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Adeno-Associated Virus Gene Expression Vector (scAAV)


The adeno-associated virus (AAV) vector system is a popular and versatile tool for in vitro and in vivo gene delivery. AAV is effective in transducing many mammalian cell types, and, unlike adenovirus, has very low immunogenicity, being almost entirely nonpathogenic in vivo. This makes AAV the ideal viral vector system for many animal studies. 

An scAAV vector is first constructed as a plasmid in E. coli. It is then transfected into packaging cells along with helper plasmids, where the region of the vector between the two inverted terminal repeats (ITRs) is packaged into live virus. Any gene(s) placed in-between the two ITRs are introduced into target cells along with the rest of viral genome. 

The wild-type AAV genome is a linear single-stranded DNA (ssDNA) with two ITRs forming a hairpin structure on each end. It is therefore also known as ssAAV. In order to express genes on ssAAV vectors in host cells, the ssDNA genome needs to first be converted to double-stranded DNA (dsDNA) through two pathways: 1) synthesis of second-strand DNA by the DNA polymerase machinery of host cells using the existing ssDNA genome as the template and the 3' ITR as the priming site; 2) formation of intermolecular dsDNA between the plus- and minus-strand ssAAV genomes. The former pathway is the dominant one.

Our scAAV transfer vector is engineered from ssAAV with two important differences. First, the trs (terminal resolution site) located in the 3' ITR is deleted in scAAV. As a result, scAAV has a tendency of forming a single-stranded DNA molecule during replication that is the concatenation of two full single-stranded genomes, one plus strand and the other minus strand. This molecule can form a self-complementary intramolecular dsDNA genome. When scAAV viral particles enter host cells, this self-complementary intramolecular dsDNA genome can skip second-strand synthesis, which is the main rate-limiting step associated with conventional ssAAV transduction, to quickly express genes carried on the scAAV vector. Therefore, scAAV has faster and increased transgene expression relative to ssAAV. Second, due to fact that wildtype AAV can carry up to about 4.7 kb of single-stranded DNA genome and yet each scAAV DNA molecule packaged into a viral particle is the concatemer of two single-stranded genomes of opposite strands, the cargo capacity of scAAV in terms of the length of the 5' ITR to 3' ITR transgene that can be properly packaged into mature virus is only about half that of ssAAV.

A major practical advantage of AAV is that in most cases AAV can be handled in biosafety level 1 (BSL1) facilities. This is due to AAV being inherently replication-deficient, producing little or no inflammation, and causing no known human disease.

Many strains of AAV have been identified in nature. They are divided into different serotypes based on different antigenicity of the capsid protein on the viral surface. Different serotypes can render the virus with different tissue tropism (i.e. tissue specificity of infection). When our AAV vectors are packaged into virus, different serotypes can be conferred to the virus by using different capsid proteins for the packaging. The serotypes currently offered by us for our ssAAV and scAAV vector systems include - serotypes 1, 2, 3, 4, 5, 6, 6.2, 7, 8, 9, rh10, DJ, DJ/8, PHP.eB, PHP.S, AAV2-retro and AAV2-QuadYF. During cloning, ITRs from AAV2 are used, as this is common practice in the field and does not impact specificity. Packaging helper plasmids include a Rep/Cap plasmid, containing the replication genes from AAV2 and the capsid proteins for a chosen serotype to determine tropism. The table below lists different AAV serotypes and their tissue tropism. 

List by Serotype
List by Tissue Type

Serotype Tissue tropism
AAV1 Smooth muscle, skeletal muscle, CNS, brain, lung, retina, inner ear, pancreas, heart, liver
AAV2 Smooth muscle, CNS, brain, liver, pancreas, kidney, retina, inner ear, testes
AAV3 Smooth muscle, liver, lung
AAV4 CNS, retina, lung, kidney, heart
AAV5 Smooth muscle, CNS, brain, lung, retina, heart
AAV6 Smooth muscle, heart, lung, pancreas, adipose, liver
AAV6.2 Lung, liver, inner ear
AAV7 Smooth muscle, retina, CNS, brain, liver
AAV8 Smooth muscle, CNS, brain, retina, inner ear, liver, pancreas, heart, kidney, adipose
AAV9 Smooth muscle, skeletal muscle, lung, liver, heart, pancreas, CNS, retina, inner ear, testes, kidney, adipose
AAVrh10 Smooth muscle, lung, liver, heart, pancreas, CNS, retina, kidney
AAV-DJ Liver, heart, kidney, spleen
AAV-DJ/8 Liver, brain, spleen, kidney
AAV2-retro Spinal nerves
AAV2-QuadYF Endothelial cell, retina
AAV2.7m8 Retina, inner ear

