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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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Li J, Liu Q, Xi H, Wei X, Chen Z. Y-Shaped DNA Duplex Structure-Triggered Gold Nanoparticle Dimers for Ultrasensitive Colorimetric Detection of Nucleic Acid with the Dark-Field Microscope. Anal Chem 2017; 89:12850-12856. [PMID: 29120162 DOI: 10.1021/acs.analchem.7b03391] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Herein, we present a novel gold nanoparticle (AuNP) enumeration-based colorimetric aptamer biosensor for ultrasensitive detection of nucleic acid. This AuNP enumeration-based colorimetric method takes advantages of the distinctive and strong localized surface plasmon resonance light scattering with the dark-field microscope. In our model system, first, cost-effective DNA1 instead of expensive 2-thioethyl ether acetic acid was capped on the surface of AuNPs to form a dense DNA1 layer. Then, two DNA strands (DNA2 and DNA3) in two different solutions were separately asymmetrically functionalized on the AuNPs capped dense DNA1 layer. The subsequent binding of the target DNA could trigger the formation of perfect complementary DNA with a Y shape and adjust the distance between nanoparticles to form AuNP dimers, accompanied by a color change from green to yellow as observed, and thereby modulated the performance of the sensor, which resulted in the ultrahigh sensitivity. With this design, a 43 aM limit of detection was obtained, which exhibited an increase of at least 5-9 orders of magnitude in sensitivity over other colorimetric sensors fabricated using conventional strategies.
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Affiliation(s)
- Jingjing Li
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Qingyun Liu
- College of Chemistry and Environmental Engineering, Shandong University of Science and Technology , Qingdao, Shandong 266510, China
| | - Hongyan Xi
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Xiangcong Wei
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
| | - Zhengbo Chen
- Department of Chemistry, Capital Normal University , Beijing, 100048, China
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Scott AW, Garimella V, Calabrese CM, Mirkin CA. Universal Biotin-PEG-Linked Gold Nanoparticle Probes for the Simultaneous Detection of Nucleic Acids and Proteins. Bioconjug Chem 2016; 28:203-211. [PMID: 27740740 DOI: 10.1021/acs.bioconjchem.6b00529] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Novel biotin-polyethylene glycol (biotin-PEG) gold nanoparticle probes have been synthesized and used as universal constructs for the detection of protein (prostate-specific antigen, PSA) and nucleic acid targets (microRNAs) from a single sample. Microarray assays based upon these probes enabled sensitive detection of biomarker targets (50 fM for nucleic acid targets and 1 pg/μL for the PSA target). Ways of detecting biomarkers, including nucleic acids and proteins, are necessary for the clinical diagnosis of many diseases, but currently available diagnostic platforms rely primarily on the independent detection of proteins or nucleic acids. In addition to the economic benefits associated with the use of a single platform to detect both classes of analytes, studies have shown that the simultaneous identification of multiple classes of biomarkers in the same sample could be useful for the detection and management of early stage diseases, especially when sample amounts are limited. Therefore, these new probes and the assays based upon them open the door for high-sensitivity combination-target assays for studying and tracking biological pathways and diseases.
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Affiliation(s)
- Alexander W Scott
- International Institute for Nanotechnology, ‡Department of Biomedical Engineering, and §Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Viswanadham Garimella
- International Institute for Nanotechnology, ‡Department of Biomedical Engineering, and §Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Colin M Calabrese
- International Institute for Nanotechnology, ‡Department of Biomedical Engineering, and §Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Chad A Mirkin
- International Institute for Nanotechnology, ‡Department of Biomedical Engineering, and §Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
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Jenkins S, Gibson N. High-throughput SNP genotyping. Comp Funct Genomics 2010; 3:57-66. [PMID: 18628885 PMCID: PMC2447245 DOI: 10.1002/cfg.130] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2001] [Accepted: 11/19/2001] [Indexed: 12/24/2022] Open
Abstract
Whole genome approaches using single nucleotide polymorphism (SNP) markers have the
potential to transform complex disease genetics and expedite pharmacogenetics research.
