Fluorescent western blotting is growing in popularity because it allows the ability to perform multiplex detection, where multiple proteins can be detected at the same time. Historically, the instrumentation available for fluorescent detection was not able to offer the sensitivity required by many researchers or was prohibitively expensive. With the introduction of advanced digital imaging instruments like the Invitrogen iBright FL1500 Imaging System, and improvements in fluorescent conjugate technologies, scientists now have the necessary tools to take advantage of the range of fluorescent dyes and antibodies for western blot detection. These advancements provide access to fluorescence detection with reduced cost and improved sensitivity.
In fluorescent western blot detection systems, signal is captured in the form of light. Transient light emission from a fluorescent molecule (fluorophore) is produced by the excitation and subsequent release of photons as the excited molecule returns back to its normal state. In contrast, chromogenic and chemiluminescent western detection systems produce signals that are products of enzyme-substrate reactions. Chromogenic enzyme-substrate reactions produce colored products that precipitate onto the membrane, while chemiluminescent detection systems generate enzymatic reactions that produce energy released in the form of light. Overall, the western blotting procedure is similar between chemiluminescent and fluorescent detection methods, with each method offering specific benefits.
Similar to enzymatic reactions, fluorescent reagents must be optimized with respect to the signal-to-noise ratio. If the degree of fluorescent labeling is too low, the signal will be weak. However, if the degree of fluorescent labeling is too high, the signal can also be weak due to the inactivation of the detection reagent or quenching of the signal caused by a phenomenon known as Förster resonance energy transfer (FRET).
|Fluorescent detection||Chemiluminescent detection|
|Signal source||Direct signal from fluorophore||Indirect signal from enzymatic reaction|
|Signal duration||Extended (weeks to months)||Limited (minutes to hours)|
|Sensitivity||Good, with a large range of fluorophores available||Excellent, with a wide variety of substrates available|
|Consistency||High reproducibility between blots||Possible variation between blots|
|Detection||Requires imaging instruments with suitable light source and filters||Film or imaging instrument|
|Quantitation||Multiplexing with an internal control makes normalization simpler||Single-channel detection makes normalization challenging|
While the detection limits are not as low as chemiluminescent detection, fluorescent detection has the unique advantage of allowing multiple targets to be assayed on the same blot at the same time without the need to strip and reprobe. Multiplexing helps make research more efficient and productive. For example, one can visualize a protein of interest simultaneously with a loading control protein, or differentiate proteins of similar molecular weights, or evaluate complex biological pathways. With the iBright FL1500 Imaging System, one can perform up to a 4-plex fluorescent western blots with the appropriate experimental setup.
In addition to enabling multiplexing, fluorescent western blot detection has several other advantages compared to enzyme-based chemiluminescent substrate detection. Fluorescent western blotting provides accurate, quantitative results, stable signals, and the ability to conserve sample due to multiplexing.
Detection of targets of similar molecular weights. Fluorescent multiplexing allows clear distinction of multiple targets on the same blot, even when they are of similar molecular weights. A composite image is shown along with images showing the single-color signals of individual proteins. Visualizing the individual signals can sometimes enable assessment of details that may be harder to see in a composite.
When getting started with fluorescent western blotting, some reagents and steps will need to be optimized to help ensure background fluorescence does not interfere with detection of the protein of interest. Here are some tips for getting started:
HeLa lysates prepared with Fluorescent Compatible Sample Buffer or with sample buffer containing bromophenol blue. Samples were separated on a Tris-glycine gel and transferred to a nitrocellulose membrane. Image was captured using the appropriate filter sets for Near-IR dyes at 680 nm.
Background fluorescence of common membranes. Common membranes such as PVDF have high levels fluorescence in the low visible light range (488 nm) whereas specialty low-fluorescence PVDF does not. Exposure time: 1 second. All contrasted the same to illustrate differences. Results can vary based on manufacturer.
