Hi Tasha,

Have you got sequences for the vectors or can you obtain them by performing a Google search / Genbank search - (one possible search on Google is " 'vector name' and addgene" ). This is the first step in the process.

If so, by far and away the easiest method I've come across in the last few years is to take the DNA sequence and drop it into a free piece of software such as the "snapgene viewer" download ; within a few clicks you can have a pro-grade map on your screen that can be output as a pdf / jpeg etc. It is only if you want to do some of the fancier options such as cloning plans that you need to actually buy a subscription and if you are in academia that is a lot cheaper than if you're in industry.

Reading through the materials and methods, by obtaining the genbank entry for CFLAR, then adding in the PCR primers that they quote were used for the cloning, you get the following sequence. Note that this is CFLAR, not CFLAR (S1) (residues 203-260).

>CFLAR XhoI-EcoRI 1470 bp CCGCTCGAGGCCACCATGGCCCAGAGCCCTGTGTCTGCCGAGGTCATTCACCAGGTGGAA GAGTGTCTTGATGAAGACGAGAAGGAGATGATGCTCTTCCTGTGTAGAGATGTGACTGAG AACCTGGCTGCACCTAACGTCAGGGACCTCCTGGATAGCTTAAGTGAGAGAGGCCAGCTC TCTTTTGCTACCTTGGCTGAATTGCTCTACAGAGTGAGGCGGTTTGACCTTCTCAAGAGG ATCTTGAAGACAGACAAAGCAACCGTGGAGGACCACCTGCGCAGAAACCCTCACCTGGTT TCTGATTATAGGGTCCTGCTGATGGAGATTGGTGAGAGCTTAGATCAGAACGATGTATCC TCCTTAGTTTTCCTTACAAGGGATTACACAGGCAGAGGCAAGATAGCCAAGGACAAGAGT TTCTTGGATCTGGTGATTGAATTGGAGAAACTGAATCTAATTGCTTCAGACCAATTGAAT TTGTTAGAAAAATGCCTGAAGAACATCCACAGAATAGACTTGAACACAAAGATCCAGAAG TACACCCAGTCCAGCCAAGGAGCAAGATCAAATATGAATACTCTCCAGGCTTCGCTCCCA AAATTGAGTATCAAGTATAACTCAAGGCTCCAGAATGGGCGAAGTAAAGAGCCAAGATTT GTGGAATACCGTGACAGTCAAAGAACACTGGTGAAGACATCCATCCAGGAATCAGGAGCT TTTTTACCTCCGCACATCCGTGAAGAGACTTACAGGATGCAGAGCAAGCCCCTAGGAATC TGCTTGATCATTGATTGTATTGGCAACGACACAAAATATCTTCAAGAGACCTTCACTTCC CTGGGCTATCATATCCAGCTTTTCTTGTTTCCCAAGTCACATGACATAACCCAGATTGTT CGCCGATATGCAAGTATGGCCCAACATCAAGACTATGACAGCTTTGCATGTGTTCTGGTG AGCCTAGGAGGCTCCCAAAGCATGATGGGCAGAGATCAAGTTCACTCAGGGTTCTCCTTG GATCATGTCAAGAACATGTTCACGGGGGACACGTGCCCTTCTCTCAGAGGGAAGCCAAAG CTCTTTTTTATTCAGAACTATGAGTCGTTAGGTAGCCAGTTGGAAGATAGCAGCCTGGAG GTAGATGGGCCATCAATAAAAAATGTGGACTCTAAGCCCCTGCAACCCAGACACTGCACA ACTCACCCAGAAGCTGATATCTTTTGGAGCCTGTGCACAGCAGACGTATCTCACTTGGAG AAGCCCTCCAGCTCATCCTCTGTGTATCTGCAGAAGCTCTCCCAGCAGCTGAAGCAAGGC AGGAGACGCCCACTCGTGGACCTCCACGTTGAACTCATGGACAAAGTGTATGCGTGGAAC AGTGGTGTTTCGTCTAAGGAGAAATACAGCCTCAGCCTGCAGCACACTCTGAGGAAGAAA CTCATCCTGGCTCCTACGTGAGAATTCCGG

If you then have the AAV8 sequence, you should be able to find the XhoI / EcoRI cloning sites to drop the above sequence into ; then Snapgene or any other half decent software should do the rest for you.

If you can find the vector sequence, or want to discuss the above further , please by all means come back. This is a surprisingly commonplace activity in my line of work. Best, Robin

Vector sequence can be found here

Nam, Hyun-Joo, Michael Douglas Lane, Eric Padron, Brittney Gurda, Robert McKenna, Erik Kohlbrenner, George Aslanidi et al. "Structure of adeno-associated virus serotype 8, a gene therapy vector." Journal of virology 81, no. 22 (2007): 12260-12271.

Thanks Abhijeet - I read the Nam paper last night when I first started replying to this thread and found it no help at all - can you tell me where within the paper or any supplements the plasmid sequence or an accession number can be found?

@Robin This might be better article than the last one, and this time please find the attached sequence too.

Hi Abhijeet, I think we were working on this at the same time although I got delayed by my actual job!

The AAV8 sequence from the Gao paper is the un-modified AAV8 sequence as far as I can tell. I tried blasting the sequence against Genbank and found a few synthetic vectors derived from different but similar AAV family members - for instance pAAV-RC, or pAAV9-SBBANN-VBC. Although these are not the same as the AAV8-derived plasmid, they give an idea of the construction philosophy that I assume the AAV8 vector uses - https://www.ncbi.nlm.nih.gov/nuccore/14994089

https://www.ncbi.nlm.nih.gov/nuccore/572609619