Label-Free Prehybridization DNA Microarray Imaging Using Photonic Crystals for Quantitative Spot Quality Analysis

2010 ◽  
Vol 82 (20) ◽  
pp. 8551-8557 ◽  
Author(s):  
S. George ◽  
I. D. Block ◽  
S. I. Jones ◽  
P. C. Mathias ◽  
V. Chaudhery ◽  
...  
Keyword(s):  
Photonic Crystals ◽  
Dna Microarray ◽  
Quality Analysis ◽  
Label Free ◽  
Spot Quality

RealSpot: software validating results from DNA microarray data analysis with spot images

2005 ◽  
Vol 21 (2) ◽  
pp. 284-291 ◽  
Author(s):  
Zhongming Chen ◽  
Lin Liu
Keyword(s):  
Data Analysis ◽  
Dna Microarray ◽  
Microarray Data ◽  
Microarray Experiment ◽  
Current Data ◽  
Microarray Data Analysis ◽  
Quality Analysis ◽  
Biological Knowledge ◽  
Data Validation ◽  
Spot Quality

The spot images from DNA microarray highly affect the discovery of biological knowledge from gene expression data. However, results from quality analysis, normalization, differential expression, and cluster analysis are rarely validated with spot images in current data analysis methods or software packages. We designed RealSpot, a software package, to validate the results by directly associating spot quality and data with spot images in a spreadsheet table. RealSpot splits hybridization images into individual spots stored in a spreadsheet table. It subsequently associates microarray data with spot images and performs data validation through the standard table operation such as sorting, searching, and editing. RealSpot has several built-in functions to facilitate data validation, including spot quality analysis, data organization, one-way ANOVA, gene ontology association, verification, import, and export. We used RealSpot to evaluate 77 slides (30,000 features each) from real hybridization experiments and to validate results from each step of data analysis. It took ∼10 min to validate results of spot quality after initial evaluation and correct ∼0.3% of falsely assigned qualities of 10,000 spots. We validated 1,641 of 2,110 differentially expressed genes identified by SAM analysis in ∼1/2 h by comparing each gene with its respective spot image. Furthermore, we found that 6 of 48 genes in one cluster from k-mean clustering method showed inconsistent trends of spot images. RealSpot is efficient for validating microarray results and thus helpful for improving the reliability of the whole microarray experiment for experimentalists.

Photonic crystals: A platform for label-free and enhanced fluorescence biomolecular and cellular assays

2008 ◽  
Vol 1133 ◽  
Author(s):  
Brian T. Cunningham ◽  
Leo Chan ◽  
Patrick C. Mathias ◽  
Nikhil Ganesh ◽  
Sherine George ◽  
...  
Keyword(s):  
Photonic Crystal ◽  
Photonic Crystals ◽  
High Throughput Screening ◽  
High Sensitivity ◽  
Excitation Wavelength ◽  
Label Free ◽  
Crystal Surfaces ◽  
Enhanced Fluorescence ◽  
Preferred Direction ◽  
Label Free Detection

Abstract Photonic crystal surfaces represent a class of resonant optical structures that are capable of supporting high intensity electromagnetic standing waves with near-field and far-field properties that can be exploited for high sensitivity detection of biomolecules and cells. While modulation of the resonant wavelength of a photonic crystal by the dielectric permittivity of adsorbed biomaterials enables label-free detection, the resonance can also be tuned to coincide with the excitation wavelength of common fluorescent tags - including organic molecules and semiconductor quantum dots. Photonic crystals are also capable of efficiently channeling fluorescent emission into a preferred direction for enhanced extraction efficiency. Photonic crystals can be designed to support multiple resonant modes that can perform label free detection, enhanced fluorescence excitation, and enhanced fluorescence extraction simultaneously on the same device. Because photonic crystal surfaces may be inexpensively produced over large surface areas by nanoreplica molding processes, they can be incorporated into disposable labware for applications such as pharmaceutical high throughput screening. In this talk, the optical properties of surface photonic crystals will be reviewed and several applications will be described, including results from screening a 200,000-member chemical compound library for inhibitors of protein-DNA interactions, gene expression microarrays, and high sensitivity of protein biomarkers.