Explore:Fluorescence friendly reagents
The selection of appropriate primary antibodies and fluorescently labeled secondary antibodies is critical when designing a fluorescent multiplex western blot experiment. Here are some guidelines to consider:
In a multiplex western blot, ideally each target protein is captured independently in separate images under conditions that eliminate any crosstalk between the fluorescent probes. Therefore, it is essential to know the configuration of the western blot imaging instrument before you begin, most importantly the available excitation and emission filter sets. Many imaging systems use a combination of excitation and emission filter sets that can be chosen to allow a narrow range of light wavelengths to pass through to excite the fluorophore and for the specific fluorophore emission to enter the camera’s detector. Instead of filter sets, some instruments may use independent narrow-spectrum light sources for excitation. The specific combination of excitation and emission conditions used is often referred to as a “channel” or “layer” and determines what fluorescent probes can be imaged separately. Depending on the instrument, the available filters may come preinstalled or require installation.
|Excitation channel||Filter range (nm)||Emission channel||Filter range (nm)||Example compatible fluorophores|
|EX1||455-485||EM1||515-564||Alexa Fluor Plus 488, Alexa Fluor 488|
|EX2||515-545||EM2||568-617||Alexa Fluor Plus 555, Alexa Fluor 546|
|EX3||608-632||EM3||675-720||Alexa Fluor Plus 647, Alexa Fluor 594|
|EX4||610-660||EM4||710-730||Alexa Fluor Plus 680, Alexa Fluor 680|
|EX5||745-765||EM5||800-850||Alexa Fluor Plus 800, Alexa Fluor 790|
|Filter sets pre-installed in iBright FL1500 Imaging Systems for visible light range (RGB) and near infrared range (NIR) fluorescent western blotting applications.|
Use a tool like the Fluorescence SpectraViewer to determine excitation and emission spectral overlap among the fluorophores available, in the context of the specific imaging instrument’s equipped excitation and emission filters. Ideally, the fluorophores used in a multiplex experiment have distinct regions of either excitation or emission spectra that are compatible with the imaging system’s filters. Note, only a region of either the excitation or the emission spectrum needs to be distinct (not both).
An example of two fluorophores with a high degree of excitation and emission spectral overlap. This type of combination should be avoided. Portions of the excitation and emission spectra of both Alexa Fluor Plus 647 and Alexa Fluor 680 fluorophores are within the ranges of the excitation and emission filters, so both fluorophores would be excited and their emissions would reach the camera’s detector under these conditions, making it difficult to distinguish the source of the detected fluorescence.
An example of a combination of fluorophores with minimal excitation spectral overlap. the excitation spectra (dashed lines) of Alexa Fluor Plus 488 and Alexa Fluor 546 fluorophores have minimal overlap within the range of the excitation filter. Despite both fluorophores having part of their emission spectra (solid lines) within the range of the emission filter, Alexa Fluor 546 would not be excited by the excitation filter that has been selected for Alexa Fluor Plus 488, so no fluorescence from Alexa Fluor 546 would be present to go through the emission filter.
An example of a combination of fluorophores with minimal emission spectral overlap. the emission spectra (solid lines) of Alexa Fluor Plus 680 and Alexa Fluor 790 have no overlap within the ranges of the two emission filters. Despite both fluorophores having part of their excitation spectra (dashed lines) within the range of excitation filter 1, any Alexa Fluor 790 fluorescence generated by that excitation range is not within the wavelengths allowed to pass through emission filter 1, so no fluorescence from Alexa Fluor 790 would reach the camera detector in that channel.
|Example fluorophore combinations|
|Number of targets||Conjugate 1||Conjugate 2||Conjugate 3||Conjugate 4|
|1||Alexa Fluor Plus 647|
|2||Alexa Fluor Plus 647||Alexa Fluor Plus 546|
|3||Alexa Fluor Plus 647||Alexa Fluor Plus 546||Alexa Fluor Plus 488|
|4||Alexa Fluor Plus 647||Alexa Fluor Plus 546||Alexa Fluor Plus 488||Alexa Fluor Plus 790|
Secondary antibody conjugates with Invitrogen Alexa Fluor Plus dyes are designed for a variety of multiplex fluorescent protein immunoassay methods, including multiplex western detection. Alexa Fluor Plus secondary antibodies have up to 4.2 times higher signal-to-noise in immunofluorescence imaging and up to 5.8 times higher signal-to-noise ratio in western fluorescent blotting while having lower cross-reactivity compared to leading Alexa Fluor secondary antibodies.
