Fact-checked by Grok 2 weeks ago

Northern blot

The Northern blot, also known as an RNA blot, is a classical molecular biology technique used to detect, identify, and quantify specific RNA sequences, such as messenger RNA (mRNA), in a biological sample by separating RNA molecules based on size and hybridizing them with complementary probes.^[1] Developed in 1977 by James C. Alwine, David J. Kemp, and George R. Stark at Stanford University, the method was named as a playful pun on the earlier Southern blot technique for DNA, adapting the transfer and hybridization principles to RNA analysis while protecting against degradation by ribonucleases.^[2] The procedure begins with the extraction and denaturation of total RNA or mRNA from cells or tissues to prevent secondary structure formation, followed by size-based separation via electrophoresis in a denaturing agarose gel, typically containing formaldehyde or glyoxal to maintain single-stranded RNA.^[3] The separated RNA is then transferred (or "blotted") from the gel to a solid support, such as a nitrocellulose or nylon membrane, using capillary action, vacuum, or electroblotting, preserving the RNA's positional order.^[3] Finally, the membrane is hybridized with a labeled nucleic acid probe—often radioactively or enzymatically tagged DNA or RNA complementary to the target sequence—allowing visualization and quantification of the specific RNA through autoradiography, chemiluminescence, or fluorescence detection.^[3] Northern blotting has been instrumental in studying gene expression by measuring steady-state levels of transcripts, determining RNA sizes, and identifying alternative splicing variants or processing events, though its sensitivity is limited compared to modern methods like quantitative reverse transcription PCR (qRT-PCR) or RNA sequencing (RNA-seq).^[3] Despite these limitations, including labor-intensive steps and requirements for relatively high RNA amounts, the technique remains valuable for validating RNA integrity and providing direct evidence of transcript abundance without amplification biases.^[3]

Background and Principle

History

The Northern blot technique was invented in 1977 by James C. Alwine, David J. Kemp, and George R. Stark at Stanford University as an analog to the Southern blot for detecting RNA sequences rather than DNA.^[4] Their method involved transferring RNA from agarose gels to diazobenzyloxymethyl-paper for hybridization with labeled probes, enabling specific RNA detection with high sensitivity.^[4] This innovation was detailed in their seminal publication in the Proceedings of the National Academy of Sciences that same year, which described the procedure for identifying specific RNA sequences in complex samples through gel electrophoresis, transfer, and hybridization.^[4] The technique emerged amid the burgeoning field of molecular biology following the recombinant DNA revolution of the early 1970s, providing a crucial tool for RNA analysis in an era when direct amplification methods were unavailable.^[5] It saw early adoption in the late 1970s and throughout the 1980s as the primary method for studying gene expression levels and RNA abundance, particularly before the widespread use of polymerase chain reaction (PCR) technologies in the 1990s. Key milestones included the routine integration of radioactive labeling, such as 32P-labeled probes with autoradiographic detection, which became standard in the 1980s for enhancing sensitivity in gene expression studies.^[4] By the 1990s, safety concerns over radioactive materials drove a shift toward non-radioactive probes, including chemiluminescent detection systems like those using horseradish peroxidase or alkaline phosphatase, which offered comparable sensitivity without radiological hazards.

Underlying Mechanism

The Northern blot technique relies on the size-based separation of RNA molecules through gel electrophoresis, followed by their immobilization onto a solid membrane and specific detection via hybridization with complementary probes. This process enables the identification and quantification of particular RNA species within a complex mixture, preserving the relative positions of separated molecules to infer their sizes. The method was developed as an adaptation for RNA analysis, building on principles of nucleic acid transfer and hybridization.^[4] To achieve accurate separation, RNA samples are denatured into single strands using denaturing agents such as formaldehyde, which disrupts secondary structures like hairpins and loops that could otherwise cause anomalous migration during electrophoresis. In a denaturing agarose gel, RNA molecules migrate based on their molecular weight under an electric field, with smaller fragments moving faster toward the anode due to the negatively charged phosphate backbone. This electrophoretic separation ensures that RNA is resolved primarily by size rather than conformation.^[3] Following separation, the RNA is transferred from the gel to a membrane—typically nitrocellulose or nylon—via capillary action or electroblotting, where it becomes covalently bound or adsorbed, immobilizing the molecules in their size-ordered positions. Detection occurs through hybridization, where a labeled probe (usually single-stranded DNA or RNA complementary to the target sequence) binds specifically to the immobilized RNA via Watson-Crick base pairing: adenine with uracil (or thymine in DNA probes) and guanine with cytosine, forming stable hydrogen-bonded duplexes under controlled stringency conditions. This specificity allows discrimination of closely related RNA sequences.^[4]^[3] The bound probe-target complexes are then visualized using various labeling strategies, such as radioactivity (e.g., phosphorus-32 incorporated into the probe, detected by autoradiography), fluorescence (via fluorescent dyes attached to the probe), or enzymatic methods (e.g., horseradish peroxidase conjugates producing chemiluminescent signals). A critical feature of the technique is the retention of size information after transfer, as the relative migration distances from gel standards (RNA ladders of known lengths) correspond directly to the positions on the membrane, enabling estimation of target RNA molecular weights in kilobases.^[4]^[3]

