Cloning strategy

July

06.07.09

Four forward primers were designed to amplify:
1.Promoter T7, RBS, CBP and LOVTAP:

gtttcttcgaattcgcggccgcttctagagtaatacgactcactataggggaattgtg

2.RBS, CBP and LOVTAP:

gtttcttcgaattcgcggccgcttctagagtgtttaactttaagaaggag

3.CBP and LOVTAP:

gtttcttcgaattcgcggccgcttctagatgaagcgacgatggaaaaagaatttcatag

4.LOVTAP:

gtttcttcgaattcgcggccgcttctagatgctactacacttgaacgtattgagaagaac

One reverse primer were designed:

gtttcttcctgcagcggccgctactagtatcaatcgcttttcagcaacacctcttc

The recipient IGEM part have been chosen: [http://partsregistry.org/partsdb/get_part.cgi?part=BBa_B0010 BBa_B0010], well 13D in the received kit plate 1

07.07.09

To design plasmids : software Vector NTI

08.07.09

Inducible LOVTAP biobrick strategy

• Problem to overcome:

PstI sites in LOVTAP sequence.

• Our goal:

Biobrick consisted of LacI promoter-RBS-LOVTAP-Term (in this order).

• Material:

Biobrick of LacI promoter, RBS, LOVTAP, Term seperatedly ( LOVTAP obtained from previous section and the rest from iGEM Spring 2009 distribution Kit plate).

• Strategy:

LacI promoter-RBS ligation with iGEM protocol (LacI promoter digested with ES, RBS digested with XP, plasmid containing an other antibiotic digested with EP).

LOVTAP is digested with ES and inserted into Term plasmid (which was digested with EX previously).

Finally, LacI promoter-RBS digested with ES to be inserted into LOVTAP-Term plasmid, digested with EX.

09.07.09

Partial digestion strategy

• Problem to overcome:

PstI sites in LOPTAP sequence -> Impossible to use iGEM protocol for ligation (where downstream part must be cut with XP)

• Strategy:

Cut with X first.

Divide into several solutions and add different concentrations of P (by dilution series)

• Results:

Most concentrated tube: all P sites are recognized and cut, so the number of parts diminishes with the concentration value.

Run an agarose gel and extract the right piece (recognized by the segment's length).

10.07.09

13.07.09

Restriction enzymes on [http://www.neb.com/nebecomm/products/category1.asp?#2 Biolabs website] and [http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/cleavage_olignucleotides.asp clevage oligonucleotides]

TRP promoter biobrick strategy'

• Problem to overcome:

SpeI sites on TRP promoter sequence.

14.07.09

Primers designed for LOVTAP read-out and RBphP project:

1.Forward primer Trp promoter:

gtttcttc gaattcgcggccgcttctagagtggcaaatattctgaaatgagctgttgacaattaatcatcgaactagttaactagtacgc

2.Reverse primer Trp promoter:

ctagctagctaggtcgataccctttttacgtgaacttgcgtactagttaactagttcgatgattaattgtca

3.1st Forward primer Inverter TetR:

aatcatcgaactagttaactagtacgcaagttcacgtaaaaagggtatcgacaaagaggagaaatactagatgtcc

4.2nd Forward primer Inverter TetR:

gtttcttcgaattcgcggccgcttctagagtggcaaatattctgaaatgagctgttgacaattaatcatcgaactagttaactagta

5.Reverse Primer Inverter TetR:

ctagctagctag tttctcctctttctctagtagtgc

6.Forward primer ppsR1 R.Palustris CGA009:

gtttcttcgaattcgcggccgcttctagatgctggaggatatttgccctggtg

7.Reverse primer ppsR1 R.Palustris CGA009:

gtttcttcctgcagcggccgctactagtattactcatcggctccgtctccttc

8.Forward primer ppsR2 R.Palustris CGA009:

gtttcttcgaattcgcggccgcttctagatggcgtcaaagtccgttcatgcc

9.Reverse primer ppsR2 R.Palustris CGA009:

gtttcttcctgcagcggccgctactagtatcaatcctctgcgtcgtctgagg

10.Forward primer BrBphP Bradyrhizobium ORS278:

gtttcttcgaattcgcggccgcttctagatgcccgttccgctgacgac

11.Reverse primer BrBphP Bradyrhizobium ORS278:

gtttcttcctgcagcggccgctactagtatcactcctcgctctgcgagc

12.Forward primer ppsR1 Bradyrhizobium ORS278:

gtttcttcgaattcgcggccgcttctagatgagggcgttcagagctcc

13.Reverse primer ppsR1 Bradyrhizobium ORS278:

gtttcttcctgcagcggccgctactagtactattccaactgactgtcttcttcgc

14.Forward primer ppsR2 Bradyrhizobium ORS278:

gtttcttcgaattcgcggccgcttctagatggccgagtttcacggtccac

15.Reverse primer ppsR2 Bradyrhizobium ORS278:

gtttcttcctgcagcggccgctactagtactagctccccttttcggtttcctc

15.07.09

16.07.09

17.07.09

August