Tissue type Recommended AAV serotypes
Smooth muscle AAV1, AAV2, AAV3, AAV5, AAV6, AAV7, AAV8, AAV9, AAVrh10
Skeletal muscle AAV1, AAV9
Brain AAV1, AAV2, AAV5, AAV7, AAV8, AAV-DJ/8
Retina AAV1, AAV2, AAV4, AAV5, AAV7, AAV8, AAV9, AAVrh10, AAV2-QuadYF, AAV2.7m8
Inner ear AAV1, AAV2, AAV6.2, AAV8, AAV9, AAV2.7m8
Lung AAV1, AAV3, AAV4, AAV5, AAV6, AAV6.2, AAV9, AAVrh10
Liver AAV1, AAV2, AAV3, AAV6, AAV6.2, AAV7, AAV8, AAV9, AAVrh10, AAV-DJ, AAV-DJ/8
Pancreas AAV1, AAV2, AAV6, AAV8, AAV9, AAVrh10
Heart AAV1, AAV4, AAV5, AAV6, AAV8, AAV9, AAVrh10, AAV-DJ
Kidney AAV2, AAV4, AAV8, AAV9, AAVrh10, AAV-DJ, AAV-DJ/8
Adipose AAV6, AAV8, AAV9
Testes AAV2, AAV9
Spleen AAV-DJ, AAV-DJ/8
Spinal nerves AAV2-retro
Endothelial cells AAV2-QuadYF

For further information about this vector system, please refer to the papers below.

References Topic
Expert Rev Hematol. 4:539 (2011) Progress & challenges of scAAV vectors in gene therapy
Mol Ther. 16:1648 (2008) Review on advances & applications of scAAV vectors
Gene Ther. 10:2112 (2003) Generation of scAAV vectors by mutating AAV terminal repeat
Mol Ther. 16:1648 (2008) Self-complementary AAV vectors; advances and applications.


Our scAAV vector system is optimized for high copy number replication in E. coli, high-titer packaging of live virus, efficient transduction of host cells, and high-level transgene expression. This viral vector can be packaged into virus using all known capsid serotypes, is capable of very high transduction efficiency, and presents low safety risk.


Efficiency: Unlike traditional ssAAV vectors, our scAAV vectors are designed to produce fully functional infectious viral particles without depending on the host cell DNA polymerase machinery. This can help to achieve faster and higher levels of gene expression compared to ssAAV vectors.

Safety: AAV is the safest viral vector system available. AAV is inherently replication-deficient and is not known to cause any human diseases.

Low risk of host genome disruption: Upon transduction into host cells, AAV vectors remain as episomal DNA in the nucleus. The lack of integration into the host genome can be a desirable feature for in vivo human applications, as it reduces the risk of host genome disruption that might lead to cancer.

High viral titer: Our scAAV vector can be packaged into high titer virus. When scAAV virus is obtained through our virus packaging service, titer can reach >1013 genome copy per ml (GC/ml).

Broad tropism: A wide range of cell and tissue types from commonly used mammalian species such as human, mouse and rat can be readily transduced with our scAAV vector when it is packaged into the appropriate serotype. But some cell types may be difficult to transduce, depending on the serotype used (see disadvantages below).

Effectiveness in vitro and in vivo: Our vector is often used to transduce cells in live animals, but it can also be used effectively in vitro.


Very limited cargo capacity: The cargo capacity of our scAAV vector is half of that of ssAAV vector. Therefore, it can accommodate a maximum of only ~ 2.2 kb of sequence between the ITRs, which leaves ~1.7 kb of cargo space for the user's DNA of interest.

Difficulty transducing certain cell types: Our scAAV vector system can transduce many different cell types including non-dividing cells when packaged into the appropriate serotype. However, different AAV serotypes have tropism for different cell types, and certain cell types may be hard to transduce by any serotype.

Technical complexity: The use of viral vectors requires the production of live virus in packaging cells followed by the measurement of viral titer. These procedures are technically demanding and time consuming relative to conventional plasmid transfection. These demands can be alleviated by choosing our virus packaging services when ordering your vector.

Key components

5' ITR: 5' inverted terminal repeat. In wild type virus, 5' ITR and 3' ITR are essentially identical in sequence. They reside on two ends of the viral genome pointing in opposite directions, where they serve as the origin of viral genome replication.

Promoter: The promoter that drives your gene of interest is placed here.

Kozak: Kozak consensus sequence. It is placed in front of the start codon of the ORF of interest because it is believed to facilitate translation initiation in eukaryotes.

ORF: The open reading frame of your gene of interest is placed here.

SV40 late pA: Simian virus 40 late polyadenylation signal. It facilitates transcriptional termination of the upstream ORF.

3' ITR-Δtrs: AAV 3' ITR with a deleted terminal resolution site. The presence of the mutated 3’ITR leads to the generation of single-stranded, inverted repeat genomes with a mutated ITR in the middle and a wild type ITR at each end. This facilitates intramolecular base pairing within the mutant ITR extending through the genome resulting in the folding of the viral DNA to form a double-stranded molecule.

Ampicillin: Ampicillin resistance gene. It allows the plasmid to be maintained by ampicillin selection in E. coli.

pUC ori: pUC origin of replication. Plasmids carrying this origin exist in high copy numbers in E. coli.

Representative vector design

VB ID Vector name Descriptions
VB010000-9304aud pscAAV[Exp]-CMV>EGFP A self-complementary (scAAV) mammalian gene expression vector encoding CMV-driven EGFP.
VB231214-1690djz pscAAV[Exp]-CBA>hSMN2[NM_017411.4] A self-complementary AAV (scAAV) vector expressing a human survival motor neuron gene SMN2, which contributes to ~15% of the functional SMN protein, driven by CBA.
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