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Walton Jones Methods edit
almost 9 years ago
Commit id: 1d15090ec8dc21625baf282986065ceced2ebd8f
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\subsection*{Cloning
and subcloning of the fly T-type Ca\textsuperscript{2+} channel (DmCa\textsubscript{v}3)} DmCa\textsubscript{v}3}
Full length cDNA clone of We generated a full-length DmCa\textsubscript{v}3 (CG15899)
was generated cDNA by
piecemeal PCR
amplification and subcloning. amplification.
Total RNA
were extracted from adult heads using Trizol reagents (Invitrogen)
and was reverse transcribed
into cDNA using RevertAid First Strand cDNA Synthesis Kit (Fermentas).
Six adjacent DNA fragments
(clone 1 – clone 6) that cover
full-length the entire DmCa\textsubscript{v}3
CDS cDNA were obtained by PCR
amplification using cDNA as a template. amplification.
Primer sets were designed based on
the FlyBase
gene annotation.
\textcolor{red}{Which version of FlyBase? FlyBase changes over time.}
Hind III and Xba I
sites were inserted at
the 5'
end of clone 1 and 3'
end of clone 6, respectively.
Primer
sets used : sets: clone 1
(5'-CGAGATAAGCTTAAAATGCTGCCACAGCCA-3' and (5'-CGAGATAAGCTTAAAATGCTGCCACAGCCA-3', 5'-GCATCAGACTACATCGCTGTC-3'), clone 2
(5'-CTGGACACGCTGCCCATGCTG-3' and (5'-CTGGACACGCTGCCCATGCTG-3', 5'-TTCCAGCTCCTCCACTTGCAC-3'), clone 3
(5'-CAACGGTGGCTCCAACAGTCG-3' and (5'-CAACGGTGGCTCCAACAGTCG-3', 5'-CCACTGGCGGAAGCTCATGCC-3'), clone 4
(5'-GCCACGCCTCTCCAAGATCCG-3' and (5'-GCCACGCCTCTCCAAGATCCG-3', 5'-GACGATAAGAGCGTTTGCACG-3'), clone 5
(5'-TCTGAAACTAGTCGTGCAAAC-3' and 5'-TGGAAGTACTGGACGGTCTGC-3') (5'-TCTGAAACTAGTCGTGCAAAC-3', 5'-TGGAAGTACTGGACGGTCTGC-3'), and clone 6
(5'-AATCCCAGCCTGACCAGCTCG-3' and (5'-AATCCCAGCCTGACCAGCTCG-3', 5'-TCTAGATTAGTCCATGGAGGATTGGGGTGA-3').
Amplified PCR fragments were sequenced and assembled into pBlueScript II KS (+)
vector by using sequential restriction enzyme
digestion sequentially.
Among various isoform-specific fragments of clone digests.
Clones 2 and
clone 3, RC-specific fragments 3 contained isoform-specific exons.
Of the combinations that were
used. amplified by PCR, we chose to proceed to assembling the RB and RC isoforms.
Frequent A to G RNA editing sites were
found identified in
clone clones 3 and 5.
One RNA editing site in clone
3(5'-AGTTCAGAGC-3') 3 (5'-AGTTCAGAGC-3') was reversed to A by site-directed
mutagenesis based on genomic sequence.
Due to several RNA editing mutagenesis.
Since there were too many edited sites in clone 5,
we reverted to using genomic DNA
was used a as template for clone 5 instead of cDNA.
Assembled full length \textcolor{red}{Why did you do this? If it came from cDNA
and you found the same edits several times, then what makes you think it wasn't supposed to be there? Maybe this was
why your UAS rescue didn't work?}
The final assembled full-length cDNAs were cut
out of the vector by digestion of with HindIII
and / XbaI and
then subcloned into pcDNA3-HE3
where 5' untranslated region downstream of
the 5'-UTR from the \emph{Xenopus laevis} $\beta$-globin
was included for better gene to improve expression in \emph{Xenopus} oocytes.