1
|
Fu R, Li Q, Wang R, Xue N, Lin X, Su Y, Jiang K, Jin X, Lin R, Gan W, Lu Y, Huang G. An interferometric imaging biosensor using weighted spectrum analysis to confirm DNA monolayer films with attogram sensitivity. Talanta 2017; 181:224-231. [PMID: 29426505 DOI: 10.1016/j.talanta.2017.12.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/13/2017] [Accepted: 12/21/2017] [Indexed: 11/28/2022]
Abstract
Interferometric imaging biosensors are powerful and convenient tools for confirming the existence of DNA monolayer films on silicon microarray platforms. However, their accuracy and sensitivity need further improvement because DNA molecules contribute to an inconspicuous interferometric signal both in thickness and size. Such weaknesses result in poor performance of these biosensors for low DNA content analyses and point mutation tests. In this paper, an interferometric imaging biosensor with weighted spectrum analysis is presented to confirm DNA monolayer films. The interferometric signal of DNA molecules can be extracted and then quantitative detection results for DNA microarrays can be reconstructed. With the proposed strategy, the relative error of thickness detection was reduced from 88.94% to merely 4.15%. The mass sensitivity per unit area of the proposed biosensor reached 20 attograms (ag). Therefore, the sample consumption per unit area of the target DNA content was only 62.5 zeptomoles (zm), with the volume of 0.25 picolitres (pL). Compared with the fluorescence resonance energy transfer (FRET), the measurement veracity of the interferometric imaging biosensor with weighted spectrum analysis is free to the changes in spotting concentration and DNA length. The detection range was more than 1µm. Moreover, single nucleotide mismatch could be pointed out combined with specific DNA ligation. A mutation experiment for lung cancer detection proved the high selectivity and accurate analysis capability of the presented biosensor.
Collapse
Affiliation(s)
- Rongxin Fu
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Qi Li
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ruliang Wang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ning Xue
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xue Lin
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ya Su
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kai Jiang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiangyu Jin
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Rongzan Lin
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wupeng Gan
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Ying Lu
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Guoliang Huang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China; National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China.
| |
Collapse
|
2
|
Li Q, Fu R, Zhang J, Wang R, Ye J, Xue N, Lin X, Su Y, Gan W, Lu Y, Huang G. Label-Free Method Using a Weighted-Phase Algorithm To Quantitate Nanoscale Interactions between Molecules on DNA Microarrays. Anal Chem 2017; 89:3501-3507. [PMID: 28230978 DOI: 10.1021/acs.analchem.6b04596] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
White light interference is used as a label-free method to detect nanoscale changes on surfaces. However, the signal-to-noise ratio of the white light interference method is very low, thus resulting in inaccurate results. In this paper, we report a corrected label-free method based on hyperspectral interferometry to overcome the shortcoming of the white light interference method. A platform based on hyperspectral interferometry was established, and a DNA hybridization microarray was constructed to quantitate thickness variation of molecules on a solid surface. We used fluorescence resonance energy transfer (FRET) to validate the results of our method. Compared to conventional fluorescence-labeled method like FRET, our method has advantages because it does not require a fluorescent label and has a detection limit of 1.78 nm, a high accuracy, and wide detection range (5-64 bp).
