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Contents 1 Protocols 1.1 Start to Finish Protocol 1.1.1 Overview 1.1.1.1 The Hierarchy of Build-A-Genome Synthetic Biology 1.1.1.2 The Nomenclature 1.1.1.3 The Workflow 1.1.2 Oligos 1.1.2.1 Diluting oligos to the proper concentration for future use 1.1.2.2 Templateless primer mix 1.1.2.3 Outer primer mix 1.1.3 Templateless PCR 1.1.3.1 Reaction Setup 1.1.3.2 Reaction Conditions 1.1.4 Finish PCR 1.1.4.1 Reaction Setup 1.1.4.2 Reaction Conditions 1.1.5 Gel Electrophoresis I 1.1.6 Ligation 1.1.6.1 Reaction Setup 1.1.6.2 Reaction Conditions 1.1.7 Bacterial Transformation 1.1.7.1 Preparation 1.1.7.2 Reaction Conditions 1.2 The Ligase Chain Reaction Protocol 1.2.1 INTRODUCTION 1.2.2 THEORY 1.2.3 COMPLETE OVERLAP PROTOCOL 1.2.4 DILUTION PROCEDURE/ GENERAL OPTIMIZATION 1.2.5 2009 ACCOMPLISHMENTS 1.2.6 ANALYSIS- Clone QC 1.2.7 Examples of ClustalW alignments for the 3R.3_23.C2.01 clones 1.2.8 MUTATIONS TABLE 1.2.9 Results/Discussion

Protocols

Start to Finish Protocol

Overview

The Hierarchy of Build-A-Genome Synthetic Biology

You will be building segments of synthetic DNA from small oligonucleotides (around 60 nucleotides long). These building blocks (BBs) will ultimately be incorporated into larger synthetic constructs, then integrated into the yeast genome.

• • From smallest to largest: Size
  • Oligos (ordered from a commercial supplier) 60 nucleotides
  • Building Blocks (constructed by Build-A-Genome students) 750 bp
  • Chunks (constructed from building blocks) 30 kb
  • Genome 12 Mb

The Nomenclature

Chunks, BBs, and Oligos In all cases, the chromosome number and arm (left or right) is listed first, followed by the design version, the chunk, the BB, then the oligo (which is prefaced with an "o" -- that's the letter "o" not a zero).For example, to refer to a... ...chunk: 3L.3_23.B3 This is chunk B3 from the left arm of chromosome 3, design version 3_23. ...BB: 3L.3_23.B3.1 This is BB 1 of chunk B3 from the left arm of chromosome 3, design version 3_23. ...oligo: 3L.3_23.B3.1.o01 This is the first (most 5') oligo of BB1 of chunk B3, from the left arm of chromosome 3, design version 3_23.

Oligo Plates 96-well plates of oligos are labeled as above, but designated "p" for plate. Multiple plates exist for each chunk, and are labeled p1, p2, p3, etc. For example: 3L.3_23.B3.p2 This is plate 2 of chunk B3, from the left arm of chromosome 3, design version 3_23.

Clones Applicable when sending clones (white colonies) off for sequencing. You will pick approximately 24 clones per BB for CSPCR, and send at least 12 off for sequencing. These 12 are labeled according to the convention laid out above, but have the designation "c" for clone. For example: 3L.3_23.B3.11.c05 This is clone 5 of BB 11 from chunk B3, from the left arm of chromosome 3, design version 3_23.

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The Workflow

1. Oligo mixes – Oligos are distributed by the instructors in 96 well plates. You will first make templateless PCR oligo mixes (TPMs) and outer primer mixes (OPMs) for use in the templateless PCR (TPCR) and finish PCR (FPCR), respectively.

2. Templateless PCR (TPCR) – The TPCR is performed to form a larger construct (the BB) from the oligo mixes.

3. Finish PCR (FPCR) – The FPCR is performed to amplify the full-length BB produced in small quantities during the TPCR.

4. Gel Electrophoresis I - You will gage the success of your FPCRs by running small samples of the TPCR and FPCR on a gel.

5. Cloning BBs – BBs which have been determined to be of the correct size will be cloned into a generic cloning vector and used to transform bacteria.

6. Bacterial Transformation – Bacteria will be transformed with the cloned construct to create a population of clones available for sequencing and future use.

7. Colony Screening PCR (CSPCR) – CSPCR will be used to determine which clones have the transformed plasmid.

8. Gel Electrophoresis II – You will analyze the results of the CSPCR by running a small volume of the CSPCR on a gel.

9. Sequencing – Clones which are shown to contain plasmids with an insert of the intended size will be sent for sequencing. You will perform sequence analysis to identify “perfect” clones.

Oligos

Oligos will be dispensed in 96 well plates. Each plate will contain two or more complete BBs. You will be given a diagram of the oligos on each plate.

Diluting oligos to the proper concentration for future use

Oligos are delivered to us at a concentration of 60uM. We have diluted them 1/10 to give you a working stock of 6uM. You will need to create a template primer mix (TPM) and an outer primer mix (OPM).

Templateless primer mix

All primers must be present at a concentration of 300nM (the oligos must all be diluted by 1/20) before use in the TPM. These dilutions should be done in a 1.7ml eppendorf tube, and primer mixes should be stored at -20ºC when not in use.