Because the signal output from fluorescent western blotting is proportional to the amount of protein present, it is possible to make quantitative measurements from western blot experiments. This aspect of western blotting can be useful when looking at treatments that cause changes in expression levels of proteins. However, to verify that any change is the result of the treatment and not changes in the amount of sample loaded, the protein target signals must be normalized.
Normalization has been traditionally performed using a housekeeping protein, normally expressed at consistent levels to normalize results. GAPDH, beta-actin, and beta-tubulin are housekeeping proteins that are commonly used for loading normalization and are typically referred to as loading control proteins. The choice of which of these loading control proteins to include in western blot detection depends on whether there is a chance that any experimental treatment impacts the expression of the housekeeping protein. When detecting housekeeping proteins, a different conjugate or color is used from the target protein detection. The fluorescent intensities are measured and then expressed as a ratio of target intensity to normalizing protein intensity. When running these multiplexed experiments, it is important to choose secondary antibodies that do not cross-react. Pre-conjugated loading control antibodies can be used to simplify these quantitative experiments by removing the need for a secondary antibody for these highly abundant targets.
Simultaneous detection of protein of interest and loading control protein. The signal of the loading control (GAPDH) can be used to normalize the signal of the target protein (cleaved PARP). Composite image shown, overlaying the signals from each probe.
Housekeeping proteins can often be affected by experimental conditions and can often have oversaturated western blotting signals due to high abundance. In these cases, total protein normalization is a better strategy for quantitative western blotting. Total protein analysis is independent of the shortfalls of loading control proteins, where the total protein loaded is used to normalize the target signals. Total protein loads can be determined using several different protein membrane stains or labeling reagents, such as No-Stain Protein Labeling reagent. It is important when normalizing to normalize to total protein loads on the membrane to account for variable transfer efficiencies.
For detection of any western blot, it is desirable to use prestained molecular weight markers (also called protein ladders) that are transferred to the membrane along with the protein sample. The appearance of the molecular weight markers on the membrane allows estimation of molecular weights for any protein bands that are detected and verification of the effective separation of the proteins of interest in the gel prior to the transfer step. The dyes used to make prestained molecular weight markers often have some fluorescent properties, however their signals can potentially overwhelm the fluorescence of the target proteins. Using protein ladders specifically designed for fluorescent western blotting can help balance the fluorescent signals. In addition, protein molecular weight markers that are labeled with fluorophores can provide better signal-to-noise ratios.
|iBright Prestained Protein Ladder||PageRuler Plus Prestained Protein Ladder||PageRuler Prestained NIR Protein Ladder|
|Applications||Fluorescence, chemiluminescent, direct visualization||NIR and RGB fluorescence, direct visualization||NIR fluorescence, direct visualization|
|Molecular weight range||~10-250 kDa||~10-250 kDa||~11-250 kDa|
|Number of bands||12||9||10|
|No. of colors||10 single colored bands (prestained)||9 colored bands- six blue, one green and two orange bands (prestained)||10 single colored bands (prestained)|
|Major features||Two unstained proteins (30 and 80 kDa) with IgG binding sites for chemiluminescent or fluorescent detection||Three colors for quick reference of approximate size||Reference band at 55kDa with greater intensity|
|Fluorescence wavelength||NIR (700 nm) and determined by 2° antibodies used||700 nm and 550nm||NIR (700 nm)|
For Research Use Only. Not for use in diagnostic procedures.