Experimental Procedure

RNA Sample Preparation

RNA sample preparation for Northern blotting begins with the isolation of high-quality total RNA from cells or tissues to ensure accurate detection of specific RNA transcripts. Common methods include phenol-chloroform extraction using reagents like TRIzol, which involves cell lysis in a monophasic solution of phenol and guanidine isothiocyanate, followed by phase separation, precipitation with isopropanol, and washing to yield intact RNA while minimizing protein and DNA contamination.^[6] Alternatively, column-based kits such as PureLink RNA or RNeasy employ silica-membrane binding in the presence of chaotropic salts, enabling selective RNA purification with optional on-column DNase treatment to eliminate genomic DNA carryover, which is critical for avoiding false hybridization signals.^[7] These approaches are widely adopted due to their compatibility with diverse sample types and high yield of RNase-free RNA.^[8] Following extraction, RNA quantification and quality assessment are essential to confirm suitability for blotting. Spectrophotometric measurement at 260 nm and 280 nm yields an A260/A280 ratio of approximately 2.0, indicating pure RNA free from protein contaminants, while ratios below 1.8 suggest the need for repurification.^[9] Additionally, running a small aliquot on a non-denaturing agarose gel reveals intact ribosomal RNA bands (28S and 18S), with the absence of smearing signifying minimal degradation, as even partial RNA breakdown can reduce blotting sensitivity by up to 20%.^[10]^[11] To prepare samples for gel loading, RNA must be denatured to disrupt secondary structures and ensure linear migration. Standard protocols involve mixing RNA with glyoxal and dimethyl sulfoxide (DMSO), heating to 50–60°C for 1 hour, which modifies guanosine residues to prevent base pairing and yields sharper bands compared to formaldehyde-based denaturation.^[12] Alternatively, formaldehyde in MOPS buffer can be used for denaturation at 65–70°C for 5–15 minutes, though it requires a fume hood due to toxicity.^[10] These treatments are followed by cooling on ice and brief centrifugation to collect the sample.^[13] Throughout preparation, stringent precautions prevent RNase-mediated degradation, which can compromise RNA integrity. All reagents and equipment must be RNase-free, achieved by treating solutions with diethyl pyrocarbonate (DEPC) to inactivate RNases, followed by autoclaving, and surfaces wiped with RNase decontamination sprays like RNaseZap.^[10] Work should occur on ice or at 4°C, with gloves changed frequently to avoid skin-derived RNases, and optional addition of RNase inhibitors during lysis.^[7] Finally, denatured RNA is loaded onto the gel in amounts typically ranging from 5 to 20 μg per lane for total RNA, depending on transcript abundance and detection sensitivity, with higher loads (up to 30 μg) used for low-expression genes.^[10]^[3] An RNA molecular weight ladder, such as one spanning 0.2–10 kb, is included in a separate lane to enable size estimation of hybridizing bands post-transfer.^[14] Samples are mixed with loading dye containing formamide or glycerol for even distribution in wells.^[15]

Gel Electrophoresis

In the gel electrophoresis step of Northern blotting, denatured RNA samples are loaded into wells of an agarose gel and subjected to an electric field, allowing separation of RNA molecules primarily by size under denaturing conditions that disrupt secondary structures and maintain single-strandedness.^[16] This process ensures that RNA migration is proportional to molecular weight, with smaller fragments moving faster toward the anode.^[14] Agarose gels at concentrations of 1-2% are commonly used, prepared with denaturants such as 2-6.7% formaldehyde or glyoxal (typically 1-2 M in combination with 50% DMSO) to prevent RNA folding and aggregation.^[16]^[17] Formaldehyde-based gels require running under a fume hood due to volatility, while glyoxal offers a less hazardous alternative without compromising denaturation efficiency.^[17] The gel is cast in 1× MOPS buffer (20 mM MOPS, 5 mM sodium acetate, 1 mM EDTA, pH 7.0) for formaldehyde systems, which provides a stable pH to support uniform RNA migration and minimize band broadening.^[16]^[15] Electrophoresis is performed in recirculating 1× MOPS buffer at 5-10 V/cm (typically 50-100 V total) for 4-6 hours, or until the bromophenol blue tracking dye migrates 2/3 to 3/4 of the gel length, achieving resolution of RNA species from 0.2 to 10 kb.^[16]^[15] Higher voltages can shorten run times but may generate heat, potentially causing band distortion if not managed with cooling.^[18] RNA samples, denatured in formamide or glyoxal during preparation, are mixed with loading buffer containing tracking dyes (e.g., bromophenol blue and xylene cyanol) and loaded alongside RNA ladders for size reference.^[16] For visualization of RNA integrity and loading equality prior to transfer, gels are stained post-run with ethidium bromide (0.5-1 μg/mL for 15-30 min) or safer alternatives like SYBR Green II (1:10,000 dilution), which offers up to 25-fold higher sensitivity than ethidium bromide for ssRNA without significantly altering migration.^[19]^[20] Post-staining, gels are destained briefly in buffer and imaged under UV transillumination, with precautions to limit exposure (e.g., short-wave UV at minimal intensity for seconds) to avoid UV-induced RNA photodegradation or cross-linking that could impair transfer efficiency.^[19]^[21]

