukawa K, Abe H, Wang J, Uda M, Koshino H, Tsuneda S, Ito Y. Reduction-triggered red fluorescent probes for dual-color detection of oligonucleotide sequences. Org Biomol Chem 2008; 7:671-7. [PMID: 19194582 DOI: 10.1039/b817228e] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a new red fluorogenic compound derived from naphthorhodamine for a reduction-triggered fluorescence probe to sense oligonucleotides. The fluorogenic reaction between naphthorhodamine azide derivatives and reducing reagents such as triphenylphosphine (TPP) on the DNA target does not use any enzyme or reagent, and fluoresces at 650 nm. The probes were used for dual color detection of a single nucleotide difference on the leukemia-related bcr/abl gene.
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Affiliation(s)
- Kazuhiro Furukawa
- Nano Medical Engineering Laboratory, Advance Science Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama 351-0198, Japan
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16
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Ye M, Zhang Y, Li H, Zhang Y, Tan P, Tang H, Yao S. A novel method for the detection of point mutation in DNA using single-base-coded CdS nanoprobes. Biosens Bioelectron 2008; 24:2339-45. [PMID: 19135353 DOI: 10.1016/j.bios.2008.12.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 11/14/2008] [Accepted: 12/03/2008] [Indexed: 11/29/2022]
Abstract
A novel method for DNA point mutation detection using single-base-coded CdS nanoparticle probes is proposed. Target DNA was immobilized on core/shell Fe(3)O(4)/Au magnetic nanoparticles. Single-base-coded CdS nanoparticles, such as guanosine coded CdS (G-CdS), cytidine coded CdS (C-CdS), thymidine coded CdS (T-CdS) and adenosine coded CdS (A-CdS) were used as the probes to identify the mutation sites in DNA strand. The hybridization process of single-base-coded CdS nanoparticle probes with the mutation sites in DNA was monitored using piezoelectric quartz crystal microbalance (QCM). The hybridization of the mutation base in DNA with its complementary base-coded CdS nanoprobes specifically caused significant changes in the resonance frequency of the QCM. Thus the base types of the mutation sites in DNA strand could be identified. The results were further confirmed by fluorescence measurement of CdS. Owing to its operation convenience and cost-effective, this DNA point mutation detection method is expected to hold a great promise in the detection of DNA point mutation and genetic assays.
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Affiliation(s)
- Min Ye
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China
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17
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Ge Q, Yu P, Bai Y, Lu Z. An emulsion system based on a chip polymerase chain reaction. Molecules 2008; 13:3057-68. [PMID: 19078848 PMCID: PMC6245313 DOI: 10.3390/molecules13123057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 11/30/2008] [Accepted: 12/02/2008] [Indexed: 11/16/2022] Open
Abstract
In this paper we describe a novel method for detecting many DNA fragments through efficient amplification by using an emulsion system based on “on-chip” PCR instead of conventional multiplex polymerase chain reaction (PCR). During the preparation of on-chip PCR, a set of primers were immobilized on a slide and other sets were in an emulsion system. Different emulsion phase primers and other related PCR components were dispersed in different droplets of the emulsion system, and then, due to the thermal instability of emulsion droplets, they would be released onto the surface of the slide after preheating in the first PCR step. To test the above method, we used plasma DNAs from pregnant women who was carrying a male fetus for gender identification. Four different Y chromosome DNA fragments were selected. Results showed that different DNA fragments could be simultaneously amplified with satisfactory results. It is suggested that a simple, convenient and inexpensive on-chip PCR method has been developed.
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Affiliation(s)
- Qinyu Ge
- Key Laboratory of Child Development and Learning Science, Ministry of Education, Southeast University, Nanjing, 210096, P.R. China; E-mails: (Q-Y. G.), (P-F. Y.)
| | - Pinfei Yu
- Key Laboratory of Child Development and Learning Science, Ministry of Education, Southeast University, Nanjing, 210096, P.R. China; E-mails: (Q-Y. G.), (P-F. Y.)
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, P.R. China; E-mail: (Y-F. B.)
| | - Zuhong Lu
- Key Laboratory of Child Development and Learning Science, Ministry of Education, Southeast University, Nanjing, 210096, P.R. China; E-mails: (Q-Y. G.), (P-F. Y.)
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, P.R. China; E-mail: (Y-F. B.)
- Author to whom correspondence should be addressed; E-mail: (Z-H. L.); Phone: +86-25-83792396; Fax: +86-25-83793779
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