Griffin:shRNA Transfection

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Lentivirus, shRNA plasmid, or siRNA?

It all depends on what you are seeking to accomplish. Are you trying to create stable knockdown? If you can run your assays under a transient RNAi event, then siRNA at present is clearly the way to go in my opinion. Now if you are working with a primary cell, neuron, generally hard to transfect cell, or in vivo, then lentiviral particles are a solution to introducing shRNA. The shRNA transfer vector alone in theory should be easy to work with insofar as culturing the cell, a simple transfection, antibiotic selection, and then collect data. However I have yet to see a definitive protocol that clearly shows this as being 'easy'; off-targeting is a big deal.

IF you are trying to create stable knockdown then the lentiviral particles are the way to go. Viral particles that have a VSV-G coat protein will have broad tropism, and contain the guts to integrate the shRNA cassette into the host genome such as lentiviruses do in nature (ie HIV-1). Otherwise if you are studying effects that can be measured with transient knockdown, then siRNA is the much more simple and straightforward approach. siRNA is a user friendly technique since you can calculate empirical moles of duplex/# cells or total volume (molarity), with a minimal number of steps and peripheral controls toward achieving results.

shRNA transfer vectors are ~10 kb DNA constructs that can give less stability problem since it is DNA instead of RNA, and albeit in transfecting with more prolonged and sustainable knockdown effects. However there are considerable nuances in the actual design and cloning of these vectors, in the actual establishment of antibiotic resistance toward generating a stable cell, and in controlling for the specific silencing/reproducible results. shRNA seems to be more prone to off-targeting effects because there is no empirical control of the promoter strength even if you can select for a line of cell that harbors even a single vector (ie promoter methylation), and due to the nature of having such a large delivery vector producing such a small hairpin substrate over several passages under antibiotic selective pressure (ie puro resistance may not = Pol III shRNA cassette expression). For these reasons at present, shRNA advantage seems to be when packaged into a lentivirus. Otherwise be prepared to run a gambit of control experiments.

Transient shRNA Transfection

Instead of chemically synthesizing the siRNAs before introducing it in the cell, the siRNAs are made directly by the cells through an expression vector that is transiently transfected into a dividng cell. The shRNA transfer vector alone can be transiently introduced into the dividing cell where the shRNA is synthesized by cellular machinery. While transient transfection is advantageous for fast analysis of shRNA mediated effects, stable transfection ensures long-term, reproducible as well as defined shRNA effects.

Stable shRNA Transfection

For many disease models, the most desirable cell types such as immune system or primary cells are not amenable to transfection. Viral delivery of RNAi vectors is a powerful alternative to transfection for these cell types as well as for in vivo applications. Stable expression is achieved by integration of the gene of interest into the target cell's chromosome: Initially the shRNA of interest has to be introduced into the cell, subsequently into the nucleus, and finally it has to be integrated into chromosomal DNA.

Stable expression can be influenced by two factors: The transfection method used and the vector containing the shRNA of interest. The transfection method determines which cell type can be targeted for stable integration through antibiotic selection. While many lipofection reagents transfect DNA up to a certain amount into adherent cell lines, efficient delivery of DNA into difficult-to-transfect suspension cell lines or even primary cells is only possible with viral methods and nucleofection. Nucleofection is a non-viral method of introducing DNA molecules efficiently into the nucleus of dividing cells, therefore significantly increasing the chances of chromosomal integration of the transgene. The technology was pioneered by Amaxa

Vector dependent

Although there is still some debate as to the effectiveness of this approach, a regular shRNA transfer vector may be able to integrate into the genome of the target cell by antibiotic selection alone. The process may occur randomly by the cell's machinery itself, possibly via DNA repair and recombination enzymes. If this phenomenon does occur, integration into inactive heterochromatin may result in little or no shRNA expression, whereas integration into active euchromatin may allow for shRNA expression. However, random integration could also lead to silencing of the shRNA cassette. Several strategies have been developed to overcome the negative position effects of random integration: Site-specific, homologous and transposon-mediated integration strategies are used but require the expression of integration enzymes or additional sequences on the plasmid.

