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Team:Alberta/Notebook/Assembly Method
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25-05-2010
Discussed an assembly method. Will start with a polyA tail Anchor oligo which will connect to a polyT tail which is bound to the bead. The anchor will consist of a primer region, a BsaI cut site, a buffer region, and finally, an A prime or B prime end. A byte with an appropriate end can be added to this anchor, and another byte can be added onto that, etc... The last thing to be added to the construct is a Terminator byte consisting of a buffer region, bsaI cut site, primer region and a polyT tail. This second primer sequence must be as uncomplimentary as possible to the anchor's primer site so as to minimize primers binding to each other when PCRing the assembled construct. The primers melting point must be around 65 C. After the construct is assembled on the bead, it is heated off and the polyA tail of the anchor binds to the polyT tail of the terminator and a plasmid is born.
We will purchase NEB oligo dT magnetic and cellulose beads which have a polyT tail (5' to 3') 25 nucleotides long. They are meant for mRNA isolation, but should work fine for our purposes. Used the IDT Analyzer software to determine what length of polyA tail is required for our anchor to have a melting temperature of 30 degrees Celcius (decided to change this melting temp later). This melting temp is sensitive to Na+ and Mg++ concentrations, so referred to ligase buffer and elution buffer for these concentrations.
The BsaI A end should look like this:
Designed an anchor with a polyA10 tail with a primer (Tm=65.1 C) region and the BsaI cut site with an A' end (ACCC).
26-05-2010
Designed new anchors, ordered oligos. Designed new anchors with larger polyA tail (and without hairpins, or self dimerization).
27-05-2010
No binding capacity specified in the manual for the beads in terms of mols or mass of DNA or beads. Binding capacity is given in terms of cells (because the beads are meant for mRNA isolation from cells). Will have to quantify binding capacity later.
Derivation of mole matching equation: ssDNA is ~330 grams/(mol*bp) moles = [concentration X volume] / [(330grams/mol X bp) X length] moles1 = moles2 c1v1/[(330g/mol X bp) X l1] = c2v2/[(330g/mol X bp) X l2] v1 = v2(c2 X l1/ c1 X l2)
Ordered new primers for anchor: GCG CGC CCG GTC TCA TGG GTC ACC CTC CC GGG AGG GTG ACC CAT GAG ACC GGC GCG C[A]12
07-06-2010
Made Wash Buffer, Elution Buffer and Low Salt Buffer for the mRNA Isolation Kit.
08-06-2010
Produce a modified protocol for Anchor binding to cellulose beads.
Protocol Preparation: Allow everything to come to room temperature. Spin 2000 to 5000g of beads in microcentrifuge for 10 seconds. Remove supernatant without disturbing the beads. Add 200:u;l of Wash Buffer to beads and agitate. Centrifuge for 10 seconds and remove supernatant. Prewarm Elution Buffer in a 70 degrees Celsius water bath.
Isolation Procedure: Apply DNA Anchor to cellulose beads, agitate and let it stand at room temperature for 5 minutes. Microcentrifuge for 10 seconds. Pipette supernatant back into original microcentrifuge. [Add 4:u;l Wash Buffer to beads and agitate to resuspend. Transfer beads and wash buffer to column reservoir of spin column. Let it stand at room temperature for 2 minutes while agitating. Microcentrifuge for 10 seconds.] X3 Add 400:u;l Low Salt Buffer, resuspend by agitation for 2 seconds and microcentrifuge for 10 seconds. Transfer and place spin column reservoir in a clean microcentrifuge tube. [Add 200:u;l pre-warmed Elution Buffer to column reservoir. Agitate to resuspend beads and let it stand for 2 minutes. Microcentrifuge for 10 seconds] X2 Place eluent on ice.
09-06-2010
<p>Calculated the mass of beads to determine the range of mg RNA could be isolated.