This has led to a requirement for high-throughput SNP genotyping platforms.
Development of a successful high-throughput genotyping platform depends on coupling
reliable assay chemistry with an appropriate detection system to maximise efficiency with
respect to accuracy, speed and cost. Current technology platforms are able to deliver
throughputs in excess of 100 000 genotypes per day, with an accuracy of >99%, at a cost
of 20–30 cents per genotype. In order to meet the demands of the coming years, however,
genotyping platforms need to deliver throughputs in the order of one million genotypes per
day at a cost of only a few cents per genotype. In addition, DNA template requirements
must be minimised such that hundreds of thousands of SNPs can be interrogated using a
relatively small amount of genomic DNA. As such, it is predicted that the next generation
of high-throughput genotyping platforms will exploit large-scale multiplex reactions and
solid phase assay detection systems.
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Affiliation(s)
- Suzanne Jenkins
- R&D Genetics, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.
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Nomura S, Kondo M, Nagano M, Matsui K, Egashira T. Development of a novel nano-Invader DNA chip system. ACTA ACUST UNITED AC 2007; 70:787-95. [PMID: 17597221 DOI: 10.1016/j.jbbm.2007.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 05/24/2007] [Accepted: 05/24/2007] [Indexed: 10/23/2022]
Abstract
By taking advantage of a homogeneous Invader assay, a miniaturized genotyping chip system termed nano-Invader was developed. The system is sensitive to 0.1 zeptomole of genomic DNA per well without prior PCR amplification. Its accuracy was determined by comparing both the genomic DNA chip and probe chip formats to PCR-RFLP. To determine the assay's capabilities in large-scale analysis, DNA samples from the Coriell Cell Repository and an additional 62-probe sets were tested with the genomic DNA and probe chip nano-Invader formats, respectively. Several hundred samples were genotyped in less than an hour, from purified genomic DNA to data analysis. With its ease of handling, speed, accuracy, sensitivity and cost-effectiveness, this chip system, especially its probe chip format, will meet a demand for high-throughput multiple genotyping in the coming era of personalized medicine.
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Affiliation(s)
- Sachio Nomura
- Division of Advanced Technology and Development, BML, 1361-1 Matoba, Kawagoe-shi, Saitama, 350-1101, Japan.
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Li JG, Liljedahl U, Heng CK. Tag/anti-tag liquid-phase primer extension array: a flexible and versatile genotyping platform. Genomics 2005; 87:151-7. [PMID: 16311014 DOI: 10.1016/j.ygeno.2005.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Revised: 09/07/2005] [Accepted: 09/19/2005] [Indexed: 11/28/2022]
Abstract
This study demonstrates an array-based platform to genotype simultaneously single nucleotide polymorphisms (SNPs) and some short insertions/deletions (indels) by the integration of the universal tag/anti-tag (TAT) system, liquid-phase primer extension (LIPEX), and a novel two-color detection strategy on an array format (TATLIPEXA). The TAT system permits a universal chip to be used for many applications, and the LIPEX simplifies the sample preparation but improves the sensitivity significantly. More importantly, all SNPs and some short indels can be interrogated in a single reaction with only two fluorescent ddNTPs. The concept of TATLIPEXA is demonstrated for nine SNPs (eight point mutations and one single-base insertion), and genotypes obtained show a remarkable concordance rate of 100% with both DNA sequencing and restriction fragment length polymorphism. Moreover, TATLIPEXA is able to provide quantitative information on allele frequency in pooled DNA samples, which could serve as a rapid screening tool for SNPs associated with diseases.