Transfer to Membrane

Following gel electrophoresis, which separates RNA molecules by size under denaturing conditions, the RNA must be transferred from the agarose gel to a solid membrane support to enable immobilization and subsequent analysis.^[9] This transfer step preserves the spatial separation of RNA fragments while facilitating their binding to the membrane through passive or active methods.^[22] The standard technique for RNA transfer is capillary blotting, a passive process originally described in the seminal Northern blot method, where RNA migrates from the gel to the membrane via capillary action driven by a buffer gradient and gravity.^[4] In this setup, the gel is placed on a wick saturated with transfer buffer, such as 10× SSPE or 20× SSC, which provides high ionic strength to promote RNA elution without excessive diffusion; stacks of absorbent paper towels or a buffer reservoir above the membrane draw the buffer upward, typically completing the transfer overnight (approximately 12–18 hours) for fragments up to 15 kb.^[9] For faster results, electroblotting applies an electric field to drive negatively charged RNA toward the membrane, using a buffer like 0.5× TBE and constant current (e.g., 200 mA) for 30–60 minutes at 10–20 V, though this method requires specialized equipment and is more common for polyacrylamide gels.^[22] Common membrane materials include nitrocellulose, which binds RNA via hydrophobic interactions and is suitable for smaller RNA molecules (<5 kb) due to its high binding capacity but lower durability, and nylon membranes, which are preferred for most applications as they offer electrostatic binding—especially positively charged variants that attract the negatively charged RNA backbone—for improved retention of larger transcripts.^[9] Positively charged nylon, such as BrightStar-Plus, enhances sensitivity by minimizing RNA loss during transfer and handling.^[22] After transfer, RNA is covalently fixed to the membrane to prevent dissociation during subsequent washes; this is achieved by UV crosslinking at 120 mJ/cm² (e.g., 1–3 minutes under 254–302 nm light) for nylon membranes or baking at 80°C for 15–30 minutes in a vacuum oven for both nitrocellulose and nylon, ensuring stable immobilization.^[22]^[9]

Hybridization and Detection

Following the transfer of RNA to a membrane, the hybridization and detection phase begins with the preparation of a specific probe designed to recognize the target RNA sequence. Probes are typically synthesized as single-stranded DNA or RNA oligonucleotides, or as complementary DNA (cDNA) fragments ranging from 200 to 1000 base pairs in length, ensuring complementarity to the RNA of interest for stable duplex formation.^[10]^[12] These probes are labeled either radioactively, most commonly with phosphorus-32 (³²P) via random priming or end-labeling methods, or non-radioactively using haptens such as digoxigenin (DIG) incorporated during in vitro transcription or chemical modification.^[23] The choice of labeling influences sensitivity and safety, with radioactive probes offering high specific activity for detecting low-abundance transcripts, while non-radioactive alternatives like DIG enable chemiluminescent detection without handling isotopes.^[23]^[24] Hybridization occurs by incubating the membrane in a buffer containing the denatured probe, typically composed of 50% formamide, 5× saline-sodium citrate (SSC), and blocking agents like Denhardt's solution or salmon sperm DNA to reduce non-specific binding.^[12]^[9] This mixture is maintained at 42–65°C—adjusted based on probe length and GC content—for 12–24 hours to allow specific annealing of the probe to complementary RNA sequences immobilized on the membrane.^[12]^[25] The formamide lowers the melting temperature, facilitating hybridization under milder conditions than those for DNA, while SSC provides ionic strength to stabilize the RNA-probe hybrids.^[10] After incubation, excess probe is removed through a series of washes, starting with low-stringency steps in 2× SSC with 0.1% sodium dodecyl sulfate (SDS) at room temperature, followed by stringent washes in 0.1× SSC with 0.1% SDS at 50–68°C to dissociate weakly bound or mismatched hybrids, thereby enhancing signal specificity.^[25]^[9] Detection methods vary by probe label to visualize the hybridized RNA-probe complexes as discrete bands corresponding to transcript sizes. For ³²P-labeled probes, autoradiography exposes the dried membrane to X-ray film or phosphorimaging screens, capturing beta particle emissions to produce a permanent record with sensitivity down to femtogram levels of RNA.^[12] Non-radioactive probes, such as those conjugated to DIG or biotin, are detected via enzyme-linked immunoassays: anti-DIG antibodies coupled to alkaline phosphatase generate a chemiluminescent signal upon substrate addition, captured on film or digital imagers, while biotinylated probes bind streptavidin-horseradish peroxidase conjugates for similar enhanced chemiluminescence or fluorescence-based readout.^[23]^[24] These approaches provide comparable sensitivity to radioactivity but with shorter exposure times and reduced hazards, often achieving detection limits of 0.1–1 pg of target RNA.^[23] Quantification of hybridization signals involves densitometric analysis of band intensities on the resulting autoradiographs or digital images, using software to measure optical density and normalize against housekeeping gene controls (e.g., 18S rRNA) or total RNA loading markers to account for variations in sample amount or transfer efficiency.^[26]^[27] This relative quantification yields semi-quantitative estimates of RNA abundance, with linear dynamic ranges spanning 1–2 orders of magnitude, enabling comparisons across experimental conditions while confirming transcript integrity through size correlation with molecular weight markers.^[26]^[27]

