Team:Alberta/Notebook/protocols/invitro biobyte assembly

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==General Protocols==
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-----------------------------
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*[[Team:Alberta/Notebook/protocols/invitro_biobyte_assembly | In Vitro BioByte Assembly]]
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-----------------------------
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*[[Team:Alberta/Notebook/protocols/LB | LB Plates and Broth]]
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*[[Team:Alberta/Notebook/protocols/transformations |Transformations]]
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*[[Team:Alberta/Notebook/protocols/overnight |5mL Overnight ]]
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*[[Team:Alberta/Notebook/protocols/glycerol | Glycerol Stock ]]
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-----------------------------
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*[[Team:Alberta/Notebook/protocols/miniprep | Plasmid Miniprep ]]
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*[[Team:Alberta/Notebook/protocols/digest | Restriction Digest ]]
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*[[Team:Alberta/Notebook/protocols/vector_dephos | Vector Dephosphorylation]]
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*[[Team:Alberta/Notebook/protocols/ligation | Ligation ]]
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-----------------------------
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*[[Team:Alberta/Notebook/protocols/agarose_gel | Agarose Gel Electrophoresis ]]
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*[[Team:Alberta/Notebook/protocols/gel_extraction | Gel Extraction ]]
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-----------------------------
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*[[Team:Alberta/Notebook/protocols/pcr | PCR]]
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*[[Team:Alberta/Notebook/protocols/colony_pcr | Colony PCR ]]
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*[[Team:Alberta/Notebook/protocols/pcr_purification | PCR Purification ]]
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-----------------------------
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*[[Team:Alberta/Notebook/protocols/labelling | Sample Labelling Conventions]]
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*[[Team:Alberta/Notebook/protocols/sequencing | Fluorescent Sequencing Reaction]]
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*[[Team:Alberta/Notebook/protocols/primer_design | Primer Design]]
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-----------------------------
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==In Vitro BioBytes Assembly 2.0==
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==Protocol: In Vitro BioBytes Assembly v2
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<br>
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===Please note that the GENOMIKON kit comes with premade anchor-Byte constructs.===
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===The GENOMIKON kit supplies plastic micropipettes than can dispense 25ul per drop.===
-
===Reagents:===
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:# Mix the iron micro beads for 10 minutes.
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:# Transfer a 25 ul (one drop) aliquot of iron micro beads to a 1.5 mL tube.
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* 1.5mL eppindorf tubes
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:# Pull the beads to the side using the magnetic tube rack supplied.
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* Magnet
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:# Remove and discard the supernatant.
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* Wash/binding buffer (10mM Tris 1mM EDTA pH8.0)
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:# Add 50 ul (2 drops) of supplied Wash Buffer to the beads. Flick gently to resuspend.
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* Elution buffer ?
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:# Pull the beads to the side using the magnetic tube rack.
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* 5x ligase buffer
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:# Remove and discard the supernatant.
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* Ligase
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:# Repeat steps 5 to 7.  
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* PCR cleanup kit
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:# Add 200 ng of a premade anchor-Byte construct to the beads and top off the volume to 25ul with the TE Buffer supplied. Flick gently to resuspend.
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* Para magnetic beads (oligo-dT25mer NEB# S1419S)
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:# Allow annealing for 30 minutes, mixing by flicking every 5 minutes. Ensure that there are no droplets on the sides of the tube.
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* A18_AB anchor stock solution (0.1pM; 67ng/uL in TE)
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:# Repeat steps 6 and 7.
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* AB KanR byte @ 40 ng/uL (0.06 pM/uL; gel purified in E buffer; 0.9 kbp)
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:# Repeat steps 5 to 7.
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* BA Byte (0.1pM; 67ng/uL in TE)
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:# Add 200 ng of the next Byte of your construct, making sure that a BA Byte follows an AB Byte and vice versa. Add an appropriate amount of 2x QuickLigase Buffer, Quick Ligase and TE to a total volume of 25ul.
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::Example:
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{|style="margin-left:40px;"
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===Procedure:===
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! Reagent !! Volume (ul)
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Preparing AB byte Anchor:
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*Add in a reaction:
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{|
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|KanR AB Byte (2.2ug; 4pM) || 5uL
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|-
|-
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|Anchor (900 ng; 50pM) || 4uL
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| (40ng/ul) AB kan Byte || 5
|-
|-
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|Q-Ligase buffer (x2) || 20uL
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| 2X Quick Ligase Buffer || 13
|-
|-
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|Q-ligase || 1uL
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| TE Buffer || 6
|-
|-
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|Total || 40uL
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| Quick Ligase || 1
 +
|-
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| TOTAL || 25
|}
|}
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*5 minutes @ R/T followed by heat inactivation @65<sup>o</sup>C for 10 minutes.
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 +
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::14. Flick gently to resuspend.  Allow ligation for five minutes, flicking gently every minute.
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===Binding:===
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::15. Add 25 ul of Wash Buffer to the tube. Flick gently.  
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* Mix beads with a couple of shakes followed by 10 minutes slow rotation.
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* Wash x2 with 50uL TE buffer
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* Add anc.byte ((0.4pM;0.27ug) and top to 20uL with TE.
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* 30 minutes of repeated flicking and inversion
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* 2x Wash as above
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===Ligation:===
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::16. Repeats steps 6 and 7.
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* Add:
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{|
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::17. Repeat steps 5 to 7 twice.
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|MilliQ water || 6uL
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|-
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::18. Repeat steps 13 to 17 for each subsequent Byte addition, including the last Byte. If the last Byte is cap, it must be added in 20 X molar excess.
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|BA Byte (0.4pM;0.27ug total) || 4uL
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|-
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::19. After the last Byte has been ligated and washed, addition of 25 ul of 75C Elution Buffer. The entire tube should be kept at 75C for ten minutes to allow the DNA construct to elute off the beads.
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|2x Q-ligase buffer || 10uL
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|-
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::20. After ten minutes, put the tube into a magnetic rack in the 75C waterbath. Allow the beads to be pulled aside and collect the supernatant into a clean 1.5 mL tube. The supernatant will contain your construct.
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|Q-ligase || 1uL
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|-
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|Total || 20uL
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|}
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* 5 minutes @ R/T with gentle mixing.
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* 2x Wash as above
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===Elution:===
 
