Part:BBa_K929301

Potsdam Standard Backbone

Introduction

Potsdam Standard Cloning Vector

Potsdam Standard Cloning Vector
BioBrick Nr.	BBa_K929301
RFC standard	[http://2012.igem.org/Team:Potsdam_Bioware/Project/Potsdam_Standard RFC 10], [http://2012.igem.org/Team:Potsdam_Bioware/Project/Potsdam_Standard Potsdam Standard]
Requirement	pSB1C3
Source	existing part:(BBa_J04450)
Submitted by	[http://2012.igem.org/Team:Potsdam_Bioware Potsdam_Bioware2012]

The Potsdam Assembly Standard is a modified PLICing (Phosphorothioate-based ligase-independent gene cloning) method (Blanusa et al. (2010)). For this standard, we designed a new cloning vector with an RFP expression cassette as insert. Therefore, we expanded the prefix with an Apa I recognition site and the suffix with a Sph I recognition site. Both enzymes causing a 3’ overhang with 4 nucleotides. For the cloning process we cut the vector with Apa I and Sph I. In this assembly standard that’s the only step where we have to use restriction enzymes.

Results

For culturing E.colis transformed with Potsdam Standard Cloning Vector with RFP: The red fluorescence of the transformed colonies is obvious after 24 h incubation at 37 °C and over night incubation at 8 °C. To speed up the cloning, you can use LED light to see red fluorescence even after 16 h incubation at 37 °C. The transformed E.colis don't need any IPTG for RFP production. For the over night culture (fig. 1), we observed that it is better to incubate them with IPTG. After centrifugation, you can see the cerry-like cell pellets (fig. 3).

Fig. 1: Over night culture of Potsdam Standard Vector with RFP

Fig. 2: Red fluorescent cell pellets

Experimental Design: How to clone with the Potsdam Standard?

The insert is amplified with primers that contain 4 phosphothioate nuclheotides and the recognition sites for Apa I and Sph I at the 5’ end. After incubation in an iodine/ethanol solution, the thiophosphates were cut out resulting in a 3’ overhang which is suitable to the overhangs that was created by cutting the Potsdam Standard vector. After that, the digested vector and the PLICed insert are mixed and transformed into E. coli (Summary: fig. 1). By using the RFP expression cassette (fig. 2), we created a ligation control system. Due to the fact that red fluorescent colonies have a failed vector ligation we can tell which colonies are correctly ligated. The colonies that do not show red fluorescence are the positive clones.

Fig. 3: Summary of the experimental design

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  INCOMPATIBLE WITH RFC[25]

  Illegal AgeI site found at 699
  Illegal AgeI site found at 811
  
• 1000
  COMPATIBLE WITH RFC[1000]