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How Gene Microarrays Work & How Our Program Saves You Time & Money

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Microarray scanner diagram

A DNA microarray, also commonly known as a DNA chip or biochip, is a collection of microscopic DNA spots attached to a solid surface.

Biotech diagram

Each DNA spot contains picomoles of a specific DNA sequence, known as probes, reporters, or oligos. These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample, or target.

Scientists use DNA microarray analysis to measure the expression levels of large numbers of genes simultaneously as well as the genotyping of multiple regions of a genome.

Each DNA spot contains picomoles of a specific DNA sequence, known as probes, reporters, or oligos. These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample, or target, under high stringency conditions.

This type of sample is also referred to as antisense RNA. Probe-target hybridization is usually detected and quantified by the detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine the relative abundance of nucleic acid sequences in the target.

Microarray scanning is highly relevant in the fields of basic research, drug discovery, disease diagnostics and more.

Microarray Detection & Types

An open hand with a DNA strand coming out of the palm

The core principle behind microarrays is hybridization between two DNA strands, the property of complementary nucleic acid sequences specifically pairing with each other by forming hydrogen bonds between complementary nucleotide base pairs.

A high number of complementary base pairs in a nucleotide sequence means tighter non-covalent bonding between the two strands. After washing off non-specific binding sequences, only strongly paired strands will remain hybridized.

Fluorescently labeled target sequences that bind to a probe sequence generate a signal that depends on the hybridization conditions, such as temperature, and washing after hybridization. The total strength of the signal, from a spot (feature), depends upon the amount of target sample binding to the probes present on that spot.

Microarrays use relative quantitation in which the intensity of a feature is compared to the intensity of the same feature under a different condition, and the identity of the feature is known by its position.

Many types of arrays exist and the broadest distinction is whether they are spatially arranged on a surface or on coded beads:

Many types of arrays exist and the broadest distinction is whether they are spatially arranged on a surface or on coded beads:

  • The traditional solid-phase array is a collection of orderly microscopic “spots”, called features, each with thousands of identical and specific probes attached to a solid surface, such as glass, plastic or silicon biochip (commonly known as a genome chip, DNA chip or gene array). Thousands of these features can be placed in known locations on a single DNA microarray.
  • The alternative bead array is a collection of microscopic polystyrene beads, each with a specific probe and a ratio of two or more dyes, which do not interfere with the fluorescent dyes used on the target sequence.

DNA microarrays can be used to detect DNA (as in comparative genomic hybridization), or detect RNA (most commonly as cDNA after reverse transcription) that may or may not be translated into proteins. The process of measuring gene expression via cDNA is called expression analysis or expression profiling.

Applications include:

  • Gene expression profiling
  • Comparative genomic hybridization
  • GeneID
  • Chromatin immunoprecipitation
  • DamID
  • SNP detection
  • Alternative splicing detection
  • Fusion genes microarray
  • Tiling array
  • Double-stranded B-DNA microarrays
  • Double-stranded Z-DNA microarrays
  • Multi-stranded DNA microarrays.

Microarrays can be manufactured in different ways, depending on the number of probes under examination, costs, and customization requirements, as well as the type of scientific question being asked. Arrays may have as few as 10 probes or up to 2.1 million micrometer-scale probes from commercial vendors.

A microarray scanner, typically used in the last step of analysis, relies on a combination of lasers and an imaging system, comprised of a specialized microscope and a camera. The lasers excite the fluorescent-labeled DNA material and the imaging system provides a high-resolution, digital image of the array for image analysis. Much can be determined about the marked DNA based on calculations such as the red/green fluorescence ratio.

Many scanners include automation features, such as autoloaders, that allow for streamlined workflows when combined with liquid handling solutions. Manufacturers like Agilent Technologies, Molecular Devices, and Illumina offer high-throughput, automated microarray scanners with superior analysis software for researchers in the life sciences focusing on gene expression studies.

Spotted vs. in situ Synthesized Arrays

Microarrays can be fabricated using a variety of technologies, including printing with fine-pointed pins onto glass slides, photolithography using pre-made masks, photolithography using dynamic micromirror devices, ink-jet printing, or electrochemistry on microelectrode arrays.