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Affiliation(s)
- Jing-Guang Li
- Department of Paediatrics, National University of Singapore, 119074, Singapore
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Rockenbauer E, Petersen K, Vogel U, Bolund L, Kølvraa S, Nielsen KV, Nexø BA. SNP genotyping using microsphere-linked PNA and flow cytometric detection. Cytometry A 2005; 64:80-6. [PMID: 15729710 DOI: 10.1002/cyto.a.20123] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) represent the most frequent form of genetic variations. Some of the most sensitive methods for SNP genotyping employ synthetic oligonucleotides, such as the peptide nucleic acid (PNA). We introduce a new method combining allele-specific hybridization, PNA technology, and flow cytometric detection. We tested the design by genotyping a Danish basal cell carcinoma cohort of 80 individuals for an A/C SNP in exon 6 of the XPD gene. METHODS Genomic DNA was amplified by a two-step polymerase chain reaction (PCR) in the presence of fluorescein-dyed primers and fluorescein-12-dUTP. The allele-specific PNA molecules were covalently coupled to carboxylated microspheres with and without rhodamine. Allele-specific hybridization between PCR products and immobilized PNA was carried out at 60 degrees C followed by flow cytometric detection. RESULTS We present a fully functional two-bead genotyping system based on PNA capture and flow cytometric detection used for the correct and fast regenotyping of a Danish basal cell carcinoma cohort. CONCLUSIONS This new assay presents a simple, rapid, and robust method for SNP genotyping for laboratories equipped with a standard flow cytometer. Moreover, this system offers potential for multiplexing and will be operational for middle-scale genotyping.
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Abstract
The Invader assay uses a structure-specific flap endonuclease (FEN) to cleave a three-dimensional complex formed by hybridization of allele-specific overlapping oligonucleotides to target DNA containing a single nucleotide polymorphism (SNP) site. Annealing of the oligonucleotide complementary to the SNP allele in the target molecule triggers the cleavage of the oligonucleotide by cleavase, a thermostable FEN. Cleavage can be detected by several different approaches. Most commonly, the cleavage product triggers a secondary cleavage reaction on a fluorescence resonance energy transfer (FRET) cassette to release a fluorescent signal. Alternatively, the cleavage can be detected directly by use of fluorescence polarization (FP) probes, or by mass spectrometry. The invasive cleavage reaction is highly specific, has a low failure rate, and can detect zeptomol quantities of target DNA. While the assay traditionally has been used to interrogate one SNP in one sample per reaction, novel chip- or bead-based approaches have been tested to make this efficient and accurate assay adaptable to multiplexing and high-throughput SNP genotyping.
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Affiliation(s)
- Michael Olivier
- Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant and simple form of DNA variation. Analyses of SNPs in the human population have the potential to greatly improve human health, both by predicting susceptibility to disease and guiding choice of therapy. This review describes new tools for SNP discovery, and current and emerging technologies for large-scale SNP analysis, as well as providing a guide to choosing the best approach for SNP analysis.
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Wu X, Zhou Y, Xu S. Chemiluminescent detection of genetic polymorphisms based on mismatch hybridization: application to cytochrome P4501A1. Mol Cell Probes 2004; 18:17-22. [PMID: 15036365 DOI: 10.1016/j.mcp.2003.07.005] [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] [Received: 04/29/2002] [Accepted: 07/11/2003] [Indexed: 11/23/2022]
Abstract
An assay that makes use of differences in thermal stability between perfectly and imperfectly matched hybrids in combination with a sensitive chemiluminescence detection system was developed and applied to the identification of CYP1A1 polymorphisms. In this assay, two oligonucleotide probes for each polymorphic site were designed: one perfectly matching the wild type allele, the other perfectly matching the mutant allele. The genotypes were determined by calculating the ratio of signals obtained from the two probes. The method described here allows for the rapid, simple and cost-effective detection of DNA polymorphisms. Compared with fluorescence- and microarray-based assays, this method provides an alternative for genotyping where costly equipment or specialized reagents are not available.