0.06g beads = 0.0599g; therefore, 0.06g can isolated 0.1 to 1 mg RNA.Calculated the minimal and maximal rpm for 2000 to 5000g of beads using the following formula: a = 4(pi)^2r(rpm)^2 / 60^2 So, when centrifuging the beads, the rpm must stay between 4700 to 7400 rpm. In the modified mRNA procedure, the centrifuge is set to 5500 rpm.
10-06-2010
Attempted to find binding capacity (in moles per mass of beads) by binding known masses of anchor to the bead, following the protocol, then qantifying the mass of DNA recovered off of the beads after eluting the DNA off of the bead. The cellulose beads settle very quickly without agitation. Measuring precise volumes of the beads was done by pipetting the cellulose bead slush into pcr tubes that were marked at 16 uL. To quantify the masses of DNA that: did not bind to the bead, came through the washes, and were eluted from the beads, the nano-drop 1000 spectrophotometer was used. The results showed that most of the anchor did not bind to the cellulose beads, and a very small amount of DNA was bound and eluted off of the beads. Possible reasons could be that the anchor was not binding, or there was too much anchor relative to the beads. A gel was also done. It showed that there was a lot of anchor that did not bind, and no anchor band was visible in the elution lane (which was expected based on the nanodrop reading).
11-06-2010
Repeated yesterday's experiment, but with a much larger amount of DNA. 1500 ng of anchor DNA to 16 uL of cellulose bead slush. There were no significant nanodrop readings except for the measurement of the amount of DNA that did not bind to the beads. Based on the nanodrop reading, over 1100 ng of DNA did not bind to the beads. The rest must have been washed away in the wash. Perhaps the melting temperature of the polyA12 tail is too low. We'll order one with a polyA18 tail and repeat the experiment.
14-06-2010
-Attempted to bind various masses of anchor to 16 uL of beads. Used 500, 1000, and 1500 ng of beads. Followed the modified mRNA isolation protocol created last week. Based on nanodrop readings, we recovered 560 ng from 1500 ng of initial DNA, 63 ng of 1000 ng of initial DNA, and 244 ng of 500 ng of DNA. Strange result of the 1000 ng of DNA, but a good sign that something appears to be binding to the cellulose beads. -To attempt to find the amount of anchor that will saturate the beads binding capacity, we used 1, 1.5, 2, and 2.5 ug of anchor and attempted to bind them to 16 uL of cellulose beads. Nanodrop readings multiplied by volume gave 600, 763, 1102, and 1730 ng of DNA not binding to the bead. What bound to the bead was 248, 1935, 4032, and 2470 ng of DNA. Obviously, something has caused the DNA readings to imply that more DNA was recovered than was put in initially. Later we found out that the readings are extremely sensitive to the small amount of residual washing solutions left over, causing the blanking process of the nanodrop to not accurately represent what solution the DNA was in.
15-06-2010
-The cellulose mRNA isolation kit came with a small amount of columns enough for only 8 trials. More were ordered. Will use magnetic beads in the meantime. -Created modified magnetic bead protocol based on the mRNA isolation protocol. Enough beads present in kit for 100 trials. -Magnetic Bead Trial #1: attempt to bind 100, 500, 1000, and 2500 ng of polyA12 anchor to 20 uL of polyT magnetic beads. Followed the modified magnetic bead protocol and eluted in 50 uL of elution buffer in a 50 C water bath. When nanodropping, apply magnet in case a small amount of magnetic particles were caught in the elution. Results: 80, 250, 305, and 460 ng of DNA were recovered from the beads after applying 100, 500, 1000 and 2500 ng of DNA initially. The magnetic beads appear to be more efficient at lower masses of DNA being bound. This appears encouraging, however, the nanodrop readings multiplied by the solution volume for the amount of DNA which did not bind initially were 335, 785, 970, and 2140 ng of DNA. The amount of DNA which did not bind and the amount that did does not add up to the amount of DNA added. This could be due to the residual solution left behind after washes. Will redo the experiment with less concentrated anchor and careful washes.
