Key elements of plasmids

Plasmids are named by indicating the viral backbone (e. g. pAAV) and the elements included in the
expression cassette in the correct order, starting from the promoter.
Elements are separated by hyphens: pAAV-hCMV-EGFP-hGHp(A) contains the hCMV promoter, the
EGFP ORF and the hGH poly(A) signal.
Fusion proteins are denoted with an underscore: pAAV-hCMV-iCre_EGFP-SV40p(A) contains a fusion
protein consisting of iCre with a C-terminal EGFP.
In DIO/FLEX constructs, the single double lox sites are denoted as dlox. Thus, each DIO/FLEX
construct has two dlox sites. This annotation makes it easier to determine from the plasmid name,
which part is double floxed. Similarly, drox and dFRT sites are annotated.
Fusion proteins in reverse orientation, which can be found in plasmids containing recombinase
recognition sites, are marked with “(rev)” like in pAAV-hCMV-dlox-FLPo_EGFP(rev)-dlox-SV40p(A).
The single elements of a fusion protein in reverse orientation are denoted within the plasmid name
in the same order as they appear in the native protein (e. g. in the above plasmid, FLPo_EGFP(rev)
means, that after recombination the protein FLPo_EGFP is produced, and not EGFP_FLPo).

ITR inverted terminal repeat

AAV-2 ITR ITR of AAV-2
deltaAAV-2 ITR 5'-ITR of AAV-2 devoid of the terminal resolution site (trs) and the D-
sequence; leads to scAAV
delta11nt AAV-2 ITR 5’-ITR of AAV-2 that is missing 11 nucleotides; so far, no major influence on
virus production or titers has been observed
2A 2A peptide from virus; functions as peptide separation site (similar to an IRES
sequence, but with a different mechanism)
2A (FMDV) 2A peptide of the Foot-and-Mouth Disease Virus
2A (PTV) 2A peptide of the Porcine Teschovirus-1
2A (TAV) 2A sequence of the Thosea asigna virus
AAV adenovirus-associated virus
AAV-2 adenovirus-associated virus serotype 2
AmpR ampicillin resistance (β-lactamase)
BDNF brain-derived neurotrophic factor
bGHp(A) bovine growth hormone polyadenylation signal
CAG artificial promoter consisting of a shortened hCMVe, a shortened CBA, a part of the
chicken beta-actin intron and parts of the rabbit beta-globin 1 intron and exon 3
CB4 artificial, calcium-dependent promoter consisting of hCMVe, a part of the hCMV
promoter, a shortened version of the murine BDNF exon IV promoter and a chimeric
intron (chI)
CBA chicken beta-actin promoter
(cd) codon diversified
chI chimeric intron (Promega)
(5´-donor site from the first intron of the human β-globin and the branch and 3´-acceptor site
from the intron located between the leader and body of an immunoglobulin gene heavy chain
variable region)

ChR Channelrhodopsin
CMV see: hCMV
CMVe see: hCMVe
Cre Cre recombinase; recognizes different kinds of lox sites
DIO double inverted ORF (open reading frame)
Dre site-specific DNA recombinase from phage D6; recognizes rox sites
DreO mammalian codon optimized version of Dre
DsRed2Mono monomeric mutant of DsRed2 (the wild-type protein as well as the codon-optimized
and engineered variant DsRed2 form tetramers)
DTA diphtheria toxin subunit A
dFRT a single double FRT site, consisting of one FRT or FRT5 site and one FRT3 site
dlox a single double lox site, usually consisting of one loxP and one lox2272 site
drox a single double rox site, usually consisting of one rox1 and one rox2 site
EGFP enhanced green fluorescent protein (GFP)
FLAG 3xFLAG-tag, includes an enterokinase cleavage site at its 3' end
FLEX flip-excision switch
FLP flippase
(recombinase that recognizes FRT sites)

FLPe FLP variant with enhanced thermostability

FLPo codon optimized FLPe
FRT flippase recognition target; recognition site for FLP, FLPe and FLPo
hCMV human cytomegalovirus (CMV) promoter
hCMVe human CMV immediate/early enhancer
hEF1α human elongation factor-1α promoter
hGHp(A) human growth hormone polyadenylation signal
hPDGFβ human platelet-derived growth factor (PDGF) β-chain promoter
hSyn1 human synapsin-1 promoter
HygroB R Hygromycin B resistance
ITR inverted terminal repeat
KanR Kanamycin resistance
loxP recognition site for Cre recombinase
lox2272 recognition site for Cre recombinase
LTR long terminal repeat
NLS nuclear localization signal
(rev) reverse orientation
(e. g. pAAV-hSyn1-floxedEGFP(rev)-SV40p(A) contains an EGFP ORF in reverse orientation
with respect to the promoter which is flanked by loxP sites)

rox recognition site for Dre recombinase

scAAV self-complementary AAV
(contains deltaAAV-2 ITR, which is a 5'-ITR of AAV-2 devoid of trs and D-sequence)

ssAAV single-stranded AAV

SV40p(A) simian virus (SV) 40 late polyadenylation signal
TeTxLC tetanus toxin light chain; altered codon usage for expression in eukaryotic cells
trs terminal resolution site
(part of wild-type AAV-ITRs; deleted in ΔAAV-2 ITR)
WPRE Woodchuck hepatitis virus (WHV) posttranscriptional regulatory element