Microarrays

2429 KiB

Open AccessArticle

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

by Ahsan Munir, Hassan Waseem, Maggie R. Williams, Robert D. Stedtfeld, Erdogan Gulari, James M. Tiedje and Syed A. Hashsham

Microarrays 2017, 6(2), 9; https://doi.org/10.3390/microarrays6020009 - 29 May 2017

Cited by 8 | Viewed by 7090

Abstract

Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R² = 0.8131). Full article

(This article belongs to the Special Issue Microfluidics Technology)

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1836 KiB

Open AccessArticle

Microarray Selection of Cooperative Peptides for Modulating Enzyme Activities

by Jinglin Fu

Microarrays 2017, 6(2), 8; https://doi.org/10.3390/microarrays6020008 - 26 Apr 2017

Cited by 2 | Viewed by 5372

Abstract

Recently, peptide microarrays have been used to distinguish proteins, antibodies, viruses, and bacteria based on their binding to random sequence peptides. We reported on the use of peptide arrays to identify enzyme modulators that involve screening an array of 10,000 defined and addressable peptides on a microarray. Primary peptides were first selected to inhibit the enzyme at low μM concentrations. Then, new peptides were found to only bind strongly with the enzyme–inhibitor complex, but not the native enzyme. These new peptides served as secondary inhibitors that enhanced the inhibition of the enzyme together with the primary peptides. Without the primary peptides, the secondary effect peptides had little effect on the enzyme activity. Conversely, we also selected peptides that recovered the activities of inhibited enzyme–peptide complex. The selection of cooperative peptide pairs will provide a versatile toolkit for modulating enzyme functions, which may potentially be applied to drug discovery and biocatalysis. Full article

(This article belongs to the Special Issue Microarrays for Drug Discovery and Development)

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383 KiB

Open AccessReview

Avian and Mammalian Facilitative Glucose Transporters

by Mary Shannon Byers, Christianna Howard and Xiaofei Wang

Microarrays 2017, 6(2), 7; https://doi.org/10.3390/microarrays6020007 - 5 Apr 2017

Cited by 22 | Viewed by 7925

Abstract

The GLUT members belong to a family of glucose transporter proteins that facilitate glucose transport across the cell membrane. The mammalian GLUT family consists of thirteen members (GLUTs 1–12 and H⁺-myo-inositol transporter (HMIT)). Humans have a recently duplicated GLUT member, GLUT14. Avians express the majority of GLUT members. The arrangement of multiple GLUTs across all somatic tissues signifies the important role of glucose across all organisms. Defects in glucose transport have been linked to metabolic disorders, insulin resistance and diabetes. Despite the essential importance of these transporters, our knowledge regarding GLUT members in avians is fragmented. It is clear that there are no chicken orthologs of mammalian GLUT4 and GLUT7. Our examination of GLUT members in the chicken revealed that some chicken GLUT members do not have corresponding orthologs in mammals. We review the information regarding GLUT orthologs and their function and expression in mammals and birds, with emphasis on chickens and humans. Full article

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Microarrays, Volume 6, Issue 2 (June 2017) – 3 articles

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