Catherine Shaffer holds a master's degree in biological chemistry and has worked as a research scientist. She is also an award-winning science fiction author and part-time reporter for local public radio.
Gel documentation systems are a necessity in any laboratory that works with DNA. Equipment for gel documentation has evolved from simple UV lights and Polaroid cameras to advanced digital data-acquisition and -analysis systems. The purpose of a gel documentation system is to capture information from DNA separated on an agarose or polyacrylamide gel. The position of the DNA band on a gel yields qualitative information, and the intensity of the signal (usually fluorescent) can be captured to give highly accurate quantitative data. Common detection methods for DNA gel documentation include CCD digital cameras, laser detection and phosphorimaging. Custom software automates many of the tasks of gel detection, including image capture, background correction and quantitation.
It can be difficult to narrow down such a broad field of commercially available instruments. According to Raymond Miller, a global product manager for Bio-Rad, it’s difficult to study the market and identify who the customers are for gel documentation systems, because the systems are so widely used. “This is such a ubiquitous technology. If you’re in life science, you need access to a gel doc system. It’s almost mandatory at this point in almost every group that I’ve ever encountered.”
Here we discuss some key features, including versatility, sensitivity, dynamic range and ease of use, as important considerations when selecting a DNA gel documentation system.
Sensitivity and dynamic range
Although some DNA-imaging applications require only a crude measurement or a “yes or no” result, most researchers using gel documentation systems are looking for the best possible data quality.
Sensitivity and dynamic range are two aspects of data quality to consider in the context of the specific application when choosing a system.
A lot of people assume that camera resolution is the best parameter to look at for assessing sensitivity in a system with a CCD camera, according to Karine Victory, Managing Director at Uvitec Ltd. “When, in fact,” she says, “Sensitivity is ensured by a large lens aperture, an excellent low noise camera, a further deep cooling of any camera electronic noise, and the closest distance sample to lens.” She cautions that a practice called binning can sacrifice the resolution of the CCD camera. Binning is a process where the sensitivity of a camera is increased by converting the total pixels to larger pixels. It allows more light to be collected at the time of image capture, but decreases the total resolution by reducing the total number of pixels. “It is good to have the binning option, but full resolution mode should always be possible by any gel doc system, especially when publication quality images are needed.”
Uvitec’s chemiluminescence imaging range from a dedicated chemi system (Minihd9), a stand alone system (Minihd9 touch) optional to fluorescence , or the combined system for chemi+ UV fluorescence and optional epi fluorescence on blot (alliance 9.7 and 9.7 chroma) all include a native 9 megapixel CCD camera with three stage peltier cooling to -60 degrees.
Sensitivity is a priority for gel documentation systems developed by UVP (an Analytik Jena company). The GelDoc-It TS3 is a stand-alone imaging system for DNA and protein gels. It is equipped with a 5.0-MP camera and a wide-angle f/1.2 lens to offer high resolution and rapid image capture. The system can also be upgraded with a CCD camera cooled to -57°C for chemiluminescent imaging.
Sarah Chaudhury, product manager at UVP, shares that advances incorporated into the latest generation of the GelDoc-It series of imagers include “more sensitive cameras and optics, combined with one-touch automation for image capture and analysis.”
Dynamic range goes hand in hand with sensitivity. A large dynamic range allows samples at low and high levels to be detected in the same image. Dynamic range can be an important consideration for some applications, such as monitoring the effects of a stimulating compound or an inhibitor on the expression of a target of interest.
LI-COR Biosciences offers instruments with more than six logs of dynamic range. According to Jeff Harford, a senior product marketing manager with LI-COR, that means images are never saturated. LI-COR’s Odyssey Fc imager is designed for use with ethidium-bromide-stained DNA gels or with other dyes such as SYTO 60 or SYBR and is equipped with disposable trays to reduce contamination. The Odyssey CLx is designed for use with SYTO 60 dye.
According to Harford, consistency in data acquisition is an important consideration when evaluating technology in gel documentation systems. “Technology that has a wide dynamic range can get consistent data from gel to gel,” he says. “Make sure that the technology is future-proof. Publishers are very concerned about reliable and reproducible data, so you need to make sure your system is going to provide solid data day in and day out. Anything the system can do to eliminate gel or blot-to-blot variability is going to be important.”
