Jie:LabNotes/ASE/2008-2-29
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Optimization of the padlock captureing efficiency
Design the optimization of the padlock capturing efficiency
1. set three standard tubes. S1 is the standard system as control for the whole experiment. S2 use the AluI to cut the circle DNA after Lambda exonuclease incubation, try to increase the efficiency of PCR. S3 use the ddH2O as the control of AluI. 2. set four optimization tubes Tube 1 decrease the dNTP concentration in the SLE mix, try to decrease the possible activity of to cut the circle. Tube 2 decrease the dNTP concentration with cascade in the SLE mix. Tube 3 change the annealing step from 60C overnight to several steps to increase the chance of correct annealing among probes and targets. Tube 4 increase the probe concentration to increase the efficiency of annealing.
during the circularization reaction, the ratio of probe/target should be at least 125:1 or 250:1.
for example: genomic DNA is 100ng/ul. How much CES22K probe(360, concentration is 9.3ng/ul) is needed?
since the molecular wight of one genome is 3pg, 200ng DNA is equal to 200ng/3pg.
the probe molecule needed is 200ng/3pg x 250. For each target and the total probe molecule is 200ng/3pg x 250 x 22,000.
the Mol of the probe is 200ng/3pg x 250 x 22,000 / (6x10 23) the concentration of probe is 9.3ng/ul. The length of each probe is approximately 90base (single strand oligoDNA). Since 1base = 330Da, the concentration of probe is 9.3ng/ul /(90x330) = 300nM the volume the probe needed is 400ng/3pg x 250 x 22,000 / {(6x10 23 阿佛加德罗常数)x70nM} = 2.0ul
Now add 1.5ul probe in reaction, the ratio of probe/DNA = 1.5x250/2 =188
set the following circularization reactions: tube Standard 1: Standard reaction system tube Standard 2: Standard reaction system, Alu I incubation before PCR tube Standard 3: Standard reaction system, control for Alu I incubation before PCR tube 1: decrease dNTP concentration from to 0.2uM to 4nM (This probe set is SNP probes, so the dNTP as Standard is 0.2uM instead of 50uM for exon probes) tube 2: decrease dNTP concentration from to 0.2uM to 0.08nM tube 3: change the annealing steps from 60C overnight to the mutiple steps tube 4: increase probe concentration from ratio 188:1 to 752:1
reaction system Stad tube 1 Stad tube 1 Stad tube 3 tube 1 tube 2 tube 3 tube 4 H2O 5.5ul 5.5ul 5.5ul 5.5ul 5.5ul 5.5ul 1ul 10x Ampligase Buffer 1ul 1ul 1ul 1ul 1ul 1ul 1ul probe (CES22K,#390) 1.5ul 1.5ul 1.5ul 1.5ul 1.5ul 1.5ul 6ul Jurkat Genomic DNA(100ng/ul) 2ul 2ul 2ul 2ul 2ul 2ul 2ul
Reaction program:
Standard 1: 95c 10min -> 60C overnight -> add 1ul SLN mix(2U/ul AmpliTaq Stoffel fragment; 0.5U/ul AmpLigase; 0.2uM dNTP) -> 60C 1h -> 37C 1min
-> add 2ul Exonuclease I/III mix -> 37C 2h -> 94C 5min -> 4C hold.
Standard 2: 95c 10min -> 60C overnight -> add 1ul SLN mix(2U/ul AmpliTaq Stoffel fragment; 0.5U/ul AmpLigase; 0.2uM dNTP) -> 60C 1h -> 37C 1min
-> add 2ul Exonuclease I/III mix -> 37C 2h -> 94C 5min -> add 0.5ul RE-AluI (100nM), the ALuI guide oligo -> denaturing at 94C 3min -> 37C 1min -> add AluI 1ul -> 37C 1h -> 75C 10min -> 4C hold.
Standard 3: 95c 10min -> 60C overnight -> add 1ul SLN mix(2U/ul AmpliTaq Stoffel fragment; 0.5U/ul AmpLigase; 0.2uM dNTP) -> 60C 1h -> 37C 1min
-> add 2ul Exonuclease I/III mix -> 37C 2h -> 94C 5min -> add 0.5ul ddH2O -> denaturing at 94C 3min -> 37C 1min -> add AluI 1ul -> 37C 1h -> 75C 10min -> 4C hold.
tube 1: same as standard 1 except that dNTP in SLN mix is 4nM (2U/ul AmpliTaq Stoffel fragment; 0.5U/ul AmpLigase; 4nM dNTP)
tube 2: same as standard 1 except that dNTP in SLN mix is 0.08nM (2U/ul AmpliTaq Stoffel fragment; 0.5U/ul AmpLigase; 0.008nM dNTP)
tube 3: 95c 10min -> 60C 1h -> add 1ul SLN mix(2U/ul AmpliTaq Stoffel fragment; 0.5U/ul AmpLigase; 0.2uM dNTP) -> 60C 1h -> (95c 1min -> 60C 1h x 20cycles)
-> 37C 1min -> add 2ul Exonuclease I/III mix -> 37C 2h -> 94C 5min -> 4C hold.
tube 4: 95c 10min -> 60C overnight -> add 1ul SLN mix(2U/ul AmpliTaq Stoffel fragment; 0.5U/ul AmpLigase; 0.2uM dNTP) -> 60C 1h -> 37C 1min
-> add 2ul Exonuclease I/III mix -> 37C 2h -> 94C 5min -> 4C hold.
prepartion of SLN is needed calculated. 2U/ul AmpliTaq Stoffel fragment; 0.5U/ul AmpLigase; 0.2uM dNTP 2U/ul AmpliTaq Stoffel fragment; 0.5U/ul AmpLigase; 4nM dNTP 2U/ul AmpliTaq Stoffel fragment; 0.5U/ul AmpLigase; 0.08nM dNTP
PCR
PCR reaction system
reaction system x14 H2O 36.2ul 36.2ul 10x JumpStartTaq Buffer 4.5ul 4.5ul MgCl2() dNTP(10mM) 1ul 1ul AmpSolV6F2/R2 mix(10uM) 2ul 2ul 50x SYBG I 0.2ul 0.2ul JumpStartTaq 1ul 1ul Products of Circluarization 5ul 5ul
Run the program on Opticon4 realtime thermocycler 94C 3min -> 8 cycles of (94C 45sec -> 57C 1min -> 72C 1min) -> 14 cycles of (94C 30sec -> 72C 1min) -> 72C 3min -> 4C hold
waiting for Alu 2 oligo