Lentiviral particle dependent

Lentiviral particles are highly efficient at infection and stable integration of the shRNA into a cell system. To obtain the lentiviral particle, the transfer vector that contains the shRNA cassette is already flanked by LTRs and the Psi-sequence of HIV. The LTRs are necessary to integrate the shRNA cassette into the genome of the target cell, just as the LTRs in HIV integrate the dsDNA copy of the virus into its host chromosome. The Psi-sequence acts as a signal sequence and is necessary for packaging RNA with the shRNA into pseudovirus particles. Viral proteins which make virus shells are provided in the packaging cell line (HEK 293T), but are not in context of the LTRs and Psi-sequences and so are not packaged into virions. Thus, virus particles are produced that are replication deficient. Lentiviral particles can infect both dividing and nondividing cells because their preintegration complex (virus “shell”) can get through the intact membrane of the nucleus of the target cell.

  • Lentiviral systems efficiently transduce both dividing and non-dividing cells
  • Study long-term gene knockdown with stable expression
  • Reproducibly transduce cell populations
  • Inducible or constitutive gene knockdown

shRNA Transfer Vector Transfection Reagents

Transient gene silencing using RNAi is critically dependent on highly efficient delivery of the shRNA transfer vector or siRNAs into cells. The two conventional reagent types are Cationic lipid-based and Polymeric formulations. All commercial transfection reagents are proprietary formulations that are competing for market share by claiming certain advantages (ie, broad cell type compatibility, low cytotoxicity, high efficiency).

Cationic lipid


Cationic lipid transfection reagents are suitable for transfecting into a wide variety of dividing cell cultures. Commercial examples include: Lipofectamine / L2000, Dharmafect, iFect, and TransIT TKO. Cationic lipids work by forming lipsomal vesicles that house the siRNA payload and bleb their way through the living cell membrane and into the cytoplasm. The efficiency of this process must be determined in order to have confidence in the knockdown effects. There are numerous commercial sources for transfection reagents for good reason; there are numerous cell types and lipsome structure will influence transfection efficiency in the multitude of experimental cell types that exist.


Polymeric formulations have been developed and optimized for transfection of shRNA plasmid DNA into the nucleus of cultured eukaryotic cells by vendors such as Open Biosystems. Cationic lipids but not polyethylenimine or polylysine prevent transgene expression when complexes are injected in the nucleus (Pollard et al 1998). Polymers but not cationic lipids promote gene delivery from the cytoplasm to the nucleus and transgene expression in the nucleus is prevented by complexation with cationic lipids but not with cationic polymers.

shRNA Transfer Vector Transient Transfection Procedure

  • In a six well tissue culture plate, grow cells to a 50-70% confluency in antibiotic-free normal growth medium supplemented with FBS.

NOTE: This protocol is recommended for a well from a 6 well tissue culture plate. Adjust cell and reagent amounts proportionately for wells or dishes of different sizes.

NOTE: Healthy and subconfluent cells are required for successful transfection experiments. It is recommended to ensure cell viability one day prior to transfection.

Prepare the following solutions:

NOTE: The optimal shRNA Plasmid DNA:shRNA Plasmid Transfection Reagent ratio should be determined experimentally beginning with 1 μg of shRNA Plasmid DNA and between 1.0 and 6.0 μl of shRNA Plasmid Transfection Reagent as outlined below. Once the optimal shRNA Plasmid DNA:shRNA Plasmid Transfection Reagent ratio has been identified for a given cell type, the appropriate amount of shRNA Plasmid DNA/shRNA Plasmid Transfection Reagent complex used per well should be tested to determine which amount provides the highest level of transfection efficiency. For example, if the optimal shRNA Plasmid DNA:shRNA Plasmid Transfection Reagent ratio is 1 μg:1 μl, then amounts ranging from 0.5 μg/0.5 μl to 2.0 μg/2.0 μl should be tested.

Solution A: For each transfection, dilute 10 μl of resuspended shRNA Plasmid DNA (i.e. 1 μg shRNA Plasmid DNA) into 90 μl shRNA Plasmid Transfection Medium (serum antibiotic free medium).

Solution B: For each transfection, dilute 1 - 6 μl of shRNA Plasmid Transfection Reagent with enough shRNA Plasmid Transfection Medium to bring final volume to 100 μl.

NOTE: Do not add antibiotics to the shRNA Plasmid Transfection Medium.

NOTE: Optimal results may be achieved by using siliconized microcentrifuge tubes.

NOTE: Although highly efficient in a variety of cell lines, not all shRNA Plasmid Transfection Reagents may be suitable for use with all cell lines.