Applications

Gene Expression Analysis

Northern blotting serves as a foundational technique for quantifying specific mRNA abundance to assess gene expression levels in response to various biological stimuli, such as hormone treatments or disease states. By hybridizing labeled probes to blotted RNA samples, researchers can measure changes in transcript levels, providing insights into regulatory mechanisms. For instance, in studies of thyroid hormone effects, Northern blot analysis revealed distinct temporal patterns of gene expression, with some mRNAs upregulated within hours of hormone administration, verifying differential responses in liver tissues. Similarly, in cancer contexts, this method has quantified elevated mRNA levels under pathological conditions, enabling correlation with cellular phenotypes. The technique also facilitates the detection of alternative splicing isoforms through the identification of band size differences on the gel, allowing differentiation of mature mRNA variants produced from a single gene. Probes specific to common exons hybridize to multiple bands corresponding to isoform lengths, thus revealing splicing patterns influenced by cellular conditions. This approach has been applied to confirm the generation of specific spliced mRNAs in cell lines, where Northern blots distinguished isoforms based on migration patterns post-electrophoresis. Such analysis is crucial for understanding isoform-specific functions in gene regulation. Tissue-specific expression profiling is another key application, where Northern blotting compares mRNA levels across different cell types or developmental stages to map gene activity spatially and temporally. By loading RNA from varied tissues onto the same gel, relative abundance can be assessed via band intensity, highlighting genes active in particular organs. For example, analysis of the C/EBP transcription factor demonstrated high mRNA expression in liver and adipose tissues but low levels elsewhere in adult mice, underscoring its role in metabolic regulation. This profiling has been instrumental in elucidating developmental gene cascades. To ensure accurate quantification, Northern blots incorporate normalization using probes for housekeeping genes like GAPDH or β-actin, which provide stable reference signals to account for variations in RNA loading or transfer efficiency. These controls help adjust for technical inconsistencies, yielding reliable relative expression data. Early applications in oncogene research, such as the 1985 study of c-myc in breast cancer, utilized Northern blotting to detect overexpressed 2.4 kb transcripts in lymph node-positive tumors, linking elevated levels to metastatic potential and establishing the method's value in cancer diagnostics during the 1980s.

RNA Characterization

Northern blotting serves as a key technique for characterizing RNA molecules by leveraging the size-based separation achieved during gel electrophoresis, which is preserved during transfer to a membrane, allowing direct assessment of transcript length and structural features.^[12] This method enables researchers to estimate the size of RNA transcripts in kilobases (kb) by comparing the migration distance of hybridized bands to known RNA ladders run alongside the samples.^[28] For instance, in studies of noncoding RNAs, northern blots have confirmed transcript lengths around 1.4 kb through precise band positioning relative to markers.^[29] Verification of RNA integrity is another critical application, where the presence of discrete, sharp bands indicates intact molecules, while degraded RNA produces characteristic smear patterns due to fragmentation.^[30] In high-quality samples, ribosomal RNA (rRNA) bands appear prominent and well-defined, contrasting with the diffuse smears observed in partially degraded RNA, which lack the typical 2:1 ratio of 28S to 18S rRNA.^[31] This visual assessment via northern blot hybridization helps identify degradation artifacts before downstream analyses, ensuring reliable structural evaluation.^[32] The technique also distinguishes polyadenylated from non-poly(A) RNAs by employing oligo(dT) probes that specifically hybridize to the poly(A) tails of mature mRNAs.^[33] In northern blots, oligo(dT) hybridization reveals bands corresponding to poly(A)+ transcripts, while the absence of signal in treated samples confirms non-polyadenylated species, such as certain noncoding RNAs.^[34] For viral RNAs and rRNAs, northern blotting facilitates identification of full-length genomes or ribosomal components, particularly in infection contexts.^[35] Probes targeting specific regions detect intact viral subgenomic RNAs, confirming their size and presence in infected cells. Similarly, for rRNAs, northern blots verify packaging of full-length 18S and 28S species in viral ribonucleoprotein complexes during infection.^[36] In mapping transcription units, northern blotting confirms start and end sites by strategically positioning probes along the gene locus to detect specific transcript boundaries.^[37] For example, probes near promoter regions hybridize to 5' ends, while those at terminators identify read-through versus terminated products, delineating unit extents as in type 3 polymerase III transcripts.^[38] This probe-based localization has clarified heterogeneous transcription start sites in zinc-responsive genes.^[39]

