Construction of pYPK0_PDC1_HIS3_RPS19b



In [1]:

    
from pydna.all import *



In [2]:

    
p567,p577,p468,p467,p568,p578,p775,p778,p167,p166 = parse("yeast_pahtway_kit_standard_primers.txt")

Yeast Pathway Kit Standard Primers



In [3]:

    
from Bio.Restriction import ZraI, AjiI, EcoRV



In [4]:

    
pYPK0 =read("pYPK0.gb")



In [5]:

    
promoter_clone = pYPKa_Z_PDC1 =read("pYPKa_Z_PDC1.gb")



In [6]:

    
gene_clone =read("pYPKa_A_ScHIS3.gb")



In [7]:

    
terminator_clone = pYPKa_E_RPS19b =read("pYPKa_E_RPS19b.gb")



In [8]:

    
p  =pcr( p167, p567, promoter_clone)
g  =pcr( p468, p467, gene_clone)
t  =pcr( p568, p166, terminator_clone)



In [9]:

    
pYPK0_E_Z, stuffer = pYPK0.cut((EcoRV, ZraI))



In [10]:

    
(pYPK0_E_Z, p, g, t)









    Out[10]:





(Dseqrecord(-5681), Amplicon(1117), Amplicon(761), Amplicon(731))



In [11]:

    
asm =Assembly((pYPK0_E_Z, p, g, t), limit=31)



In [12]:

    
asm









    Out[12]:





Assembly
fragments..: 5681bp 1117bp 761bp 731bp
limit(bp)..: 31
G.nodes....: 8
algorithm..: common_sub_strings



In [13]:

    
candidate = asm.assemble_circular()[0]
candidate.figure()









    Out[13]:





 -|name|98
|       \/
|       /\
|       98|1117bp_PCR_prod|50
|                          \/
|                          /\
|                          50|761bp_PCR_prod|37
|                                            \/
|                                            /\
|                                            37|731bp_PCR_prod|61
|                                                              \/
|                                                              /\
|                                                              61-
|                                                                 |
 -----------------------------------------------------------------



In [14]:

    
result = candidate.synced(pYPK0)

The new construct should have cseguid m-7lOIJ60aZl4b7rN4vanlD7OWk and 9404 bp.



In [15]:

    
result.write("pYPK0_PDC1_HIS3_RPS19b.gb")









    




pYPK0_PDC1_HIS3_RPS19b.gb

Download



In [16]:

    
from pydna.all import *
reloaded =read("pYPK0_PDC1_HIS3_RPS19b.gb")



In [17]:

    
reloaded =read("pYPK0_PDC1_HIS3_RPS19b.gb")