Team:Newcastle/19 August 2010

From 2010.igem.org

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(Aims)
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{{Team:Newcastle/mainbanner}}
{{Team:Newcastle/mainbanner}}
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=Gel extraction of ''yneA'', pGFPrrnB and pSB1C3=
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=''yneA''=
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==Aims==
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==Gel extraction==
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 +
===Aims===
To extract the correct size bands for ''yneA'', pGFPrrnB and PSB1AT3 from the gel after running gel electrophoresis. Concentration of the DNA and vectors are also checked with nanodrop.
To extract the correct size bands for ''yneA'', pGFPrrnB and PSB1AT3 from the gel after running gel electrophoresis. Concentration of the DNA and vectors are also checked with nanodrop.
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==Materials and Protocol==
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===Materials and Protocol===
Please refer to [[Team:Newcastle/Gel_electrophoresis|gel electrophoresis]], [[Team:Newcastle/Gel_extraction|gel extraction]], [[TeamNewcastleNanoDrop_Spectrophotometer|nanodrop spectrophotometer]].
Please refer to [[Team:Newcastle/Gel_electrophoresis|gel electrophoresis]], [[Team:Newcastle/Gel_extraction|gel extraction]], [[TeamNewcastleNanoDrop_Spectrophotometer|nanodrop spectrophotometer]].
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==Results==
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===Results===
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==Discussion==
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===Discussion===
The bands we extracted from the gel was good for pGFPrrnB, but not so strong for ''yneA'' and PSB1C3.  
The bands we extracted from the gel was good for pGFPrrnB, but not so strong for ''yneA'' and PSB1C3.  
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The results we got from the nanodrop were not as good as expected for ''yneA'' and PSB1C3.
The results we got from the nanodrop were not as good as expected for ''yneA'' and PSB1C3.
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==Conclusion==
+
===Conclusion===
We will proceed with digestion, but another set of ligation will be set up to repeat the process again.
We will proceed with digestion, but another set of ligation will be set up to repeat the process again.
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=Ligation for pGFPrrnB with ''yneA'' and pSB1C3 with ''yneA''=
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==Ligation==
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==Aims==
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===Aims===
To ligate ''yneA'' into both vectors pGFPrrnB and pSB1C3.
To ligate ''yneA'' into both vectors pGFPrrnB and pSB1C3.
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==Materials and Protocol==
+
===Materials and Protocol===
Please refer to [[Team:Newcastle/Ligation|ligation]].
Please refer to [[Team:Newcastle/Ligation|ligation]].
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===Ligation mix for pSB1C3 with ''yneA''===
+
====Ligation mix for pSB1C3 with ''yneA''====
The concentration of pSB1C3 and ''yneA'' that we got from the gel extraction earlier today was very low, so we used a different mixture set up for ligation.
The concentration of pSB1C3 and ''yneA'' that we got from the gel extraction earlier today was very low, so we used a different mixture set up for ligation.
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==Results and Conclusion==
+
===Results and Conclusion===
Please refer to [[Team:Newcastle/20_August_2010|20.08.10]].
Please refer to [[Team:Newcastle/20_August_2010|20.08.10]].
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=Digestion of ''yneA'', pGFPrrnB and pSB1C3=
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==Digestion==
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==Aim==
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===Aim===
To repeat digestion from [[Team:Newcastle/18_August_2010|18.08.10]].
To repeat digestion from [[Team:Newcastle/18_August_2010|18.08.10]].
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==Materials and Protocol==
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===Materials and Protocol===
Please refer to [[Team:Newcastle/Restriction_digests|restriction digest]].
Please refer to [[Team:Newcastle/Restriction_digests|restriction digest]].
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=Setting up Overnight Cultures for miniprep=
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==Setting up Overnight Cultures==
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==Aims==
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===Aims===
To prepare cultures for miniprep of ''yneA'', pGFPrrnB and pSB1C3 [[Team:Newcastle/20_August_2010|tomorrow]].
To prepare cultures for miniprep of ''yneA'', pGFPrrnB and pSB1C3 [[Team:Newcastle/20_August_2010|tomorrow]].
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==Materials and Protocol==
+
===Materials and Protocol===
Please refer to [[Team:Newcastle/Growing_an_overnight_cultures|growing an overnight culture]].
Please refer to [[Team:Newcastle/Growing_an_overnight_cultures|growing an overnight culture]].