Advantages and Limitations

Key Strengths

Northern blotting offers high specificity through the use of complementary nucleic acid probes that hybridize to target RNA sequences, enabling the detection of single-nucleotide mismatches and minimizing non-specific binding that can lead to false positives in amplification-based methods like PCR.^[40] This hybridization-based approach ensures that only closely related sequences are identified, providing a reliable confirmation of RNA presence without the artifacts often associated with primer mismatches or off-target amplification in RT-PCR.^[41] A key strength of the technique is its ability to simultaneously provide information on both the size and relative abundance of RNA transcripts from a single sample, which is not possible with quantitative reverse transcription PCR (qRT-PCR), as the latter focuses solely on abundance and loses spatial resolution regarding transcript length.^[42] By separating RNAs via gel electrophoresis prior to transfer and detection, Northern blotting allows visualization of transcript integrity, splice variants, and multigene family members on the same blot, offering a comprehensive profile of RNA species in contexts like gene expression studies.^[30] The method supports the detection of multiple transcripts using a single gel by employing sequential or multiplexed probing strategies, where different probes can be applied to the same membrane after stripping, facilitating efficient analysis of gene families or co-expressed RNAs without requiring separate gels for each target.^[43] Additionally, unlike amplification-dependent techniques, Northern blotting avoids biases introduced by reverse transcription or PCR efficiency variations, delivering a direct measurement of steady-state RNA levels that accurately reflects the cellular RNA pool.^[44] Since the 1990s, Northern blotting has benefited from versatile non-radioactive labeling options, such as digoxigenin or biotin incorporation during probe synthesis, which enhance safety by eliminating the hazards of radioisotopes while maintaining detection sensitivity through chemiluminescent or enzymatic systems.^[45] These advancements have made the technique more accessible and practical for routine laboratory use, preserving its utility in verifying RNA expression patterns.^[46]

Principal Drawbacks

Northern blotting suffers from low sensitivity, typically requiring 10–30 μg of total RNA per sample for reliable detection, which limits its utility for low-abundance or rare transcripts.^[25] In contrast, PCR-based methods like RT-qPCR require only nanogram quantities of RNA, enabling analysis of scarce material.^[30] This higher RNA demand arises from inefficiencies in gel separation, transfer, and hybridization steps, often resulting in weak signals for minor RNA species.^[47] The technique is labor-intensive and time-consuming, typically requiring multiple days to complete the full workflow from RNA preparation to detection, compared to the few hours needed for RT-qPCR.^[10] This extended timeline stems from sequential manual steps, including electrophoresis, blotting, and prolonged hybridization periods, which demand significant hands-on effort and increase the risk of procedural errors.^[48] Quantitation via Northern blotting is semi-quantitative at best, hampered by inconsistencies in transfer efficiency, probe hybridization, and background noise that introduce variability across samples.^[48] Unlike absolute quantification possible with qPCR, these factors make precise measurement of RNA levels challenging without extensive normalization controls.^[49] RNA's vulnerability to degradation by RNases poses a major challenge, requiring rigorous RNase-free conditions throughout handling to avoid loss of sample integrity and signal.^[10] Even minor contamination can compromise results, as a single RNase-induced cleavage can substantially reduce detectable RNA bands.^[30] In the modern genomics era, Northern blotting has become largely obsolete for routine use, supplanted by high-throughput RNA sequencing (RNA-seq) since the late 2000s due to the latter's superior scalability and sensitivity.^[50] While it retains niche applications, the shift to RNA-seq has diminished its prevalence in gene expression studies.^[51]

Variants

Reverse Northern Blot

The reverse northern blot is a variant of the northern blot technique in which the roles of the target and probe are reversed to facilitate analysis of multiple gene candidates. In this method, cDNA fragments or PCR-amplified products derived from a cDNA library or differential display are immobilized by spotting them onto a nylon or nitrocellulose membrane in an array format. Labeled cDNA probes, synthesized from total RNA or mRNA of the sample via reverse transcription, are then hybridized to these immobilized DNA targets under stringent conditions to detect binding signals indicative of gene expression levels. This reversal allows for the direct assessment of RNA abundance against numerous predefined DNA sequences without prior separation by electrophoresis.^[52] Developed for high-throughput screening of differentially expressed genes, the reverse northern blot emerged as a key tool in the late 20th century alongside techniques like differential display and subtractive hybridization. It enables researchers to test hundreds of candidate clones simultaneously using minimal amounts of RNA, reducing the labor-intensive need to sequence each potential differentially expressed gene individually. By comparing hybridization intensities from probes derived from control and experimental RNA samples on duplicate membranes, the technique identifies upregulated or downregulated transcripts efficiently.^[53] A primary application of the reverse northern blot is in identifying upregulated clones from expression libraries, particularly in studies of cellular responses to stimuli or developmental processes, where it confirms true positives and filters false artifacts from initial screens like differential display PCR. For instance, in neuronal regeneration research, candidate genes from cDNA libraries are screened via this method to validate differential expression before full cloning and sequencing, streamlining the discovery of novel transcripts. It is especially useful in subtractive hybridization workflows, where abundant common sequences are removed, allowing focused detection of rare, condition-specific RNAs.^[54]^[55] Compared to the standard northern blot, the reverse northern offers advantages in scalability and RNA economy, as it screens many targets at once rather than analyzing one RNA species per blot, though it does not provide information on transcript size or integrity. Detection follows similar principles to the conventional approach, involving autoradiography, chemiluminescence, or fluorescence after hybridization, often with radioactive or digoxigenin-labeled probes, but the immobilized DNA array format positions it as an early precursor to high-density microarray technologies for genome-wide expression profiling.^[52]