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Affiliation(s)
- Xiaoming Wu
- Institute of Environmental Medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
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Chen X, Sullivan PF. Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. THE PHARMACOGENOMICS JOURNAL 2004; 3:77-96. [PMID: 12746733 DOI: 10.1038/sj.tpj.6500167] [Citation(s) in RCA: 184] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The large number of single nucleotide polymorphism (SNP) markers available in the public databases makes studies of association and fine mapping of disease loci very practical. To provide information for researchers who do not follow SNP genotyping technologies but need to use them for their research, we review here recent developments in the fields. We start with a general description of SNP typing protocols and follow this with a summary of current methods for each step of the protocol and point out the unique features and weaknesses of these techniques as well as comparing the cost and throughput structures of the technologies. Finally, we describe some popular techniques and the applications that are suitable for these techniques.
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Affiliation(s)
- X Chen
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA 23298-0424, USA.
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Lu M, Knickerbocker T, Cai W, Yang W, Hamers RJ, Smith LM. Invasive cleavage reactions on DNA-modified diamond surfaces. Biopolymers 2004; 73:606-13. [PMID: 15048784 DOI: 10.1002/bip.20007] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recently developed DNA-modified diamond surfaces exhibit excellent chemical stability to high-temperature incubations in biological buffers. The stability of these surfaces is substantially greater than that of gold or silicon surfaces, using similar surface attachment chemistry. The DNA molecules attached to the diamond surfaces are accessible to enzymes and can be modified in surface enzymatic reactions. An important application of these surfaces is for surface invasive cleavage reactions, in which target DNA strands added to the solution may result in specific cleavage of surface-bound probe oligonucleotides, permitting analysis of single nucleotide polymorphisms (SNPs). Our previous work demonstrated the feasibility of performing such cleavage reactions on planar gold surfaces using PCR-amplified human genomic DNA as target. The sensitivity of detection in this earlier work was substantially limited by a lack of stability of the gold surface employed. In the present work, detection sensitivity is improved by a factor of approximately 100 (100 amole of DNA target compared with 10 fmole in the earlier work) by replacing the DNA-modified gold surface with a more stable DNA-modified diamond surface.
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Affiliation(s)
- Manchun Lu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1396, USA
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Affiliation(s)
- Sambasivarao Damaraju
- Polyomx Program (www.polyomx.org), Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
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de Arruda M, Lyamichev VI, Eis PS, Iszczyszyn W, Kwiatkowski RW, Law SM, Olson MC, Rasmussen EB. Invader technology for DNA and RNA analysis: principles and applications. Expert Rev Mol Diagn 2003; 2:487-96. [PMID: 12271820 DOI: 10.1586/14737159.2.5.487] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Concomitant advances made by the Human Genome Project and in the development of nucleic acid screening technologies are driving the expansion of pharmacogenomic research and molecular diagnostics. However, most current technologies are restrictive due to their complexity and/or cost, limiting the potential of personalized medicine. The invader assay, which can be used for genotyping as well as for gene expression monitoring without the need for intervening target amplification steps, presents an immediate solution that is accurate, simple to use, scaleable and cost-effective.
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Affiliation(s)
- Monika de Arruda
- Third Wave Technologies, 502 South Rosa Road, Madison, WI 53719-1256, USA.
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Albert TJ, Norton J, Ott M, Richmond T, Nuwaysir K, Nuwaysir EF, Stengele KP, Green RD. Light-directed 5'-->3' synthesis of complex oligonucleotide microarrays. Nucleic Acids Res 2003; 31:e35. [PMID: 12655023 PMCID: PMC152820 DOI: 10.1093/nar/gng035] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Light-directed synthesis of high-density microarrays is currently performed in the 3'-->5' direction due to constraints in existing synthesis chemistry. This results in the probes being unavailable for many common types of enzymatic modification. Arrays that are synthesized in the 5'-->3' direction could be utilized to perform parallel genotyping and resequencing directly on the array surface, dramatically increasing the throughput and reducing the cost relative to existing techniques. In this report we demonstrate the use of photoprotected phosphoramidite monomers for light-directed array synthesis in the 5'-->3' direction, using maskless array synthesis technology. These arrays have a dynamic range of >2.5 orders of magnitude, sensitivity below 1 pM and a coefficient of variance of <10% across the array surface. Arrays containing >150,000 probe sequences were hybridized to labeled mouse cRNA producing highly concordant data (average R(2) = 0.998). We have also shown that the 3' ends of array probes are available for sequence-specific primer extension and ligation reactions.