In spotted microarrays, the probes are oligonucleotides, cDNA, or small fragments of PCR products that correspond to mRNAs. The probes are synthesized prior to deposition on the array surface and are then “spotted” onto glass.

These arrays may be easily customized for each experiment, because researchers can choose the probes and printing locations on the arrays, synthesize the probes in their own lab (or collaborating facility), and spot the arrays. They can then generate their own labeled samples for hybridization, hybridize the samples to the array, and finally read the arrays with their own microarray scanner.

In oligonucleotide microarrays, the probes are short sequences designed to match parts of the sequence of known or predicted open reading frames. Although oligonucleotide probes are often used in “spotted” microarrays, the term “oligonucleotide array” most often refers to a specific technique of manufacturing.

Oligonucleotide arrays are produced by printing short oligonucleotide sequences designed to represent a single gene or family of gene splice-variants by synthesizing this sequence directly onto the array surface instead of depositing intact sequences.

Two-Channel vs. One-Channel Detection

Two-color microarrays or two-channel microarrays are typically hybridized with cDNA prepared from two samples to be compared (e.g. diseased tissue versus healthy tissue) and that are labeled with two different fluorophores.

Fluorescent dyes commonly used for cDNA labeling include Cy3, which has a fluorescence emission wavelength of 570 nm (corresponding to the green part of the light spectrum), and Cy5 with a fluorescence emission wavelength of 670 nm (corresponding to the red part of the light spectrum).

The two Cy-labeled cDNA samples are mixed and hybridized to a single microarray that is then scanned in a microarray scanner to visualize fluorescence of the two fluorophores after excitation with a laser beam of a defined wavelength. Relative intensities of each fluorophore may then be used in ratio-based analysis to identify up-regulated and down-regulated genes.

In single-channel microarrays or one-color microarrays, the arrays provide intensity data for each probe or probe set indicating a relative level of hybridization with the labeled target.

However, they do not truly indicate abundance levels of a gene but rather relative abundance when compared to other samples or conditions when processed in the same experiment. Each RNA molecule encounters protocol and batch-specific bias during amplification, labeling, and hybridization phases of the experiment making comparisons between genes for the same microarray uninformative.

The comparison of two conditions for the same gene requires two separate single-dye hybridizations.

Flexible DNA Microarray Reader Leases

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Founder-Friendly Leases

Our lease agreements are founder-friendly and flexible, helping you preserve working capital, strengthen the cash flow of your business, and keep business credit lines open for expansions, staffing, and other crucial operational expenses and business development opportunities.

2-5 Year Lease Lengths

Leases range from 2 to 5 years. Length will depend on several factors, including how long you want to use the equipment, equipment type, and your company’s financial position. These are standard factors leasing companies consider and help us tailor a lease agreement to fit your needs.

Your Choice of Manufacturer

We don’t carry an inventory. This means you’re not limited to a specific set of manufacturers. Instead, you can pick the equipment that aligns with your business goals and preferences. We’ll work with the manufacturer of your choice to get the equipment in your facility as quickly as possible.

Maintenance & Repair Coverage

Bundle preventive maintenance and repair coverage with your lease agreement. You can spread those payments over time. Easily maintain your equipment, minimize the chances something will break down, repair instrumentation quickly, and simplify your payment processes.

End-of-Lease Options

At the end of your lease, you have multiple options. You can either renew the lease at a significantly lower price, purchase the machine outright based on the fair market value of the original pricing, or call it a day and we’ll come the pick up the equipment for you free of charge.

No Loan-Like Terms

Our leases do not include loan-like terms, which can be restrictive or harmful in certain situations. We do not require debt covenants, IP pledges, collateral,  or equity participation. Our goal is to maximize your flexibility. When you lease with us, you’re collaborating with a true business partner.

In-House Underwriting Process

Our underwriting is done in-house. You can expect quicker turnaround, allowing you respond to your equipment needs as they arise. We require less documentation than traditional lenders and financiers and can get the equipment you need in operation more quickly.

Popular Microarray Scanner Manufacturers

Agilent
Applied Microarrays
Bio-Rad
Illumina
Innopsys
Molecular Devices
Perkin Elmer
Thermo Fisher Scientific