If you have up to 20 primers in a BB:

   * Label your TPM tube with the BB number and oligo concentration (300 nM)
   * Add 10 ul each primer
   * If necessary (if under 20 primers), add H2O to a final volume of 200ul.
   * Mix thoroughly 

If you have >20 primers in a BB

   * Label your TPM tube with the BB number and oligo concentration (see below)
   * Add 10 ul each primer to an eppendorf tube.
   * Do not add any water. Your final volume should be >200 ul, with the concentration 
     of each primer at ~250 - ~275 nM.
   * Record the different concentration of this TPM in your lab notebook.

Outer primer mix

The outer primers (first and last: x.01 and x.18, x.20, x.22, or x.22) must be present at a concentration of 3uM (the oligos must both be diluted by 1/2) in the OPM. Again, these dilutions should be done in a 1.7ml eppendorf tube, and primer mixes should be stored at -20oC when not in use.

   * Add 25 ul each of first and last primers to a labeled eppendorf tube.

• Mix thoroughly
• Label your OPM tube with the concentration (3uM)

Templateless PCR

Reaction Setup

Reaction Conditions

Finish PCR

Reaction Setup

Reaction Conditions

Gel Electrophoresis I

Ligation

Reaction Setup

Reaction Conditions

Bacterial Transformation

Preparation

Reaction Conditions

The Ligase Chain Reaction Protocol

INTRODUCTION

The Ligase Chain Reaction Protocol (LCR) is designed to replace and improve the current Templateless Chain Reaction Protocol (TPCR). The LCR is thought to have many distinct advantages:
1.) Accuracy of BB sequence should be increased (theoretically).
2.) The actual construction of the BB should be considerably easier thanks to the overlapping feature of the oligonucleotides.
3.) Money should be saved throughout the entire workflow because the LCR only needs to be run once to produce workable results.
In order to make a working protocol we must first subject the given protocol to stress tests to test for robustness. The second part of our experiments should be to test known working samples of the LCR trials in order to prove that the experimental procedure works correctly. (We did this because our oligonucleotides were built incorrectly) We used samples from Jennifer Tullman’s batch of 3L.3_23.A1 BB. The third part of our testing will be to assemble the failed BB’s from the Intersession 2009 work that Mary and I worked on.

THEORY

The theoretical background for the efficiency and accuracy of the LCR is based on the un-gapped oligonucleotides and manner of construction of the BB.

Step 1
Build un-gapped oligonucleotides that are around 60bp each
Step 2a
Mix the oligonucleotides together.
Step 2b
Phosphorylate the 5’ ends of the oligonucleotides so that the Taq DNA Ligase (Thermostable) can work on ligating the spaces
<PICTURE>
Step 3 Use a chained reaction to allow the overlapping pieces to anneal and then use the ligase to join the DNA backbone.
<PICTURE>
This is the step where the efficiency and the accuracy are most obvious. The oligonucleotides have a very high specificity for their complementary strand. This is thanks to the ~30bp stretch of complementary DNA. There is also a very low possibility for loxP sites since a palindrome sequence is much harder to find as the stretch of complementary sites for annealing grow longer.

Step 4
Every step thereafter is the same as the old BAG protocol.

COMPLETE OVERLAP PROTOCOL

DILUTION PROCEDURE/ GENERAL OPTIMIZATION

2009 ACCOMPLISHMENTS

ANALYSIS- Clone QC

Examples of ClustalW alignments for the 3R.3_23.C2.01 clones

MUTATIONS TABLE

Results/Discussion

From our construction successes (< 95%) and our lack of perfect clones we must conclude a mixed result from our experiments. This method has many advantages and disadvantages that need to be accounted for in order to assess the ultimate efficiency and accuracy of the protocol.

First and foremost, this is a very costly protocol (refer to Jasper’s report) and even with one pass through the FPCR to CSPCR workflow, the price of the reagents cannot be reconciled with the lack of successes on our sequencing results. We use more BBs since it costs more to overlap every part of BB. This extra cost cannot be offset by the increased efficiency since my results suggests that even with the new protocol, a single perfect clone cannot be found out of 12 submitted clones. The increased accuracy was supposed to improve the parts where the overlapped regions met.

We must also take into account the relative difficulty that these BBs offer in their construction. They are all of the ones that have failed previous years. There are quite a few that are over 800bp in length. From our sequence data, transversions were the #1 type of mutations found in the LCR sequences followed by deletions which are then followed by transitions. These mutations occurred in very random places and never at the same place among same BBs. All the highlighted areas were based on the abi sequence files that had clear well-defined ratings for each mutation. All in all, these BBs were poor examples in terms of relative design and composition of BBs encountered by BAG students over the course of a semester.

The time that it takes the LCR to progress is staggering considering the workflow jams that might occur if more PCR machines are not introduced into the classroom. Testing for shortened annealing times in which 5 minutes instead of 15 minutes is used should be conducted. This would require a comparative study among the same BBs.

Next time a negative control is also needed for every step in order to prove that this LCR is created from contaminated reagents.

This protocol is excellent for pushing BBs through the FPCR stage. It’s ultimate accuracy is still up for debate as we have a very bad sample to draw any reasonable conclusions from. Ultimately, it may be that the commercial markets have not deemed the LCR reaction reagents as a low cost alternative to the Taq polymerase driven reactions of our TPCR.