Gene Delivery Using Viral Vectors - Challenges in Delivery of Therapeutic Genomics and Proteomics - page 238

Table 5.6 Conserved Noncoding Sequences

Conserved
Noncoding
Sequence

Location Function

R Repeated at both ends of the

genomic RNA

Essential for reverse transcription and
to control genomic RNA size, as it
contains the polyadenylation signal

U5 Unique in the 5 region, is

guanethidine (GU) rich

Improves recognition of the R
polyadenylation signal

PBS Binding site, contains a

complementary sequence for
a specific tRNA (tRNApro for
MoMLV viruses) copackaged
with the retroviral genome

Complementary sequence is essential
for a specific tRNA (tRNApro for
MoMLV viruses) copackaged with
the retroviral genome

SD Splice donor (SD) site exists

between the 5b LTR and the gag
gene

Allows the formation of subgenomic
mRNA species in the producing cells

SA Splice acceptor (SA) site exists

in the 3b end of the pol gene
upstream of the env gene. The
splice donor site is followed by a
region called Cc, that overlaps the
5b end of gag

Required in cis for encapsidation of
the viral RNA

 Organized in several stem loops

recognized by viral proteins

Allows the specific packaging of
viral genomic mRNA and partially
overlaps the dimerization signal (DIS)

Polypurine track
(PPT)

- A purine-rich sequence that is less

sensitive to RT Rnase H degradation.
The remaining sequence is used to
prime second-strand synthesis of the
viral genome. Some retroviruses have
two ppt (e.g., lentiviruses)

U3 Unique in the 3 region within the

RNA genome

Duplicated in the provirus and
contains a promoter and an
enhancer recognized by the cellular
transcription machinery

Generally three strategies have been used for the design of retroviral vectors that
express two or more proteins:

1. Expression of different proteins from alternatively spliced messenger RNAs transcribed
from one promoter
2. Use of the promoter in the LTR and internal promoters to drive transcription of different
cDNAs
3. Use of internal ribosome entry site (IRES) elements to allow translation of multiple coding
regions from a single mRNA