siRNA/siAb™ Assay Kits provide convenience and economy by combining into one format products that are guaranteed to knock-down the targeted mRNA and detect the level of the targeted protein. The kit's siRNA SMARTpool®s and antibodies have been extensively validated and together with the included positive and negative controls, they make data generation easier and more trusted. Components available separately. Capacity dependent on choice of plate format, see COA.
To assist researchers in addressing and minimizing potentially confounding issues associated with siRNA-dependent gene silencing.; 5X Universal Buffer is no longer supplied with this kit, however, it can be made using the recipe found here.
This product is not available for sale in Australia, New Zealand, Singapore, Indonesia, Thailand, The Phillippines, Malaysia, Vietnam, Japan, Korea, and China.
Unless otherwise stated in our catalog or other company documentation accompanying the product(s), our products are intended for research use only and are not to be used for any other purpose, which includes but is not limited to, unauthorized commercial uses, in vitro diagnostic uses, ex vivo or in vivo therapeutic uses or any type of consumption or application to humans or animals.
This gene encodes a member of the neurotrophic tyrosine kinase receptor (NTKR) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. The presence of this kinase leads to cell differentiation and may play a role in specifying sensory neuron subtypes. Mutations in this gene have been associated with congenital insensitivity to pain, anhidrosis, self-mutilating behavior, mental retardation and cancer. Alternate transcriptional splice variants of this gene have been found, but only three have been characterized to date.
FUNCTION: SwissProt: P04629 # Required for high-affinity binding to nerve growth factor (NGF), neurotrophin-3 and neurotrophin-4/5 but not brain- derived neurotrophic factor (BDNF). Known substrates for the Trk receptors are SHC1, PI 3-kinase, and PLC-gamma-1. Has a crucial role in the development and function of the nociceptive reception system as well as establishment of thermal regulation via sweating. Activates ERK1 by either SHC1- or PLC-gamma-1-dependent signaling pathway. SIZE: 796 amino acids; 87497 Da SUBUNIT: Exists in a dynamic equilibrium between monomeric (low affinity) and dimeric (high affinity) structures. Binds SH2B2. Interacts with SQSTM1 which bridges NTRK1 to NGFR (By similarity). SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein (By similarity). Note=Endocytosed to the endosomes upon treatment of cells with NGF (By similarity). TISSUE SPECIFICITY: Isoform TrkA-II is primarily expressed in neuronal cells; isoform TrkA-I is found in non-neuronal tissues. PTM: Ligand-mediated auto-phosphorylation. Interaction with SQSTM1 is phosphotyrosine-dependent. DISEASE: SwissProt: P04629 # Defects in NTRK1 are a cause of congenital insensitivity to pain with anhidrosis (CIPA) [MIM:256800]. CIPA is characterized by a congenital insensitivity to pain, anhidrosis (absence of sweating), absence of reaction to noxious stimuli, self-mutilating behavior, and mental retardation. This rare autosomal recessive disorder is also known as congenital sensory neuropathy with anhidrosis or hereditary sensory and autonomic neuropathy type IV or familial dysautonomia type II. & Chromosomal aberrations involving NTRK1 are a cause of thyroid papillary carcinoma (PACT) [MIM:188550]. Translocation t(1;3)(q21;q11) with TFG generates the TRKT3 (TRK-T3) transcript by fusing TFG to the 3'-end of NTRK1; a rearrangement with TPM3 generates the TRK transcript by fusing TPM3 to the 3'-end of NTRK1. & Chromosomal aberrations involving NTRK1 are a cause of thyroid papillary carcinoma (PACT) [MIM:188550]. Intrachromosomal rearrangement that links the protein kinase domain of NTRK1 to the 5'-end of the TPR gene forms the fusion protein TRK-T1. TRK-T1 is a 55 kDa protein reacting with antibodies against the C-terminus of the NTRK1 protein. SIMILARITY: SwissProt: P04629 ## Belongs to the protein kinase superfamily. Tyr protein kinase family. Insulin receptor subfamily. & Contains 2 Ig-like C2-type (immunoglobulin-like) domains. & Contains 3 LRR (leucine-rich) repeats. & Contains 1 protein kinase domain.
What transfection reagent do you recommend?
» Answer
Upstate sells a product called siIMPORTER™. siIMPORTER™ is a Cationic lipid formulation that has been designed for efficient transfection of siRNA into a wide variety of mammalian cell lines with extremely low cytotoxicity.
What tissue culture plate format should I use?
» Answer
This will depend largely on the requirements of your experimental conditions. siRNA SMART pools® have been used successfully in a range of tissue culture dishes from 96 well plates up to 6 well plates. For each plate format, cell number and transfection conditions should be optimized.