scholarly journals How to copy and paste DNA microarrays

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Stefan D. Krämer ◽  
Johannes Wöhrle ◽  
Philipp A. Meyer ◽  
Gerald A. Urban ◽  
Günter Roth
Keyword(s):  
Real Time ◽  
Dna Microarray ◽  
Dna Microarrays ◽  
Label Free ◽  
Binding Assays ◽  
Single Stranded Dna ◽  
Whole Process ◽  
Double Stranded Dna ◽  
Cost Efficient ◽  
Copy And Paste

Abstract Analogous to a photocopier, we developed a DNA microarray copy technique and were able to copy patterned original DNA microarrays. With this process the appearance of the copied DNA microarray can also be altered compared to the original by producing copies of different resolutions. As a homage to the very first photocopy made by Chester Charlson and Otto Kornei, we performed a lookalike DNA microarray copy exactly 80 years later. Those copies were also used for label-free real-time kinetic binding assays of apo-dCas9 to double stranded DNA and of thrombin to single stranded DNA. Since each DNA microarray copy was made with only 5 µl of spPCR mix, the whole process is cost-efficient. Hence, our DNA microarray copier has a great potential for becoming a standard lab tool.

scholarly journals Label-Free Monitoring of Human IgG/Anti-IgG Recognition Using Bloch Surface Waves on 1D Photonic Crystals

Biosensors ◽  
2018 ◽  
Vol 8 (3) ◽  
pp. 71 ◽  
Author(s):  
Alberto Sinibaldi ◽  
Agostino Occhicone ◽  
Peter Munzert ◽  
Norbert Danz ◽  
Frank Sonntag ◽  
...  
Keyword(s):  
Photonic Crystals ◽  
Surface Waves ◽  
Dissociation Constants ◽  
Limit Of Detection ◽  
Detection System ◽  
Label Free ◽  
Human Igg ◽  
Surface Mass ◽  
On Chip ◽  
Antibody Interactions

Optical biosensors based on one-dimensional photonic crystals sustaining Bloch surface waves are proposed to study antibody interactions and perform affinity studies. The presented approach utilizes two types of different antibodies anchored at the sensitive area of a photonic crystal-based biosensor. Such a strategy allows for creating two or more on-chip regions with different biochemical features as well as studying the binding kinetics of biomolecules in real time. In particular, the proposed detection system shows an estimated limit of detection for the target antibody (anti-human IgG) smaller than 0.19 nM (28 ng/mL), corresponding to a minimum surface mass coverage of 10.3 ng/cm2. Moreover, from the binding curves we successfully derived the equilibrium association and dissociation constants (KA = 7.5 × 107 M−1; KD = 13.26 nM) of the human IgG–anti-human IgG interaction.

Gold Nanoparticle-Based Label-Free Detection of BRCA1 Mutations Utilizing DNA Ligation on DNA Microarray

2009 ◽  
Vol 9 (2) ◽  
pp. 1019-1024 ◽  
Author(s):  
Agnishwar Girigoswami ◽  
Taihua Li ◽  
Cheulhee Jung ◽  
Hyo Young Mun ◽  
Hyun Gyu Park
Keyword(s):  
Gold Nanoparticle ◽  
Dna Microarray ◽  
Label Free ◽  
Brca1 Mutations ◽  
Dna Ligation ◽  
Label Free Detection

scholarly journals Low-cost label-free biosensors using photonic crystals embedded between crossed polarizers

2010 ◽  
Vol 18 (18) ◽  
pp. 19120 ◽  
Author(s):  
Yousef Nazirizadeh ◽  
Uwe Bog ◽  
Sylwia Sekula ◽  
Timo Mappes ◽  
Uli Lemmer ◽  
...  
Keyword(s):  
Photonic Crystals ◽  
Low Cost ◽  
Label Free
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