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Affiliation(s)
- Thomas J Albert
- NimbleGen Systems Inc., One Science Court, Madison, WI 53711, USA.
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Brodsky AS, Silver PA. A microbead-based system for identifying and characterizing RNA-protein interactions by flow cytometry. Mol Cell Proteomics 2002; 1:922-9. [PMID: 12543929 DOI: 10.1074/mcp.t200010-mcp200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We present a high throughput, versatile approach to identify RNA-protein interactions and to determine nucleotides important for specific protein binding. In this approach, oligonucleotides are coupled to microbeads and hybridized to RNA-protein complexes. The presence or absence of RNA and/or protein fluorescence indicates the formation of an oligo-RNA-protein complex on each bead. The observed fluorescence is specific for both the hybridization and the RNA-protein interaction. We find that the method can discriminate noncomplementary and mismatch sequences. The observed fluorescence reflects the affinity and specificity of the RNA-protein interaction. In addition, the fluorescence patterns footprint the protein recognition site to determine nucleotides important for protein binding. The system was developed with the human protein U1A binding to RNAs derived from U1 snRNA but can also detect RNA-protein interactions in total RNA backgrounds. We propose that this strategy, in combination with emerging coded bead systems, can identify RNAs and RNA sequences important for interacting with RNA-binding proteins on genomic scales.
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Affiliation(s)
- Alexander S Brodsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and The Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.
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Kirk BW, Feinsod M, Favis R, Kliman RM, Barany F. Single nucleotide polymorphism seeking long term association with complex disease. Nucleic Acids Res 2002; 30:3295-311. [PMID: 12140314 PMCID: PMC137089 DOI: 10.1093/nar/gkf466] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2002] [Revised: 04/02/2002] [Accepted: 06/12/2002] [Indexed: 12/16/2022] Open
Abstract
Successful investigation of common diseases requires advances in our understanding of the organization of the genome. Linkage disequilibrium provides a theoretical basis for performing candidate gene or whole-genome association studies to analyze complex disease. However, to constructively interrogate SNPs for these studies, technologies with sufficient throughput and sensitivity are required. A plethora of suitable and reliable methods have been developed, each of which has its own unique advantage. The characteristics of the most promising genotyping and polymorphism scanning technologies are presented. These technologies are examined both in the context of complex disease investigation and in their capacity to face the unique physical and molecular challenges (allele amplification, loss of heterozygosity and stromal contamination) of solid tumor research.
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Affiliation(s)
- Brian W Kirk
- Department of Microbiology, Box 62, Hearst Microbiology Research Center, Joan and Sanford I. Weill Medical College of Cornell University, Room B-406, 1300 York Avenue, New York, NY 10021, USA
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Lu M, Hall JG, Shortreed MR, Wang L, Berggren WT, Stevens PW, Kelso DM, Lyamichev V, Neri B, Skinner JL, Smith LM. Structure-specific DNA cleavage on surfaces. J Am Chem Soc 2002; 124:7924-31. [PMID: 12095336 DOI: 10.1021/ja012082c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The structure-specific invasive cleavage reaction is a useful means for sensitive and specific detection of single nucleotide polymorphisms, or SNPs, directly from genomic DNA without a need for prior target amplification. A new approach integrating this invasive cleavage assay and surface DNA array technology has been developed for potentially large-scale SNP scoring in a parallel format. Two surface invasive cleavage reaction strategies were designed and implemented for a model SNP system in codon 158 of the human ApoE gene. The upstream oligonucleotide, which is required for the invasive cleavage reaction, is either co-immobilized on the surface along with the probe oligonucleotide or alternatively added in solution. The ability of this approach to unambiguously discriminate a single base difference was demonstrated using PCR-amplified human genomic DNA. A theoretical model relating the surface fluorescence intensity to the progress of the invasive cleavage reaction was developed and agreed well with experimental results.