  • Add the shRNA Plasmid DNA solution (Solution A) directly to the dilute shRNA Plasmid Transfection Reagent (Solution B) using a pipette. Mix gently by pipetting the solution up and down and incubate the mixture 15-45 minutes at room temperature.
  • Wash the cells twice with 2 ml of shRNA Transfection Medium. Aspirate the medium and proceed immediately to the next step. NOTE: Do not use PBS as the residual phosphate may compete with DNA and bind the shRNA Plasmid Transfection Reagent, thereby reducing the transfection efficiency.

NOTE: Do not use PBS as the residual phosphate may compete with DNA and bind the shRNA Plasmid Transfection Reagent, thereby reducing the transfection efficiency. For each transfection, add 0.8 ml shRNA Plasmid Transfection Medium to well.

  • For each transfection, add 0.8 ml shRNA Plasmid Transfection Medium to well.
  • Add the 200 μl shRNA Plasmid DNA/shRNA Plasmid Transfection Reagent Complex (Solution A + Solution B) dropwise to well, covering the entire layer.
  • Gently mix by swirling the plate to ensure that the entire cell layer is immersed in solution.
  • Incubate the cells 5-7 hours at 37° C in a CO2 incubator or under conditions normally used to culture the cells.

NOTE: Longer transfection times may be desirable depending on the cell line.

  • Following incubation, add 1 ml of normal growth medium containing 2 times the normal serum and antibiotics concentration (2x normal growth medium).
  • Incubate the cells for an additional 18-24 hours under conditions normally used to culture the cells.

Aspirate the medium and replace with fresh 1x normal growth medium.

  • Assay the cells using the appropriate protocol 24-72 hours after the addition of fresh medium in the step above.

NOTE: Controls should always be included in shRNA experiments. Control shRNAs are available as 20 μg. Each encode a scrambled shRNA sequence that will not lead to the specific degradation of any known cellular mRNA.

NOTE: For Western blot analysis prepare cell lysate as follows: Wash cells once with PBS. Lyse cells in 300 μl 1x Electrophoresis Sample Buffer (sc-24945) by gently rocking the 6 well plate or by pipetting up and down. Sonicate the lysate on ice if necessary.

NOTE: For RT-PCR analysis isolate RNA using the method described by P. Chomczynski and N. Sacchi (1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162: 156-159) or a commercially available RNA isolation kit.

Vector Titration


Vector titration typically involves PCR or flow cytometry depending on the presence of a fluorescent protein. For example, mouse NIH 3T3 or human HT1080 cells are infected for 4 hours with limiting dilutions of vector supernate in the presence of polybrene and analyzed for expression of fluorescent protein or detection of vector or packaging sequences by PCR. The titer represents the relative infectivity of the vector as measured on the target cell of choice and is expressed as Infectious Units (IU)/mL. Different target cells, or different infection protocols, may yield different results.

Vector supernate can be concentrated using ultrafiltration. Recoveries (65-90%) vary depending on the envelope used and stability of the viral particle. This technique does not separate empty from functional viral particles. Therefore, at very low titers, concentration may not always yield an improved titer due to the presence of inhibitory empty viral particles.

Packaging cells

Human HEK-293 cells are common for packaging, since they are readily subject to high transfection efficiencies. If the cells do not transfect well in control experiments using a non-viral GFP vector, consider discarding the cells and trying a different lot of cells.

  • On occasion, cells can become refractive to transfection. Consequently, use low passage cells for all transfections.
  • 293 cells are adherent, however can detach from the plate during pipetting, or shear stress of a confluent plate. For this reason, perform the transfection when the cells are approximately 30% confluent.
  • After 36-48 hours, the cells should reach confluency and be producing the maximum amount of virus. If the cells are fed fresh media, several harvests of virus can be made after the cells reach confluency.
  • If human cells are used for packaging a RNA hairpin that targets a human sequence, lower viral titers may be experienced if silencing of the targeted gene is detrimental to the cell or packaging process.

Multiplicity of infection (MOI)

Multiplicity of infection (MOI) is the ratio of transfer vector transducing particles to cells. An MOI of 10 indicates that there are ten transducing units for every cell in the well. It is important to note that different cell types may require different MOIs for successful transduction and knockdown of the target gene. For instance, HEK293T cells are highly susceptible to lentiviral transduction (MOI of 5-20) while neuronal cells such as SHSY5Y often require higher MOIs of 10-50.

In most cases of transducing 42 different human cancer cell lines, MOI 3 yielded 50-90 % transduction efficiency with both vectors. In vivo studies with nude mouse s.c. tumor model (A549 lung cancer cells) revealed that lentiviruses were more efficient vehicles than adenoviruses when same amount of virus was used Molecular Therapy (2004) 9, S281.