Quantitative Northern Blot

The quantitative Northern blot enhances the standard technique by incorporating methods for accurate measurement of RNA abundance, addressing limitations in sensitivity and reproducibility of traditional film-based detection. A key improvement involves the addition of internal standards, such as in vitro-transcribed RNA spikes, which are added to samples prior to processing to normalize for variations in RNA loading, transfer efficiency, and hybridization conditions. These exogenous controls, often non-homologous to the target RNA, enable relative quantification by comparing signal intensities of the target to the known amount of spike-in RNA, improving the reliability of expression level comparisons across samples.^[56] Phosphorimaging represents a significant advancement over film autoradiography for digital quantification in Northern blots, offering a linear dynamic range of up to five orders of magnitude (10^5-fold), which allows detection of both low- and high-abundance RNAs in a single exposure without saturation. In this method, radiolabeled probes hybridize to the blotted RNA, and the membrane is exposed to a storage phosphor screen that captures emitted radiation as a latent image, which is then scanned to produce quantifiable digital data. This replaces the non-linear response of X-ray film, enabling precise densitometric analysis and reducing exposure times by 10- to 100-fold compared to traditional methods.^[57]^[58] Slot and dot blots integrate with Northern blotting protocols as simplified variants for direct RNA quantification, bypassing gel electrophoresis to focus solely on abundance rather than size separation. In these approaches, denatured RNA samples are applied directly to a membrane via slots or dots under vacuum, hybridized with probes, and detected similarly to traditional blots, allowing high-throughput screening of multiple samples for relative expression levels. Since the 1990s, improvements have included non-radioactive detection systems akin to ELISA, using enzyme-conjugated antibodies or streptavidin for chemiluminescent or colorimetric signals, which provide faster processing (hours instead of days) and enhanced reproducibility without handling radioactivity.^[59]02219-8/fulltext) For data analysis, software tools like ImageJ facilitate band or spot volume measurement by selecting regions of interest, subtracting background noise, and integrating pixel intensities to yield quantitative values normalized against internal standards or loading controls. These open-source programs process scanned images from phosphorimagers or chemiluminescent detectors, supporting statistical comparisons and error estimation for robust interpretation of RNA levels.^[60]