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Affiliation(s)
- Manchun Lu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1396, USA
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Nicewarner Peña SR, Raina S, Goodrich GP, Fedoroff NV, Keating CD. Hybridization and enzymatic extension of au nanoparticle-bound oligonucleotides. J Am Chem Soc 2002; 124:7314-23. [PMID: 12071740 DOI: 10.1021/ja0177915] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated the impact of steric effects on the hybridization and enzymatic extension of oligonucleotides bound to 12-nm colloidal Au particles. In these experiments, a nanoparticle-bound 12-mer sequence is hybridized either to its solution phase 12-mer complement or to an 88-mer template sequence. The particle-bound oligonucleotide serves as a primer for enzymatic extension reactions, in which covalent incorporation of nucleotides to form the complement of the template is achieved by the action of DNA polymerase. Primers were attached via-C(6)H(12)SH, -C(12)H(24)SH, and -TTACAATC(6)H(12)SH linkers attached at the 5' end. Primer coverage on the nanoparticles was varied by dilution with (5')HSC(6)H(12)AAA AAA(3'). Hybridization efficiencies were determined as a function of linker length, primer coverage, complement length (12-mer vs 88-mer), and primer:complement concentration ratio. In all cases, hybridization for the 88-mer was less efficient than for the 12-mer. Low primer surface coverage, greater particle-primer separation, and higher primer:complement ratios led to optimal hybridization. Hybridization efficiencies as high as 98% and 75% were observed for the 12-mer and 88-mer, respectively. Enzymatic extension of particle-bound primers was observed under all conditions tested; however, the efficiency of the reaction was strongly affected by linker length and primer coverage. Extension of primers attached by the longest linker was as efficient as the solution-phase reaction.
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Affiliation(s)
- Sheila R Nicewarner Peña
- Department of Chemistry and Life Sciences Consortium, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Lu M, Shortreed MR, Hall JG, Wang L, Berggren T, Stevens PW, Kelso DM, Lyamichev V, Neri B, Smith LM. A surface invasive cleavage assay for highly parallel SNP analysis. Hum Mutat 2002; 19:416-22. [PMID: 11933196 DOI: 10.1002/humu.10071] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The structure-specific invasive cleavage of single-stranded DNA by 5' nucleases is a useful means for sensitive detection of single-nucleotide polymorphisms or SNPs. The solution-phase invasive cleavage reaction has sufficient sensitivity for direct detection of as few as 600 target molecules with no prior target amplification. One approach to the parallelization of SNP analysis is to adapt the invasive cleavage reaction to an addressed array format. Two surface invasive cleavage reaction strategies were designed and tested using the polymorphic site in codon 158 of the human ApoE gene as a model system, with a synthetic oligonucleotide as target. The upstream oligonucleotide, which is required for the invasive cleavage reaction, was either added in solution (strategy 1), or co-immobilized on the surface along with the probe oligonucleotide (strategy 2). Both strategies showed target-concentration and time-dependent amplification of signal. Parameters that govern the rate of the surface-invasive cleavage reactions are discussed.
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Affiliation(s)
- Manchun Lu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Abstract
Understanding the relationship between genetic variation and biological function on a genomic scale is expected to provide fundamental new insights into the biology, evolution and pathophysiology of humans and other species. The hope that single nucleotide polymorphisms (SNPs) will allow genes that underlie complex disease to be identified, together with progress in identifying large sets of SNPs, are the driving forces behind intense efforts to establish the technology for large-scale analysis of SNPs. New genotyping methods that are high throughput, accurate and cheap are urgently needed for gaining full access to the abundant genetic variation of organisms.
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Affiliation(s)
- A C Syvänen
- Department of Medical Sciences - Molecular Medicine, Uppsala University, University Hospital, 75185 Uppsala, Sweden.
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