planned out nested primers 05-14-2014d1522
2014-08-29planned out nested primers 05-14-2014d1522
see 05-14-2014d1516
Files found here
C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\05-15-2014d0934\nested primer test 05-15-2014d1104
and
05-14-2014d1516
I would like to investigate doing a nested pcr on some of the transcripts.
Maybe sample 16, 6, and 5 on 5-13-14
16 uses primer set GF021
6 uses primer set GF38
5 also uses primer set GF38
Therefore, I could just order nested primers for GF021 and GF38.
The expected PCR product sequences can be found at "\\biofs.biodesign.asu.edu\CIM\Research\labdata\Felicia Craciunescu\cancer vaccine project 2013\notebook\cancer vaccine 2013 notebook.xlsx" sheet 5-9-14
good free software for assembling dna sequences
DNA Sequence Assembly Software
05-15-2014d0937
Nested PCR test
Files found here
C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\05-15-2014d0934\nested primer test 05-15-2014d1104
18-22 bp long and should have a Tm in the 52-58 C range with a GC content of 40-60%.
All of the previous primers they used are 18-21 bp
GF021_fw CTGCTATTGGCTGCTCGG 18 52.5
GF021n_fw CCGGACGTCAAGGAGGTAG 19 55.3
GF021_rv CTTTAGGCTGCGGTCATC 19 50.2
GF021n_rv AGCTTGAGAGGCAATGTATTTAC 23 51.6
final gf021 product 824 bp
Now I'd like to make gf38 primers
>GF38_product
GCAACTTGGAGAGCGGGGCCGAGGCGCCGGCCGCCGGCAGGGCAGCCATGGAGGCAGCGGCGCGGAGGCGGCAGCATCCGGGAGCGGCGGGCGGTGCGGGCGCGCAGCCGGGCGCCTCCTTCCTGCAGGCCAGGCGACAGAGATGGGGAGCTGGATTTCTCCACTTTCCTGACCATTATGCACATGCAAATAAAACAAGAGGATCCAAAGAAAGAAATTCTCTTGGCCATGTTGATGGCAGACAAGGAGAAGAAAGGCTACATCATGGCATCTGAGCTACGGTCCAAACTCATGAAACTAGGGGAGAAACTCACCCACAAGGAAGTGGATGATCTTTTCAAGGAAGCAAATATAGAACCAAATGGCAAAGTGAAGTATGATGAATTTATCCACAAGATCACCATTCCTG
>GF38_fw
GCAACTTGGAGAGCGGGG
>GF38_rv
CAGGAATGGTGATCTTGTGG
>GF38n_fw
AGGGCAGCCATGGAGGCAG
>GF38n_rv
CTTCACTTTGCCATTTGGTTC
GF38_fw GCAACTTGGAGAGCGGGG 18 54.7
GF38n_fw AGGGCAGCCATGGAGGCAG 17 54.1
GF38_rv CAGGAATGGTGATCTTGTGG 20 51.7
GF38n_rv CTTCACTTTGCCATTTGGTTC 21 50.3
final GF38 nested product size: 337 bp