Construction of pYPK0_PDC1_HIS3_RPS19b

pYPKa_Z_PDC1

pYPKa_E_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")

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")





In [16]:
from pydna.all import *
reloaded =read("pYPK0_PDC1_HIS3_RPS19b.gb")

In [17]:
reloaded =read("pYPK0_PDC1_HIS3_RPS19b.gb")