Versatility
Although a simple, dedicated, single-use gel documentation system seems like an appealing choice, most customers are interested in a system with more versatility in terms of the types of gels that can be analyzed, detection methods and range of applications. Many manufacturers are responding with instruments that have multiple functions, such as multiplex fluorescent detection, compatibility with colorimetric samples or radiolabeled samples or even additional imaging applications, like Western blotting and tissue-section analysis.
GE Healthcare Life Sciences offers a line of laser scanners with extremely broad versatility across detection methods and applications. Its Amersham Typhoon 5 Biomolecular Imager can image fluorescent, radiolabeled and colorimetric samples. In addition to working with DNA gels, protein gels and blots, the system can be used to image and analyze microplates, culture dishes, tissue sections and many other sample types.
The heart of the laser scanner is its photomultiplier tubes. Designed to detect signals ranging from very weak to very strong, they offer a wide dynamic range, making possible the scanner’s versatility.
Laser scanners also can accommodate a range of sample formats, from small samples on glass slides to large, flat cassettes.
In addition to the laser scanners, GE also offers two CCD camera systems which can be used for DNA gel documentation, the ImageQuant LAS 500 and the more advanced Amersham Imager 600. When selecting an imager, researchers should consider whether chemiluminescent detection is desired or required, says GE Healthcare Life Sciences senior scientist Erik Bjerneld: “If the user is primarily interested in chemiluminescence, then we recommend a CCD imager. If sensitivity and resolution for fluorescent imaging or phosphorimaging are important, then we recommend this laser scanner,” says Bjerneld.
Safety and ease of use
Although data quality and versatility are crucial considerations when choosing a system, with so many instruments on the market, safety and ease of use are emerging as important factors in making a selection. One growing trend is toward automation in gel documentation. That means, ideally, being able to put a gel into the system, and at the push of a button the analysis is performed. Most systems offer some degree of automation. For example, UVP’s GelDoc-It TS3 is equipped with extensive automation features. Image capture is automated through its VisionWorks software, which uses preset capture settings such as autoexposure, focus, zoom and lighting for one-touch image capture.
Another aspect of user experience with gel documentation is safety, primarily with respect to the use of ethidium bromide. The same property that makes ethidium bromide a good dye for DNA—its ability to intercalate between the DNA bases—also makes it a strong mutagenizing agent and a health risk that requires special handling. Those precautions often include use of gloves, protective equipment and isolation of instruments contaminated with ethidium bromide. New, safer dyes are available for use with DNA gels, and many instrument vendors have optimized their systems for use with those safer options to support researchers who want to phase out ethidium bromide.
According to Miller, there’s been long-standing resistance to moving away from ethidium bromide, but that’s starting to change. “The transition is finally happening. We see a lot more researchers expressing interest in safer fluorescent dyes,” he says.
Ease of use has also been a priority for Bio-Rad. Its offerings include the basic, entry-level Gel Doc EZ system, the more fully featured Gel Doc XR+ system and the GS-900 Calibrated Densitometer for industrial-scale gel imaging. “We’ve put a lot of effort into making the systems as easy as possible,” says Miller. That includes automating much of the work of gel imaging, such as zooming and focusing.
MIT researcher Arnaud Gutierrez also cites ease of use as an attractive feature for a gel documentation system. “We are using Azure C400 for DNA gels and fluorescent Western blotting. It is a very user-friendly gel doc. We are totally happy with it. The small size of the device was a key in our choice. Fluorescent multiplexing, as well as pre-stained gel, are working fine,” says Gutierrez.
The market for DNA gel documentation systems is mature and highly competitive, with many options at multiple price points. Individual needs, as well as specific applications, should always be the primary consideration when selecting a system. Choices for a particular laboratory come down to details such as the performance of the instrument with the lab’s preferred dyes and specific applications and the ability to switch between detection methods. It is difficult to find head-to-head comparisons of instruments for specific applications, so paying close attention to product literature and communication with company representatives is important to narrow the choices. In addition, systems should be future-proof, purchased with new and developing technologies in mind.