Nonradioactive Northern Blot Research Articles

Study of Circular RNA Expression by Nonradioactive Northern Blot Procedure.

Circular RNAs (circRNAs) are covalently closed transcripts generated by back-splicing reaction. The lack of free ends endows these RNA molecules with high stability thus allowing them to accumulate in tissues and body fluids. They are widely expressed in most organisms, are modulated during development and display tissue-specific expression, resulting particularly enriched in the nervous system. Deregulation of circRNA expression has also been associated with several pathological conditions including neurological diseases and cancer.Here we present a Northern blot procedure that allows the analysis of the expression of bona fide circRNAs through the use of a digoxigenin-labeled RNA probe and the immunodetection of the signals.

Detection and quantification of glycosylated queuosine modified tRNAs by acid denaturing and APB gels.

Queuosine (Q) is a conserved tRNA modification in bacteria and eukaryotes. Eukaryotic Q-tRNA modification occurs through replacing the guanine base with the scavenged metabolite queuine at the wobble position of tRNAs with G34U35N36 anticodon (Tyr, His, Asn, Asp) by the QTRT1/QTRT2 heterodimeric enzyme encoded in the genome. In humans, Q-modification in tRNATyr and tRNAAsp are further glycosylated with galactose and mannose, respectively. Although galactosyl-Q (galQ) and mannosyl-Q (manQ) can be measured by LC/MS approaches, the difficulty of detecting and quantifying these modifications with low sample inputs has hindered their biological investigations. Here we describe a simple acid denaturing gel and nonradioactive northern blot method to detect and quantify the fraction of galQ/manQ-modified tRNA using just microgram amounts of total RNA. Our method relies on the secondary amine group of galQ/manQ becoming positively charged to slow their migration in acid denaturing gels commonly used for tRNA charging studies. We apply this method to determine the Q and galQ/manQ modification kinetics in three human cells lines. For Q-modification, tRNAAsp is modified the fastest, followed by tRNAHis, tRNATyr, and tRNAAsn. Compared to Q-modification, glycosylation occurs at a much slower rate for tRNAAsp, but at a similar rate for tRNATyr. Our method enables easy access to study the function of these enigmatic tRNA modifications.

Near-infrared fluorescent northern blot.

Northern blot analysis detects RNA molecules immobilized on nylon membranes through hybridization with radioactive 32P-labeled DNA or RNA oligonucleotide probes. Alternatively, nonradioactive northern blot relies on chemiluminescent reactions triggered by horseradish peroxidase (HRP) conjugated probes. The use of regulated radioactive material and the complexity of chemiluminescent reactions and detection have hampered the adoption of northern blot techniques by the wider biomedical research community. Here, we describe a sensitive and straightforward nonradioactive northern blot method, which utilizes near-infrared (IR) fluorescent dye-labeled probes (irNorthern). We found that irNorthern has a detection limit of ∼0.05 femtomoles (fmol), which is slightly less sensitive than 32P-Northern. However, we found that the IR dye-labeled probe maintains the sensitivity after multiple usages as well as long-term storage. We also present alternative irNorthern methods using a biotinylated DNA probe, a DNA probe labeled by terminal transferase, or an RNA probe labeled during in vitro transcription. Furthermore, utilization of different IR dyes allows multiplex detection of different RNA species. Therefore, irNorthern represents a more convenient and versatile tool for RNA detection compared to traditional northern blot analysis.

Nonradioactive Northern Blot of circRNAs.

Circular RNAs (circRNAs) are recognized as a special species of transcripts in metazoans with increasing studies, and northern blotting is a direct way to confirm the existence and to evaluate the size of individual circRNAs. Northern blotting probes can be radioactive isotope (32P) labeled, which is not environment-friendly and sometimes inconvenient to use. Here, we describe a nonradioactive northern blot protocol with digoxigenin-labeled probe to detect circRNA.