16-06-2010
-Magnetic Bead Trial 2: attempt to bind 500, 1000, 2500, and 5000 ng of anchor to 20 uL of beads. The mass of the DNA which didn't bind exceeded the mass of what was intitially mixed with the beads. This is obviously an error in measurement (caused by what!). The amount of DNA recovered was 0, 90, 70, and 250 ng of DNA. Looks like nothing bound to the beads. Possible cause of no DNA binding to bead: very low concentration of anchor meant a large reaction volume which would lead to a higher reaction time. Next time, use higher concentration anchor and increase binding time to an hour rather than 15 minutes (the mRNA isolation procedure calls for only 10 minutes).
16-07-2010
Solution Phase Assembly (Preparations)
Digested 10:u;g of pSB1C3 with Amp Resistance using BsaI. This digested DNA will be used to test: 1) whether acyl-NTPs will specifically incorporate to the cut ends of DNA by Klenow Polymerase and 2) if the acyl-NTPs block the ligation reaction between the vector (pSB1C3) and the insert (Amp Resistance).Two different minipreps of pSB1C3 with AmpR were used for the digestions.
Digestion #1 Protocol:
- 28.3:u;L pSB1C3 with AmpR (176.5ng/:u;L nanodrop concentration)
- 60.7:u;L MilliQ H20
- 10.0:u;L 10X NEBuffer 4
- 1.0:u;L BsaI
- 100:u;L Total
Digestion #2 Protocol:
- 28.7:u;L pSB1C3 with AmpR (174.1ng/:u;L nanodrop concentration)
- 60.3:u;L MilliQ H20
- 10.0:u;L 10X NEBuffer 4
- 1.0:u;L BsaI
- 100:u;L Total
Both were incubated at 50 degrees Celsius for 1 hour, were PCR Purified using the Qiagen PCR Purification Kit and ran on a 1.0% agarose gel to check for completion.
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Only lanes 6 to 8 were used. Lane 6 contains the kb+ ladder, while Lanes 7 and 8 contains the digested and purified pSB1C3 with AmpR fragments. Overall, the digestion went to completion.
19-07-2010
Solution Phase Assembly (Pre-test #1)
Protocol:
- Prepared acyl-NTPs by adding 50:u;L of MilliQ H20 to each powdered acyl-NTP (acyl-ATP, acyl-CTP, acyl-GTP and acyl-TTP). Then, add equal volume amounts of each acyl-NTP solution in an eppendorf tube to produce the complete mix to be used in the pre-test.
- Set-up 4 tubes with 2:u;L of 0.5M EDTA. The EDTA will be used to inhibit Klenow Polymerase's enzyme activity.
- Prepare Blocking Solution by adding: 85:u;L cut pSB1C3 and AmpR, 4:u;L complete acyl-NTP mix and 10:u;L Klenow Buffer.
- Transfer 20:u;L of Blocking Solution in one tube with 0.5M EDTA. This is the control of the experiment. It was placed in a 75 degrees Celsius water bath for 20 minutes to heat inactivate Klenow.
- Add 5:u;L Klenow Polymerase to the remaining Blocking Solution and incubate at 37 degrees Celsius.
- 20:u;L of the Blocking Solution was transferred to the remaining tubes with 0.5M EDTA after 5, 10 and 20 minutes incubation at 37 degrees Celsius. These tubes were also heat inactivated at 75 degrees Celsius for 20 minutes.
- All tubes were PCR Purified using the Qiagen PCR Purification Kit.
- Ligation of digested pSB1C3 and AmpR was done after purification.
- 16:u;L digested pSB1C3 and AmpR with acyl-NTP.
- 2:u;L of 5X ligase buffer
- 2:u;L of T4 ligase
- Ligations were incubated at room temperature for 1 hour.
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