  • HEK293= 5-10 particles/cell
  • SHSY5Y= 10-50 particles/cell

When transducing a lentiviral construct into a cell line for the first time, a range of volume or MOI should be tested.

Calculate MOI

(Total # cells per well)x(Desired MOI) = Total transducing units needed (TU)

(Total TU needed)/(TU/ml reported on C of A) = Total ml of lentiviral particles to add to each well


200 µl viral stock containing 10^6 (1e6) lentiviral transducing particles/1 ml

  • 70,000 cells/well x 5 MOI = 350,000 TU
  • 350,000 TU / 1e6 = 350 µl of viral stock
  • 70,000 cells/well x 0.5 MOI = 35,000 TU
  • 35,000 TU / 1e6 = 35 µl of viral stock

Lentivrus Infection

Sigma Aldrich


Prepare mammalian cells growing exponentially and are no more than 70-80% confluent before transduction. Prepare a stock solution of hexadimethrine bromide at 2 mg/ml in water.


Day 1.

  • Add 2.0e4 (20,000) cells in fresh medium to the number of wells needed for each construct in a 96-well plate. Duplicate or triplicate wells for each lentiviral construct and control should be used.
  • Incubate 18-20 hours at 37°C in a humidified incubator in an atmosphere of 5-7% CO2.

Note: The growth rates of cells vary greatly. Adjust the number of cells plated to accommodate a confluency of 70% upon transduction. Also account for the length of time the cells will be growing before downstream analysis when determining the plating density.

Day 2.

Remove medium from wells. To each well add 110 µl medium and hexadimethrine bromide (aka polybrene) to a final concentration of 8 µg/ml. Gently swirl the plate to mix.


Polybrene; 1,5-dimethyl-1,5-diazaundecamethylene polymethobromide, hexadimethrine bromide.

Polybrene (hexadimethrine bromide) is a cationic polymer used to increase the efficiency of infection of certain cells with a retrovirus in cell culture. Polybrene acts by neutralizing the charge repulsion between virions and sialic acid on the cell surface.

Hexadimethrine bromide is a small positive charged molecule that binds to cell surfaces and neutralizes surface charge. This treatment enhances transduction of most cell types by 2-10 fold. Some cells, like primary neurons, are sensitive to hexadimethrine bromide. Do not add hexadimethrine bromide to these types of cells. If working with a cell type for the first time, a hexadimethrine control only well should be used to determine cell sensitivity.

Add lentiviral particles to appropriate wells. Gently swirl the plate to mix. Incubate 18-20 hours at 37°C in a humidified incubator in an atmosphere of 5-7% CO2. Cells may be incubated for as little as 4 hours before changing the medium containing lentiviral particles. Overnight incubation may be avoided when toxicity of the lentiviral particles are a concern.

Note: When transducing a lentiviral construct into a cell line for the first time, a range of volume or MOI should be tested.

Day 3.

Remove the medium containing lentiviral particles from wells. Add fresh medium to a volume of 120 µl to each well. Note: For cell types that do not strongly adhere to the plate, 100 µl of medium may be removed and replaced with 100 µl fresh medium.

Day 4 and forward.

Replace medium every 3-4 days until cells are to be assayed. Cells may be selected and each clone may be expanded to assay for expression of shRNA. A variety of phenotypic, enzymatic, or gene expression assays may be performed. The desired assay should be optimized prior to the high-content screen with both negative and positive controls.

Note: Due to the random integration of the lentivirus into the host genome, varying levels of shRNA expression may be seen with different colonies. Testing a number of colonies will allow the optimal degree of expression to be determined.

shRNA Controls

Negative Controls

  • Untreated Cells. Untreated cells will provide a reference point for comparing all other samples.
  • Empty construct, containing no shRNA insert; The empty viral particles or DNA are a useful negative control that will not activate the RNAi pathway because it does not contain an shRNA insert. It will allow for observation of cellular effects of the transduction/transfection process. Cells transduced/transfected with the empty control provide a useful reference point for comparing specific knockdown.
  • Non-targeting shRNA; This non-targeting shRNA is a useful negative control that will activate RISC and the RNAi pathway, but does not target any human or mouse genes. The short hairpin sequence cotnains 5 base pair mismatches to any known human or mouse gene. This allows for examination of the effects of shRNA transduction/transfection on gene expression. Cells transduced/transfected with the non-target shRNA will also provide useful reference for interpretation of knockdown.