Why buy the siRNA/siAB kit?
» Answer
Dharmacon and Upstate have paired together reagents into a kit, which offer you value and convenience. There is a cost savings by buying the kit when compared to buying the kit components individually. Additionally, in most cases, Upstate antibodies are not offered with positive control cell lysates when purchased separately.
What is the difference between an siRNA SMART pool® and an siRNA?
» Answer
siRNA SMART pool® are a mixture of four individual siRNAs that have been designed with Dharmacon's proprietary algorithms, SMARTselection and SMARTpool. SMARTselection uses 34 criteria to eliminate the non-functional siRNAs. Then the SMARTpool technology uses a sophisticated algorithm to combine 4 or more SMART selected siRNA duplexes in a single pool, resulting in even greater probability that the siRNA pool reagent will reduce mRNA to low levels as compared to using a randomly designed single siRNA designed against the same gene.
How much should the protein level decrease?
» Answer
The half-life of some proteins is particularly long. The siRNA SMART pool® mediated decrease in an mRNA may not be indicative of its protein level decrease if the gene product being targeted is very stable. Although we guarantee that the siRNA SMART pool® will reduce mRNA levels by at least 50%, we cannot guarantee that the level of a protein will decrease by a proportional level due to the variance in protein stability and cell systems.
I need a control for siRNA use; do you offer a product like that?
» Answer
We recommend using the siSTARTER kit to pilot your siRNA/siAB experiments. With this kit, you will be able to determine the efficacy of your transfections by knocking-down the expression of an internal control protein that has been well characterized to respond to siRNA-mediated knock-down: Lamin A/C. Additionally, you may use a host of control siRNA's offered by Dharmacon to control and optimize your experiments. Refer to www.dharmacon.com or call Dharmacon at 800-235-9880.
When should I look for a siRNA-dependent decrease in target protein level?
» Answer
We recommend to start looking for a decrease 48 hours after transfection of the siRNA SMART pool®. However, the maximal decrease may be reached later. It is advisable to set up a time course experiment to identify optimal conditions. The cell system being used and the half-life of the specific protein being tested will determine when the maximal reduction is reached. The half-life of some proteins is particularly long and the level of its mRNA decrease may not be indicative of its protein level decrease.
When should I look for a siRNA-dependent decrease in target mRNA level?
» Answer
We recommend to start looking for a decrease 24 hours after transfection of the siRNA SMART pool. However, the maximal decrease may be reached later. It is advisable to set up a time course experiment to identify optimal conditions. The cell system being used and the half-life of the specific mRNA being tested will determine when the maximal reduction is reached.
Do the siRNA SMART pools induce an interferon-mediated PKR response?
» Answer
It is known that double-stranded RNA (dsRNA) in mammalian cells is able to trigger a strong physiological response that results in a global, translational inhibition and mRNA degradation. dsRNA can initiate interferon synthesis whereby PKR and 2', 5'-oligoadenylate synthase become activated. Activated PKR phosphorylates translational initiation factors, which causes the cell's translational machinery to stall. Activated 2', 5'-oligoadenylate synthase results in the activation of ribonuclease L that causes cellular mRNA degradation. Together, this results in a general, non-specific, dsRNA-mediated silencing of gene expression. However, using dsRNA, that is shorter than 30bp in length, allows RNAi to occur without activating the interferon response. The short length of the dsRNA allows the interferon response to be bypassed. This prevents the non-specific knockdown of gene expression. The dsRNA molecules in the siRNA SMART pools are siRNA duplexes shorter than 30bp, and therefore will not active the interferon-mediated PKR response. Please see reference: Elbashir, S. M., et al. (2001) Nature 411, 494-498.
What is the stability of the SMART pool?
» Answer
2'-ACE protected RNA, either duplexed or single stranded is completely resistant to nucleases by virtue of the protecting group. A deprotected duplex is significantly more resistant to nucleases than deprotected single strands. However, maintaining sterile, RNAse free conditions is always recommended as a precaution.
How are the siRNA SMART pools synthesized?
» Answer
The duplexes that comprise an siRNA SMARTpools are processed as Option A4 duplexes (deprotected/desalted; annealed). The duplexes all have "UU" overhangs and a 5' phosphate on the antisense strand.
When should I look for a siRNA-dependent decrease in target mRNA level?
» Answer
We recommend to start looking for a decrease 24 hours after transfection of the siRNA SMART pool®. However, the maximal decrease may be reached later. It is advisable to set up a time course experiment to identify optimal conditions. The cell system being used and the half-life of the specific mRNA being tested will determine when the maximal reduction is reached.