References

[1]
Northern Blot - National Human Genome Research Institute
Northern blot is a laboratory technique used to detect a specific RNA sequence in a blood or tissue sample.
[2]
Northern blot - PMC - NIH
Northern blot first uses denaturing gel to separate RNA according to the size. The RNA is then transferred to a nylon membrane while keeping the same ...
[3]
Method for detection of specific RNAs in agarose gels by transfer to ...
We describe a technique for transferring electrophoretically separated bands of RNA from an agarose gel to paper strips.Missing: blot | Show results with:blot
[4]
The early days of blotting - PubMed
The term Southern blotting led to a "geographic" naming tradition, with RNA blotting bearing the name Northern blotting and protein transfer to membranes ...Missing: recombinant | Show results with:recombinant
[5]
The Methodology Used to Measure Differential Gene Expression ...
Northern blot analysis is the gold standard to which newer technologies should be compared. This is because factors inherent to Northern blotting serve to ...Missing: history adoption
[6]
[PDF] TRIzol Reagent User Guide (Pub.No. MAN0001271 D)
TRIzol Reagent isolates high quality total RNA, DNA, and proteins from cell and tissue samples within one hour. It is a monophasic solution.<|separator|>
[7]
Top Ten Ways to Improve Your RNA Isolation
The easiest and safest methods available are column-based methods like the PureLink RNA ... Alternatively, for other RNA isolation methods, such as TRIzol ...
[8]
Impact of RNA isolation protocols on RNA detection by Northern ...
Our analysis included two hot phenol methods and two TRIzol extraction procedures. We found that signal intensity/detection sensitivity makes the key difference ...
[9]
Northern & Southern Blot Protocols
### Summary of Northern Blot Transfer to Membrane (Sigma-Aldrich)
[10]
The Basics: Northern Analysis | Thermo Fisher Scientific - US
RNA samples are first separated by size via electrophoresis in an agarose gel under denaturing conditions. The RNA is then transferred to a membrane, ...Introduction · Steps · RNA Isolation, Probe Generation
[11]
RNA quality control: 3 Key Considerations - Bitesize Bio
Jun 20, 2024 · The least expensive method for checking RNA integrity is to run the RNA on a 1% standard agarose gel and examine the ribosomal RNA (rRNA) bands ...Missing: Northern | Show results with:Northern
[12]
Analysis of RNA by Northern Blot Hybridization - Current Protocols
Nov 1, 2001 · This is arguably the quickest and most reliable method for northern analysis of specific sequences in RNA extracted from eukaryotic cells.
[13]
Northern blotting of RNA denatured in glyoxal without ... - PubMed
A rapid and easy procedure for preparing Northern blots is described. RNA is denatured with glyoxal in the presence of ethidium bromide and glycerol.
[14]
Northern Blotting - ScienceDirect.com
Mix 15 μg of the RNA sample with an equal volume of 2× RNA loading buffer. Dilute 3 μg Millennium RNA Markers in an equal volume of 2× RNA loading buffer.
[15]
https://goldbio.com/documents/2564/RNA%2520Gel%2520and%2520Northern%2520Blotting%2520Protocol.pdf
[16]
Agarose Gel Electrophoresis of RNA | Thermo Fisher Scientific - US
Protocol · Heat 1 g agarose in 72 ml water until dissolved, then cool to 60°C. · Add 10 ml 10X MOPS running buffer, and 18 ml 37% formaldehyde (12.3 M).
[17]
Top Ten Northern Analysis Tips | Thermo Fisher Scientific - US
Using glyoxal/DMSO instead of formaldehyde avoids the need to pour and run gels in a fume hood and eliminates safety issues associated with formaldehyde. How do ...
[18]
[PDF] Making Northern Blots of Agarose Gels
This protocol specifically deals with separating RNA by size on agarose gels, followed by transblotting to Hybond N membranes. Protocols for preparing cDNA ...
[19]
Optimal Northern Analysis | Thermo Fisher Scientific - US
Staining after the gel has been run is recommended because EtBr in the samples can supposedly alter migration of the RNA and inhibit complete transfer of the ...Missing: damage | Show results with:damage
[20]
https://www.lonzabio.jp/catalog/pdf/pd/PD056.pdf
[21]
Agarose Gel Electrophoresis, How It Works and Its Uses
Ensure you wear a UV face shield and keep skin covered while the light box is on to prevent damage to your skin or eyes by the UV light. Tap to unmute. Your ...Agarose Gel Electrophoresis... · In Agarose Gel... · What Is Agarose Gel...
[22]
Membrane Transfer and Crosslinking for RNA
Northern assays require the total RNA to be resolved on a denaturing agarose gel first, then transferred to a membrane and immobilized for subsequent ...
[23]
A sensitive non-radioactive northern blot method to detect small RNAs
Jan 15, 2010 · We describe a new northern blot-based protocol (LED) for small RNA (∼15–40 bases) detection using digoxigenin (DIG)-labeled oligonucleotide probes.
[24]
https://www.sigmaaldrich.com/US/en/technical-documents/protocol/genomics/nucleic-acid-labeling-and-detection/dig-northern-starter-kit
[25]
Modified Northern blot protocol for easy detection of mRNAs in total ...
Jan 20, 2022 · In this paper, we report modifications and tips used to improve the traditional Northern protocol for the detection of mRNAs in total RNA.
[26]
Northern blot analysis for detection and quantification of RNA in ...
In this protocol, we describe how northern blot analysis is used to identify gene expression patterns at the RNA level in human cancer cells as well as in ...
[27]
Northern blotting - Cambridge University Press & Assessment
Northern blotting is the main method for examining the expression of genes through measurement of an mRNA. Tissue specificity and the factors which regulate ...Missing: original | Show results with:original
[28]
Transcript isoform sequencing reveals widespread promoter ...
May 22, 2020 · Northern blotting revealed a broad size distribution for MPK20 sppRNAs in hen2-2, consistent with alternative sppRNA PASs (Fig. 3i). We ...Results · Methods · Northern Blotting
[29]
The long noncoding RNA ASNR regulates degradation of Bcl-2 ...
Aug 31, 2016 · Northern blot analysis confirmed the transcript size of approximately 1.4 kb (Fig. 1C). We further assessed the coding potential of the ...
[30]
Modified Northern blot protocol for easy detection of mRNAs in ... - NIH
Jan 20, 2022 · In this paper, we report modifications and tips used to improve the traditional Northern protocol for the detection of mRNAs in total RNA.
[31]
Methods of RNA Quality Assessment - Promega Corporation
In this article, we discuss the most common methods for RNA quantification and analysis. We include details about the appropriate application for each method.Absorbance · Fluorescent Dye-Based... · Agarose And Acrylamide Gel...Missing: blot | Show results with:blot
[32]
Methods to Check RNA Integrity | Thermo Fisher Scientific - US
Partially degraded RNA will have a smeared appearance, will lack the sharp rRNA bands, or will not exhibit the 2:1 ratio of high quality RNA. Completely ...
[33]
Polyadenylation-Dependent Control of Long Noncoding RNA ... - NIH
