planned out nested primers 05-14-2014d1522

2014-08-29

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

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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

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