Positive Controls

  • Positive shRNA knockdown control; This control contains shRNA sequence that targets GFP expression. This shRNA control has been experimentally shown to reduce GFP expression. This control serves to quickly visualize knockdown in cells expressing GFP.
  • Positive shRNA knockdown control; This control contains shRNA sequence that targets eGFP expression (GenBank Accession # pEGFP U476561). The shRNA has been experimentally shown to reduce eGFP expression by 90% in C166-GFP mouse fibroblast cells 48 hours post-transduction by mRNA transcript level. This control serves to quickly visualize knockdown in cells expressing eGFP.
  • Positive reporter vector or lentiviral particles; This is a useful positive control for measuring transduction/transfection efficiency and optimizing shRNA delivery. The GFP Control contains a gene encoding GFP, driven by the CMV promoter. This control provides fast visual confirmation of successful transduction/transfection.


The copGFP protein is a novel natural green monomeric green fluorescent protein cloned from copepod Pontellina plumata, a type of plankton. The copGFP protein is a non-toxic, non-aggregating protein with fast protein maturation, high stability at a wide range of pH (pH 4-12), and fluorescent properties that do not require any additional cofactors or substrates.

Due to its exceptional properties, copGFP is an excellent fluorescent marker that can be used instead of EGFP (the widely used Aequrea victoria GFP mutant) for monitoring delivery of lentiviral constructs into cells. The copGFP protein has a very bright fluorescence that exceeds the brightness of EGFP by approximately a third.

The copGFP protein emits green fluorescence with the following characteristics:

  • emmision wavelength max – 502 nm
  • excitation wavelength max – 482 nm
  • quantum yield – 0.6
  • extinction coefficient – 70,000 M-1 cm-1

When assaying cells, DO NOT fix with methanol and minimize exposure to light. PFA/Formalin fixation works.


Factors Influencing Successful Transfection

Concentration and purity of nucleic acids

Determine the concentration of your DNA using 260 nm absorbance. Avoid cytotoxic effects by using pure preparations of nucleic acids.

DNA:In terms of plasmid preparation, McManus Lab has not observed a need to use E. coli cells that are highly defective for recombination. High DNA quality usually means high transfection efficiency. All DNA preparations should be performed by Cesium prep or endotoxin-free ion exchange plasmid purification methods. If poor transfection is consistently observed, it may be worth performing a additional clean-up of the DNA. The transfection protocols described here are sensitive to the amount of DNA. It is important to optimize DNA:Transfection Reagent ratios.

Transfection in serum-free media

The highest transfection efficiencies can be obtained if the cells are exposed to the transfection complexes in serum free conditions followed by the addition of medium containing twice the amount of normal serum to the complex medium 3–5 hrs post transfection (leaving the complexes on the cells). However, the transfection medium can be replaced with normal growth medium if high toxicity is observed.

No antibiotics in transfection medium

The presence of antibiotics can adversely affect the transfection efficiency and lead to increased toxicity levels in some cell types. It is recommended that these additives be initially excluded until optimized conditions are achieved, then these components can be added, and the cells can be monitored for any changes in the transfection results.

High protein expression levels

Some proteins when expressed at high levels can by cytotoxic; this effect can also be cell line specific.

Cell history, density, and passage number

It is very important to use healthy cells that are regularly passaged and in growth phase. The highest transfection efficiencies are achieved if cells are plated the day before. However, adequate time should be allowed to allow the cells to recover from the passaging (generally >12 hours). Plate cells at a consistent density to minimize experimental variation. If transfection efficiencies are low or reduction occurs over time, thawing a new batch of cells or using cells with a lower passage number may improve the results.


  1. Murphy S, Altruda F, Ullu E, Tripodi M, Silengo L, and Melli M. . pmid:6548262. PubMed HubMed [Paper1]
  2. Czauderna F, Santel A, Hinz M, Fechtner M, Durieux B, Fisch G, Leenders F, Arnold W, Giese K, Klippel A, and Kaufmann J. . pmid:14576327. PubMed HubMed [Paper2]
  3. Koper-Emde D, Herrmann L, Sandrock B, and Benecke BJ. . pmid:15493873. PubMed HubMed [Paper3]
  4. . pmid:12776118. PubMed HubMed [Paper4]
  5. Pollard H, Remy JS, Loussouarn G, Demolombe S, Behr JP, and Escande D. . pmid:9516451. PubMed HubMed [Paper5]
All Medline abstracts: PubMed HubMed

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