AAV SagRNA Expression Vector

CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) nuclease expression vectors are among several types of emerging genome editing tools that can quickly and efficiently create mutations at target sites of a genome (the other two popular ones being ZFN and TALEN).

Cas9 is a member of a class of RNA-guided DNA nucleases which are part of a natural prokaryotic immune system that confers resistance to foreign genetic elements such as plasmids and bacteriophage. Within the cell, the Cas9 enzyme forms a complex with a guide RNA (gRNA), which provides targeting specificity through direct interaction with homologous 18-22nt target sequences in the genome. Hybridization of the gRNA to the target site localizes Cas9, which then cuts the target site in the genome.

To achieve CRISPR-mediated gene targeting it is essential for the target cells to co-express Cas9 and the target site-specific gRNA at the same time. This can be accomplished by either expressing both Cas9 and the gRNA sequence from the same vector (a.k.a. all-in-one vector) or by using separate vectors for driving Cas9 and gRNA expression (Cas9 only and gRNA only vectors, respectively). The advantage of using separate vectors over an all-in-one vector for expressing Cas9 and gRNA is that it offers the flexibility of combinatorial usage of different gRNA expression vectors in conjunction with a variety of Cas9 variants (wild type nuclease, Cas9 nickase, dCas9, etc.) depending upon the user’s experimental goal.

Our AAV SagRNA expression vectors are designed to work with SaCas9 derived from Staphylococcus aureus, which is >1 kb shorter in comparison to the conventional SpCas9 derived from Streptococcus pyogenes. SaCas9 provides a distinct advantage over SpCas9 which has limited use in AAV-based applications due its large size and the small cargo capacity of AAV vectors. SaCas9 functionally differs from SpCas9 in two major aspects – first, SaCas9 requires a different gRNA scaffold sequence from the one required by SpCas9. The gRNA compatible with SaCas9 is called as SagRNA. Secondly, the PAM sequence recognized by SaCas9 is NNGRR (NNGRRT preferred), whereas the PAM recognized by SpCas9 is NGG (preferred) and NAG (less preferred).

Our AAV SagRNA expression vectors are available for expressing either single-SagRNA or dual-SagRNA. While the single-SagRNA vector is widely used for conventional CRISPR genome editing such as generating single gene knockout, dual-SagRNA vectors are necessary for applications requiring simultaneous targeting of a pair of genomic sites. Examples of such applications include generating deletion of a fragment between two DSBs targeted by a pair of SagRNAs, and targeting two different genes simultaneously. While the single SagRNA vector consists of a single human U6 promoter driving the target site specific SagRNA sequence in between the two ITRs, the dual SagRNA vector consists of two consecutive U6 promoters driving the expression of SagRNA sequences specific to two genomic target sites of interest.

The AAV SagRNA expression 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. The SagRNA expression cassette placed in-between the two ITRs is introduced into target cells along with the rest of viral genome. A human U6 promoter drives the expression of the user-selected SagRNA sequence, which directs SaCas9 to the DNA target site of interest. 

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.

AAV genomic DNA forms episomal concatemers in the host cell nucleus. In non-dividing cells, these concatemers can remain for the life of the host cells. In dividing cells, AAV DNA is lost through the dilution effect of cell division, because the episomal DNA does not replicate alongside host cell DNA. Random integration of AAV DNA into the host genome can occur but is extremely rare. This is desirable in many gene therapy settings where the potential oncogenic effect of vector integration can pose a significant concern. 

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. Due to their low immunogenicity in host organisms, our ssAAV gRNA only vectors are the perfect tools for in vivo CRISPR-based applications.

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 AAV 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.

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

Suitable for SaCas9-based applications: Our AAV SagRNA expression vectors are designed to work with SaCas9 derived from Staphylococcus aureus, which is >1 kb shorter in comparison to the widely used SpCas9 derived from Streptococcus pyogenes. SaCas9 provides a distinct advantage over SpCas9 which has limited use in AAV-based applications due its large size and the small cargo capacity of AAV 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 AAV vector can be packaged into high titer virus. When AAV 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 AAV 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.

Difficulty transducing certain cell types: Our AAV 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 be transduced 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. 

PAM requirement: Our AAV SagRNA expression vector is designed to work with SaCas9 derived from Staphylococcus aureus. SaCas9-mediated CRISPR targeting is dependent on the presence of the PAM sequence, NNGRR (NNGRRT preferred) on the immediate 3’ end of the gRNA recognition sequence.

Single-SagRNA expression AAV vector

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.

U6 Promoter: Drives expression of the downstream SagRNA sequence. This is the promoter of the human U6 snRNA gene, an RNA polymerase III promoter which efficiently expresses short RNAs.

SagRNA: Guide RNA compatible with Cas9 derived from Staphylococcus aureus.

Terminator: Terminates transcription of the SagRNA.

CMV promoter: Human cytomegalovirus immediate early enhancer/promoter. It drives the ubiquitous expression of the downstream marker gene.

Marker: A drug selection gene (such as neomycin resistance), a visually detectable gene (such as EGFP), or a dual-reporter gene (such as EGFP/Neo). This allows cells transduced with the vector to be selected and/or visualized.

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

3' ITR: 3' inverted terminal repeat. See description for 5’ ITR.

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.