Estandarización de un protocolo para Northern blot no radioactivo usado en la detección de pequeños RNA en células Vero

<p><strong>Título en ingles:</strong> <strong>Standardization of<em> Northern blot </em>non-radioactive protocol used in the detection of small RNAs in Vero line cells</strong></p><p>El interés en la detección, identificación, y caracterización funcional de los pequeños RNAs no codificantes (sRNAs), ha generado la necesidad de optimizar las metodologías comúnmente usadas en su detección, la reacción en cadena de la polimerasa cuantitativa (RT-qPCR) y <em>Northern blot</em>, con el fin de que sean más sensibles y específicas. A pesar de la baja sensibilidad del <em>Northern blot</em>, esta metodología continúa siendo de uso común en la detección de sRNAs porque permite detectar el RNA pequeño así como a sus precursores, razón por la cual se usa como una metodología complementaria en este tipo de investigaciones. En este trabajo se describe la implementación de un nuevo protocolo para <em>Northern blot</em> no radioactivo, con modificaciones dirigidas a mejorar su sensibilidad y especificidad. El diseños de la sonda con la tecnología LNA, el marcaje de esta con Digoxigenina y por último la fijación del RNA a la membrana mediante 1-Ethyl-3-(-3-dimethylaminopropyl) carboniimide (EDC) y finalmente se discuten los fundamentos teóricos de estos cambios.</p>

Enhanced detection of small RNAs using a nonradioactive approach.

Recent advancements in high-throughput sequencing have led to the identification of many new classes of small noncoding RNAs such as endo-siRNAs. Unfortunately, reliable quantification of RNAs by sequencing is difficult due to artifacts arising from various factors involved in cDNA library preparation. Northern blot is one of the leading methods used to confirm the presence of a given RNA sequence because it can accurately quantify the cellular abundance, the size of the small RNA and reveal the presence of potential precursors and RNA isoforms. Here, we present a comprehensive description of LNA probe design along with a recently developed highly sensitive and cost-effective nonradioactive northern blot approach termed LED. LED combines a cross-linking method (EDC) and digoxigenin (DIG) labeling, and it can detect small RNAs with concentrations as low as 0.05 fmol and requires as little as a few seconds of membrane exposure for signal generation.

A sensitive non-radioactive northern blot method to detect small RNAs

The continuing discoveries of potentially active small RNAs at an unprecedented rate using high-throughput sequencing have raised the need for methods that can reliably detect and quantitate the expression levels of small RNAs. Currently, northern blot is the most widely used method for validating small RNAs that are identified by methods such as high-throughput sequencing. We describe a new northern blot-based protocol (LED) for small RNA (∼15–40 bases) detection using digoxigenin (DIG)-labeled oligonucleotide probes containing locked nucleic acids (LNA) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide for cross-linking the RNA to the membrane. LED generates clearly visible signals for RNA amounts as low as 0.05 fmol. This method requires as little as a few seconds of membrane exposure to outperform the signal intensity using overnight exposure of isotope-based methods, corresponding to ∼1000-fold improvement in exposure-time. In contrast to commonly used radioisotope-based methods, which require freshly prepared and hazardous probes, LED probes can be stored for at least 6 months, facilitate faster and more cost-effective experiments, and are more environmentally friendly. A detailed protocol of LED is provided in the Supplementary Data.

Research Article: Expression pattern of deoxyguanosine kinase3 during mouse development

The mitochondrial salvage pathway supplies deoxyribonucleotide triphosphates for mitochondrial DNA synthesis. Its rate limiting enzymes are deoxyguanosine kinase (dGK) and thymidine kinase2. Mutations in these enzymes lead to several mitochondrial diseases in infants. Deoxyguanosine kinase3 (dGK3) is an isoform of dGK that was cloned from gestational day 8 mouse embryos. The objective of this study was to characterize the developmental expression of dGK3 in mouse embryos. Non-radioactive Northern blot and reverse transcription-polymerase chain reaction analyses were used. Expression analyses showed that the smaller sized transcript of dGK3 was expressed in embryos from gestational day 8 through day 17. Expression levels were uniform from gestational day 8 to 15 with the lowest expression on gestational day 17. Further analyses showed expression of the gene in multiple adult tissues indicating the dGK3 is not an embryonic isoform of dGK. This study is the first analysis of dGK3 expression during early development.

Improved non-radioactive Northern blot protocol for detecting low abundance mRNAs from mammalian tissues

A rapid and sensitive non-radioactive Northern blot protocol is described which has been optimised in several critical steps. This is based on a formaldehyde-denaturing agarose gel electrophoresis, an alkaline transfer, hybridisation with digoxigenin-DNA probes and detection with a chemiluminescent substrate. This method allows even low abundance mRNAs to be detected in total RNA samples from mammalian tissues.

