Berkeley LBL/Laina Notebook

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== Introduction ==
== Introduction ==
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A genomic library was constructed by partial digestion with EcoRI/BamHI and BgII/XhoI followed by ligation of the DA fragments into EcoRI/XhoI abd BgII/XhoI site of the cosmid vector pET29bEBBX. Oligonucleotide primers were synthesized by Intergrated DNA technologies (IDT),Inc, Coraville, IA. Nucleotide sequence analysis was analysed using Lasergene Megasoftware. Database search was done using Basic Local Alignment Search Tool (BLAST). Sequence Compilation Sequence Alignment
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Revision as of 06:10, 27 October 2007

Contents

Introduction

A genomic library was constructed by partial digestion with EcoRI/BamHI and BgII/XhoI followed by ligation of the DA fragments into EcoRI/XhoI abd BgII/XhoI site of the cosmid vector pET29bEBBX. Oligonucleotide primers were synthesized by Intergrated DNA technologies (IDT),Inc, Coraville, IA. Nucleotide sequence analysis was analysed using Lasergene Megasoftware. Database search was done using Basic Local Alignment Search Tool (BLAST). Sequence Compilation Sequence Alignment


Materials

Plasmids, Cells, Miniprep Kits, IPTG, Antibiotics.

Methods

Primer Design

Biobricking of bch-gene cluster and crtN gene.

Plasmids:

pET29EBBX|pBR322|pHM6

Genes:

bchB bchE bchI bchL bchM bchN [[crtNgene]]

crtN

PCR of crtN an Heliobacillus mobilis G/C content an annealing region

crtN-F 40% BglII CrtN-R 50% BamHI and XhoI

Primers

crtN-F     5’gctagCTCGAGttaGGATCCtcagtaactggctgacaagcct3’
crtN-R     3’ccaaaAGATCTgtgaaacatacagcaaaaaacctgggt5’
bchB-F     5'ttaaGAATTCaagaaggagatatacatATGGGCGGAAGCGGGGTGGCTGGA3'
bchB-R     3'ttaGGATCCccgttcgccttggtttgacttact5'
bchE-F     5'ccaaagatctAAGAAGGAGATATACATatgcgcatactgatgatcca3' 
bchE-R     3'gctagCTCGAGtattttcatcatgcctctcgt5'
bchI-F     5'ttaaGAATTCaagaaggagatatacatATGACGGAAGTGCAAAACAAT3'
bchI-R     3'ttaGGATCCtcggggctgagaaggcgggagca5'
bchL-F     5'ttaaGAATTCaagaaggagatatacatATGATCATCGCGGTCTACGGA3'   
bchL-R     3'ttaGGATCCttgggcagaaggtgtggaagca5'
bchM-F     5'ttaaGAATTCaagaaggagatatacatATGGCAAACGAAGTAAATTC3'
bchM-R     3'ttaaGGATCCtctcttcggcttaatttccaacag5'
bchN-F     5'accgaattcAAGAAGGAGATATACATatggaaagggtcgaacgggaaaac3'
bchN-R     3'attaggatccTCATTCCAGCCACCCCGCTT5'

PCR

  PCR of bch-? genes using - 20ng/ul pHM6
  1ul pHM6 
  1ul dNTP
  5ul primer mix 
  0.5ul enzyme-phusion polymerase
  32.5ul H20
  50ul total
   

Digestions

  6 ul bch insert
  8ul pET29bEBBX
  2ul ligase buffer
  1ul ligase 
  3ul H20
  20ul total 

Dephosphorylation

  50 ul pBR3222
  6 ul phosphatase buffer
  1 ul phosphatase
  3 ul H20
  Incubate 30" -1hr 
  run gel

Ligations (3hrs @ R.T)

Results

Sequencing

Discussion