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* Add 20uL of élution buffer @70<sup>o</sup>C.
 
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* Mix and remove rapidly.
 
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[[Team:Alberta/Notebook/protocols| Back]]
 
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Latest revision as of 03:49, 28 October 2010

TEAM ALBERTA


In Vitro BioBytes Assembly 2.0


Please note that the GENOMIKON kit comes with premade anchor-Byte constructs.

The GENOMIKON kit supplies plastic micropipettes than can dispense 25ul per drop.

  1. Mix the iron micro beads for 10 minutes.
  2. Transfer a 25 ul (one drop) aliquot of iron micro beads to a 1.5 mL tube.
  3. Pull the beads to the side using the magnetic tube rack supplied.
  4. Remove and discard the supernatant.
  5. Add 50 ul (2 drops) of supplied Wash Buffer to the beads. Flick gently to resuspend.
  6. Pull the beads to the side using the magnetic tube rack.
  7. Remove and discard the supernatant.
  8. Repeat steps 5 to 7.
  9. Add 200 ng of a premade anchor-Byte construct to the beads and top off the volume to 25ul with the TE Buffer supplied. Flick gently to resuspend.
  10. Allow annealing for 30 minutes, mixing by flicking every 5 minutes. Ensure that there are no droplets on the sides of the tube.
  11. Repeat steps 6 and 7.
  12. Repeat steps 5 to 7.
  13. Add 200 ng of the next Byte of your construct, making sure that a BA Byte follows an AB Byte and vice versa. Add an appropriate amount of 2x QuickLigase Buffer, Quick Ligase and TE to a total volume of 25ul.
Example:
Reagent Volume (ul)
(40ng/ul) AB kan Byte 5
2X Quick Ligase Buffer 13
TE Buffer 6
Quick Ligase 1
TOTAL 25


14. Flick gently to resuspend. Allow ligation for five minutes, flicking gently every minute.
15. Add 25 ul of Wash Buffer to the tube. Flick gently.
16. Repeats steps 6 and 7.
17. Repeat steps 5 to 7 twice.
18. Repeat steps 13 to 17 for each subsequent Byte addition, including the last Byte. If the last Byte is cap, it must be added in 20 X molar excess.
19. After the last Byte has been ligated and washed, addition of 25 ul of 75C Elution Buffer. The entire tube should be kept at 75C for ten minutes to allow the DNA construct to elute off the beads.
20. After ten minutes, put the tube into a magnetic rack in the 75C waterbath. Allow the beads to be pulled aside and collect the supernatant into a clean 1.5 mL tube. The supernatant will contain your construct.


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