Collapse
Affiliation(s)
- Qi Li
- Department of Biomedical Engineering, Tsinghua University School of Medicine , Beijing 100084, PR China
| | - Rongxin Fu
- Department of Biomedical Engineering, Tsinghua University School of Medicine , Beijing 100084, PR China
| | - Junqi Zhang
- Department of Biomedical Engineering, Tsinghua University School of Medicine , Beijing 100084, PR China
| | - Ruliang Wang
- Department of Biomedical Engineering, Tsinghua University School of Medicine , Beijing 100084, PR China
| | - Jiancheng Ye
- Department of Biomedical Engineering, Tsinghua University School of Medicine , Beijing 100084, PR China
| | - Ning Xue
- Department of Biomedical Engineering, Tsinghua University School of Medicine , Beijing 100084, PR China
| | - Xue Lin
- Department of Biomedical Engineering, Tsinghua University School of Medicine , Beijing 100084, PR China
| | - Ya Su
- Department of Biomedical Engineering, Tsinghua University School of Medicine , Beijing 100084, PR China
| | - Wupeng Gan
- National Engineering Research Center for Beijing Biochip Technology , Beijing 102206, PR China
| | - Ying Lu
- Department of Biomedical Engineering, Tsinghua University School of Medicine , Beijing 100084, PR China
| | - Guoliang Huang
- Department of Biomedical Engineering, Tsinghua University School of Medicine , Beijing 100084, PR China.,National Engineering Research Center for Beijing Biochip Technology , Beijing 102206, PR China
| |
Collapse
|
3
|
Zhu J, Song X, Xiang G, Feng Z, Guo H, Mei D, Zhang G, Wang D, Mitchelson K, Xing W, Cheng J. A rapid automatic processing platform for bead label-assisted microarray analysis: application for genetic hearing-loss mutation detection. ACTA ACUST UNITED AC 2013; 19:144-52. [PMID: 23975388 DOI: 10.1177/2211068213491096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Molecular diagnostics using microarrays are increasingly being used in clinical diagnosis because of their high throughput, sensitivity, and accuracy. However, standard microarray processing takes several hours and involves manual steps during hybridization, slide clean up, and imaging. Here we describe the development of an integrated platform that automates these individual steps as well as significantly shortens the processing time and improves reproducibility. The platform integrates such key elements as a microfluidic chip, flow control system, temperature control system, imaging system, and automated analysis of clinical results. Bead labeling of microarray signals required a simple imaging system and allowed continuous monitoring of the microarray processing. To demonstrate utility, the automated platform was used to genotype hereditary hearing-loss gene mutations. Compared with conventional microarray processing procedures, the platform increases the efficiency and reproducibility of hybridization, speeding microarray processing through to result analysis. The platform also continuously monitors the microarray signals, which can be used to facilitate optimization of microarray processing conditions. In addition, the modular design of the platform lends itself to development of simultaneous processing of multiple microfluidic chips. We believe the novel features of the platform will benefit its use in clinical settings in which fast, low-complexity molecular genetic testing is required.
Collapse
Affiliation(s)
- Jiang Zhu
- 1CapitalBio Corporation, Beijing, P. R. China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Xie F, Zhu J, Deng C, Huang G, Mitchelson K, Cheng J. General and reliable quantitative measurement of fluorescence resonance energy transfer using three fluorescence channels. Analyst 2012; 137:1013-9. [PMID: 22234659 DOI: 10.1039/c2an15902c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we describe a comprehensive general system adapted for quantitative fluorescence resonance energy transfer (FRET) measurement using signals from three channels of a fluorescence instrument. The general FRET measurement system involves two established methods, as well as two novel approaches. Unlike the previous measurements, which can be taken correctly only when the quantity of the acceptor is greater than or equal to that of the donor, one of our novel methods can overcome this obstacle and take quantitative FRET measurements when the donor is in excess of the acceptor. Hence the general FRET measurement system allowed one to determine the exact distance when the donor and acceptor were present in different quantities, and integrated the methods for quantitative FRET measurements. The uniformity of measured values and utility of each method were validated using molecular standards based on DNA oligonucleotide rulers. We also discussed and validated the use of a novel method for estimating the relative quantities of the donor and acceptor fluorophores when they were not known before an appropriate method of this system can be selected.
Collapse
Affiliation(s)
- Fengbo Xie
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Haidian District, Beijing, 100084, China
| | | | | | | | | | | |
Collapse
|
5
|
Zhu J, Lu Y, Deng C, Huang G, Chen S, Xu S, Lv Y, Mitchelson K, Cheng J. Assessment of Fluorescence Resonance Energy Transfer for Two-Color DNA Microarray Platforms. Anal Chem 2010; 82:5304-12. [DOI: 10.1021/ac100804p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiang Zhu
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Ying Lu
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Cheng Deng
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Guoliang Huang
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Shengyi Chen
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Shukuan Xu
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Yi Lv
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Keith Mitchelson
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Jing Cheng
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| |
Collapse
|