Nonradioactive northern blotting for the determination of acetylcholinesterase mRNA. Comparison to the radioactive technique

Nonradioactive northern blotting for the determination of acetylcholinesterase mRNA. Comparison to the radioactive technique

Nonradioactive northern blotting for the determination of acetylcholinesterase mRNA. Comparison to the radioactive technique.

A sensitive nonradioactive northern blotting for the detection of acetylcholinesterase mRNA in mammalian tissues is described and compared to its radioactive version. Best results were obtained if digoxigenin labeled RNA probe was used for hybridization and CDP-Star™, a chemiluminescent alkaline phosphatase substrate, for detection. The described nonradioactive technique for acetylcholinesterase mRNA determination is as sensitive as the radioactive one, but requires no protection against radiation and is less time consuming. Because of higher stability of the labeled probe, nonradioactive technique is also more convenient from the standpoint of experimental planning.

Northern blot analysis of nm23 gene expression in human lung cancer

To investigate the role of nm23 gene expression in lung cancer. Forty human lung cancer tissues and 19 non-cancerous pulmonary tissues were studied for their nm23-H1 and nm23-H2 mRNA expression with nonradioactive Northern blot hybridization. Correlation of nm23 mRNA expression with clinical features of lung cancer was analyzed. The mRNA expression of nm23-H2 gene in poorly differentiated squamous-cell carcinoma was significantly decreased compared to that in moderately differentiated squamous-cell carcinoma. The mRNA expression of nm23-H1 and nm23-H2 genes in small cell lung cancer was decreased compared to that in squamous-cell carcinoma. No significant difference in nm23 mRNA expression was observed in lung cancers with and without lymph node metastasis, nor was there significant difference in patients with lung cancers in different stages. The mRNA expression of nm23 gene is correlated with the degree of differentiation of lung cancer, but there is no evidence of metastasis suppression effect by nm23 gene.

The NAD+Precursors, Nicotinic Acid and Nicotinamide Upregulate Glyceraldehyde-3-Phosphate Dehydrogenase and Glucose-6-Phosphate Dehydrogenase mRNA in Jurkat Cells

To better understand the role of nicotinic acid and nicotinamide in the regulation of the oxidative stress response, we measured the levels of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and glucose-6-phosphate dehydrogenase (G6PD) mRNA in Jurkat cells treated with these NAD+precursors. We used a modified nonradioactive Northern blot method and detected the mRNA using 18-mer digoxigenin (DIG)-labeled oligonucleotides as probes. We observed increased levels of the mRNAs for the two enzymes in treated cells. Our findings suggest that the NAD+precursors may protect against oxidative stress and DNA damage by up-regulating the stress response genes GAPDH and G6PD.

Nonradioactive Northern Blot Analysis of Plant RNA and the Application of Different Haptens for Reprobing

Northern blot analysis using radioactive probes is still the most common technique to determine the accumulation of transcripts in cells and tissues. The main disadvantages of this technique are the possible health hazard, inconvenience during handling, the high amount of RNA target necessary for detection, and difficulties with stripping and reprobing. In this paper, we propose an easily applicable protocol for Northern blot analysis of plant RNA with enhanced sensitivity using digoxigenin-, fluorescein-, or biotin-labeledin vitrotranscripts derived from PCR products. Furthermore, we show the rehybridization of Northern blots with fluorescein as a second hapten, avoiding any stripping procedure.

Nonradioactive Northern blotting with biotinylated and digoxigenin‐labeled RNA probes

The application of nonradioactive RNA probes for Northern blotting offers the advantage of a rapid turn-around time for results without the loss of sensitivity for target mRNA detection. However, a problem that has impeded the widespread use of nonradioactive RNA probes for use in Northern blotting is the difficulty in stripping these probes from nylon membranes after hybridization. In this report we describe two protocols for stripping digoxigenin (Dig)-labeled RNA probes from nylon membranes. One protocol utilizes a phosphate-buffered formamide stripping solution to remove nonchemically modified (regular) RNA probes while the other method utilizes strippable probes that were produced with a chemically modified nucleotide (CTP) and removed by a specific stripping solution. This latter method was developed by Ambion Inc. and is called Strip-EZ. We also describe a protocol for the detection of two separate rat mRNAs using both biotin and digoxigenin-labeled RNA probes that does not require stripping the membrane after hybridization. Finally, we describe the use of another new labeling technology, called Chem-Link, that quickly and conveniently labels RNA for use in Northern blotting.