Revision as of 09:57, 25 August 2010

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Contents

yneA

Gel extraction

Aims

To extract the correct size bands for yneA, pGFPrrnB and PSB1AT3 from the gel after running gel electrophoresis. Concentration of the DNA and vectors are also checked with nanodrop.

Materials and Protocol

Please refer to gel electrophoresis, gel extraction, nanodrop spectrophotometer.

Results

yneA 1 yneA 2 yneA 3 pSB1C3 pGFPrrnB
Concentration of DNA ng/µl 3.4 4.7 5.4 2.2 18.5

Discussion

The bands we extracted from the gel was good for pGFPrrnB, but not so strong for yneA and PSB1C3.

The results we got from the nanodrop were not as good as expected for yneA and PSB1C3.

Conclusion

We will proceed with digestion, but another set of ligation will be set up to repeat the process again.

Ligation

Aims

To ligate yneA into both vectors pGFPrrnB and pSB1C3.

Materials and Protocol

Please refer to ligation.

Ligation mix for pSB1C3 with yneA

The concentration of pSB1C3 and yneA that we got from the gel extraction earlier today was very low, so we used a different mixture set up for ligation.

Ligation mix:

Reagents 1:3(μl) 1:5(μl) Vector(μl)
Vector 3 2 1.5
Insert 3 6 7.5
10X BUFFER 1 1 1.1
T4 Ligase 1 1 1
H2O 2 0 0
Total Volume 10.0 10.0 10.0

Results and Conclusion

Please refer to 20.08.10.


Digestion

Aim

To repeat digestion from 18.08.10.

Materials and Protocol

Please refer to restriction digest.


Setting up Overnight Cultures

Aims

To prepare cultures for miniprep of yneA, pGFPrrnB and pSB1C3 tomorrow.

Materials and Protocol

Please refer to growing an overnight culture.



Subtilin Immunity

Aims

Newcastle 4 Primer Tubes.jpg

Today we received the four new primers that we ordered:

  • Prom_For
  • pSB1C3_for
  • pSB1C3_rev
  • Term_rev

These primers were ordered as a solution to the problem we encountered before we were about to attempt carry out the Gibson protocol for the Subtilin Immunity (and RocF) BioBrick. The primers will be used with previously rehydrated primers to try and obtain all four parts that we need to make the Subtilin Immunity BioBrick using the Gibson Protocol. So far the spaIFEG coding sequence (part 3) has already been successfully obtained. We still need to obtain the plasmid vector (part 1), promoter & RBS (part 2) and double terminator (part 4). So in order to do this the primers received today will be rehydrated and Phusion PCR will be carried out for each of the parts in order to amplify these parts.

Materials and protocol

Please refer to DNA rehydration page for the protocol for the rehydration of the four primers and to the Phusion PCR page for protocol followed for Phusion PCR. Table # below shows the different fragments, primers and conditions used for each tube.

Tube Part to be amplified DNA fragment consisting the part Forward primer Reverse Primer Melting Temperature (Tm in °C) Size of the fragment (in bp) Extension time* (in seconds)
1 Plasmid Vector pSB1C3 pSB1C3_for pSB1C3_rev 68 2046 + 70
2 Promoter and RBS (pVeg-SpoVG) BioBrick Bba_K143053 Prom_for P2P2_rev 67 139 + 15
4 Double terminator pSB1AK3 consisting BBa_B0014 P1T1_for Term_rev 63 116 + 15

Table #: This table shows the three different Phusion PCR reactions that were carried out today. If this is successful, these three parts (part 1, 2 and 4) along with (part 3) which is already obtained can be ligated together for the construction of subtilin immunity BioBrick with the help of Gibson Cloning method.

  • The extension rate of the Phusion polymerase is 1 Kb/ 30 seconds. Thus the extension time of each and every PCR reaction is slightly different.
  • The primers in bold are the new primers we received today. The primers not in bold were previously re-hydrated.


Discussion and Conclusion

Tommorrow we will carry out a test gel to check the sizes of the amplified fragments and if the sizes are correct then gel extraction will be performed

rocF BioBrick

Gel extraction of linearised pSB1C3

PCR of pSB1C3, pspac oid and double terminator with new primers

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