Nov 15, 2012 · Total RNA was treated with RNase H in the presence (+) or absence (−) of oligo(dT) before northern analysis using a SHG60-specific probe.
[34]
Complete editing is not required for long poly(A) tract addition
Northern blot analysis. For the blot presented in Figure 2A, 0.2 µg of mitochondrial oligo(dT) selected RNA was fractionated on a 6% acrylamide- ...
[35]
Efficient translation of poly(A)-deficient mRNAs in Saccharomyces ...
Total RNA was separated into poly(A)* and poly(A)-deficient RNA by oligo(dT)-cellulose chromatography and the amounts of each fraction determined by Northern ...
[36]
Structural Analysis and Whole Genome Mapping of a New ... - NIH
We report the biological and structural characterization of umbravirus-like associated RNAs (ulaRNAs), a new category of coat-protein dependent subviral RNA ...
[37]
RIG-I Detects Viral Genomic RNA during Negative-Strand RNA Virus ...
(E) Northern blot analysis of RNA associated with a-NS1 or control antibody using a full-length, internally labeled probe specific to M-vRNA. (A)–(E) show ...
[38]
Importance of the 1+7 configuration of ribonucleoprotein complexes ...
Jan 4, 2018 · Next, to clarify whether the 18S and 28S rRNAs detected by NGS were packaged in their full-length forms, we performed a northern blot analysis ...
[39]
High‐resolution transcription maps reveal the widespread impact of ...
Jan 19, 2018 · The approximate position of the oligonucleotide probe used for Northern blot analysis is indicated by a black arrow. B. Northern blot analysis ...<|control11|><|separator|>
[40]
Delineation of the Exact Transcription Termination Signal for Type 3 ...
Northern blotting was performed using a probe (position 38–56) that detects both the terminated (T) and read-through transcripts (Figure 1B). Two major ...
[41]
Changes in transcription start sites of Zap1-regulated genes during ...
Transcription start sites mapped by Deep-RACE for ... A) Diagram showing the location of RT-PCR primers and Northern blot probes used in this experiment.
[42]
https://www.thermofisher.com/us/en/home/references/ambion-tech-support/northern-analysis/tech-notes/strategies-for-detecting-mrna.html
[43]
Near-infrared fluorescent northern blot - PMC - NIH
Northern blot analysis allows for identification and quantification of RNA molecules. Unlike methods such as reverse transcription PCR (RT-PCR) and RNase ...Results · Multiplexing In Irnorthern... · Materials And Methods
[44]
Strategies for Detecting mRNA | Thermo Fisher Scientific - US
In general, Northern analysis is the only method that provides information about transcript size, whereas NPAs are the easiest way to simultaneously examine ...
[45]
A Comprehensive Analysis of Northern versus Liquid Hybridization ...
Jun 22, 2021 · Northern blotting is a more promising approach for small RNA study since it displays the size distribution of miRNA precursors and mature forms, ...
[46]
Northern Blot / RNA Blot - News-Medical
The northern blot technique is a classical way of analyzing the presence of a specific RNA sequence in a sample. Northern blotting is relatively cheap and ...
[47]
Non-radioactive labeling of RNA transcripts in vitro with the hapten ...
Abstract. We have developed a system for the enzymatic in vitro synthesis of non-radioactively labeled RNA which is derivatized with the hapten digoxigenin.
[48]
Chemi-Northern: a versatile chemiluminescent northern blot method ...
Northern blotting can be used to measure the size and level of intact RNAs, along with changes in their processing, modification, and metabolism. The procedure ...Results · Attomole Sensitivity Of... · Blotting Of Rna To Membrane
[49]
Preparation of Yeast RNA - Collart - 1993 - Current Protocols - Wiley
Ten to twenty micrograms of total RNA isolated by either procedure is sufficient for most northern blot, S1 mapping, or primer extension applications. Time ...Abstract · Disrupt The Cells · Commentary
[50]
Northern Blotting - an overview | ScienceDirect Topics
Northern blotting is a classical method extensively used for the detection of mature miRNAs as well as its precursors and it does not require specialized ...
[51]
mRNA Quantitation Techniques: Considerations for Experimental ...
However, as a quantitative technique, Northern blotting presents several limitations resulting from the inability to control for the efficiency of RNA transfer ...
[52]
[PDF] CHAPTER 3 ANALYSIS AND QC FOR REAL-TIME QPCR ARRAYS ...
QPCR has been shown to be an effective form of miRNA profiling. Northern blotting has limitations including low throughput and poor sensitivity. Alternative ...
[53]
Comprehensive molecular screening: from the RT-PCR to the RNA ...
Until the end of the 1990s, Northern blot had been used extensively for RNA quantification (1,2). ... Advantages and disadvantages of RT-PCR and RNAseq. Technique ...<|control11|><|separator|>
[54]
Cost comparison for qRT-PCR and RNA-Seq
Northern blot is a classic low-throughput technique, whereas RT-PCR and quantitative real-time polymerase chain reaction (qPCR) are medium-throughput techniques ...
[55]
In search of differentially expressed genes and proteins
On the other hand, “reverse” Northern blot allows simultaneous testing of hundreds of different DD cDNAs, with smaller amounts of RNA [21]and similar ...
[56]
High-throughput confirmation of differential display PCR ... - PubMed
... (reverse Northern blot) provide a high-throughput means to screen clones for artifacts. Reverse Northern blots also confirm differential gene expression …
[57]
Differential display cloning of genes induced in regenerating neurons
Candidate genes were screened by the reverse Northern blot method to eliminate obvious false positives and the three remaining candidates cloned and sequenced.
[58]
Differentially expressed DNA sequences following recovery from ...
Reverse Northern blot analysis. This was carried out to verify the subtractive hybridisation results and to eliminate any possibility of false positives ...
[59]
Normalization of multiple RNA samples using an in vitro ... - PubMed
... Northern blot or RNase protection. The feasibility of this approach to ... internal standard control transcript as well as the amount of RNA determined ...
[60]
Phosphorimager - Kirk - Major Reference Works - Wiley Online Library
Sep 15, 2010 · Phosphorimaging is a form of solid-state liquid scintillation where radioactive material can be both localised and quantified.
[61]
Quantitative Northern Blot Analysis of Mammalian rRNA Processing
Here, we describe the quantitative analysis of the steady-state levels of rRNA precursors, applicable to studies in mammalian cells and other organisms.
[62]
Slot Blot Analysis - an overview | ScienceDirect Topics
Slot blot analysis is defined as a method for measuring and quantifying RNA ... Northern blot analysis of RNA isolated from livers of transgenic mice. Poly ...
[63]
Analyzing gels and western blots with ImageJ - lukemiller.org
Nov 4, 2010 · ImageJ (http://rsb.info.nih.gov/ij/index.html) can be used to compare the density (aka intensity) of bands on an agar gel or western blot.Missing: northern | Show results with:northern