Electroneutral Na-coupled cotransporter expression in the kidney during variations of NaCl and water metabolism.

The purpose of the present study was to analyze the long-term regulation of renal bumetanide-sensitive Na+-K+-2Cl- cotransporter and thiazide-sensitive Na+-Cl- cotransporter gene expression during changes in NaCl and water metabolism. Male Wistar rats exposed to high or low NaCl intake, saline loading, dehydration, water loading, and furosemide administration during 7 days were studied. Control groups had access to regular food and tap water. Rats were kept in metabolic cages for 4 days before and during the experiment to determine daily urinary electrolyte excretion and osmolarity. At the end of the experiment, creatinine clearance and serum electrolyte levels were also measured. Kidneys were excised and macroscopically subdivided into cortex and outer and inner medulla. Total RNA was extracted from each individual cortex or outer medulla by use of the guanidine/cesium chloride method. The Na+-K+-2Cl- cotransporter expression in outer medulla total RNA was assessed by nonradioactive Northern blot analysis and the Na+-Cl- cotransporter expression in renal cortex total RNA was assessed by semiquantitative polymerase chain reaction. Experimental maneuvers were adequately tolerated, and all groups developed the appropriate renal response to each challenge. However, the level of expression of both cotransporters did not change in any model, except for a 2.8-fold increase in the Na+-Cl- cotransporter expression during dehydration. We conclude that nephron adaptation to 7-day modifications in NaCl and water metabolism does not include changes in the amount of electroneutral sodium-coupled cotransporter gene expression at the mRNA level.

Increased gene expression of β-amyloid precursor protein and its homologues APLP1 and APLP2 in human neuroblastoma cells in response to retinoic acid

β-Amyloid precursor protein (APP) belongs to a family of homologous β-amyloid precursor-like proteins (APLPs) including APLP1 and APLP2. Previously it has been shown that APP is subject to regulation by retinoic acid (RA). In this paper we show that APLP1 and APLP2 mRNA expression is upregulated during RA-induced differentiation of human SH-SY5Y neuroblastoma cells. The cells were treated with RA (10 μM) for 3 and 6 days and mRNA levels were analysed by a non-radioactive Northern blot assay. RA induced a 2- to 3-fold increase in the gene expression of both APLP2 and APP, whereas the increase in APLP1 mRNA expression was significantly higher. Our results support a role for APLPs during neuronal differentiation.

A reliable and sensitive method for non-radioactive Northern blot analysis of nerve growth factor mRNA from brain tissues

This report describes a sensitive, rapid and reproducible protocol for non-isotopic Northern blotting analysis. Church buffer and probes labeled with digoxigenin (DIG) were used for studying the expression of nerve growth factor (NGF) in the rat brain. Using the described method, NGF cRNA probe was hybridized to blotted RNA and the results were compared to Northern blot obtained using the method recommended by the manufacturer (Boehringer Mannheim). Comparison revealed that the blot treated with Church buffer detected at least 10-fold more NGF mRNA as compared to blot hybridized with formamide buffer. In summary, we have developed an optimal hybridization protocol to perform non-radioactive Northern blot analysis using antisense RNA as a probe. This method allowed us to detect the specific low-abundant mRNA and analyze the expression of neurotrophic factors in the rat brain.

Reduction of Background Problems in Nonradioactive Northern and Southern Blot Analyses Enables Higher Sensitivity Than 32P-Based Hybridizations

An improved chemiluminescence-based RNA/DNA detection procedure offering a widely applicable alternative to the conventional 32P labeling employed in molecular biology is described. Even highly sensitive applications such as Northern blot analysis of low-copy RNAs are shown to be feasible now without radioactive labeling. Improved quality of nonradioactive detection was obtained by the use of digoxigenin-labeled nucleotides in combination with dioxetane substrates which are decomposed by the hydrolysis of alkaline phosphatase. Previously existing problems involving unacceptably high background signals in nonradioactive labeling procedures were eliminated by the application of a modified RNA/DNA transfer, hybridization, and detection protocol. The data presented here delineate a system consistently superior to radioactivity and should considerably increase the usefulness of nonradioactively labeled probes detected by chemiluminescence.