Boston UniversityStatus
From 2007.igem.org
Contents |
What We've Accomplished
Primer Design
SO1415
Gene sequence: overhangof the actual gene
This sequence was found on http://www.ncbi.nlm.nih.gov/
Megablast was used to compare the designed primer against the s. oneidensis genome
The length, gc content, melt temp etc info was found on www.idtdna.com
The site used to find parameters of a well-designed primer: http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html
SO_1415 gene sequence: 5’ GAATGAATAA ATGAAATGTCCTTCGGACTCCCTGTCCATTTTACGTTGTAATCAAATATTGGATGCGGCTGAAAAGCTCA TTGAGTCACAAGGTGTTGTATCTTTTAAGTTTTCTCAGCTTGCGCATGAGGTGGGATGCTCTACGGGTAC TTTATATAAATTTTTTGAACGTAAAGAAGATGTGTTGGTTTGTTTATTTTTAAGAAGCGCAACCTCAAAT CACTTACCGATATTTATCCATAAAAATCCAGAGTTAACTGCGCAAGAGAAGGTGCTGTTACCCATTTTAT TTACCTTTGAAACCATTAAGCGCAGTAGTAGCTTTTTTACGCTGCGTTCGGTGTCGGTCAATACCATGGT GTGGAAACTGGCCAGTGACGAAAAAGTGGAGCGGTTTAAAAAACGCATTAATGCTTTTTGGAGTTGGTTT ACAGACTCACTGCATTTAGCTGTTGAAAACGGCGAATTAGTGGCAACACCATTACAAATTAAAGAATTGG TCCAAGGGATAACGTTTTATTTAACAGGGTCTTTGACACAATTTGAAAGTCAATTGATTGCCCCAGAGTT TTTGTCTGATCGCCGTGAAACCTGTTATCGACATTTAGCAAACCTGATGGAGCGATACGAGTGGAAAAAG CCTTTAACTCTTGCGCTGTTTGATTCGTTAGAGGCGAGAACTATTAAGTTTTTTGACCAACATTATCGTG ACCATATGACCTGCGCGGCTTGTAGTGCGCTGTCAAATACCGACACTAAGACATCATCTCCCTGTACTCG TCAGTGTGGTTAG ‘’’GGCGTCCTGC’’’ 3’
Primer 1: TGA ATA AAT GAA ATG TCC TTC GGA CTC CCT G LENGTH:31 GC CONTENT:41.9 % MELT TEMP:59.9 ºC MOLECULAR WEIGHT:9494.2 g/mole EXTINCTION COEFFICIENT:298500 L/(mole·cm) nmole/OD260:3.35 µg/OD260:31.81
Primer 2: GAC GCC CTA ACC ACA CTG ACG LENGTH:21 GC CONTENT:61.9 % MELT TEMP:60.2 ºC MOLECULAR WEIGHT:6345.2 g/mole EXTINCTION COEFFICIENT:197000 L/(mole·cm) nmole/OD260:5.08 µg/OD260:32.21
SO4157
5’ AAGGAAAACC ATGTCCACCATGCTGCCACTGTATTTAGTCGATGATGATGAAGCGATTCTCGACTCCTTAGGGTTTATGC TCAGGCAATTTGGTTACCAAGTACAAACCTTTAGCAGTGGACGGGATTTTTTAGCCCAATGTCCGTTAAC ACAGGCTGGCTGCGTGATTTTAGATAGCCGAATGCCGGAGATCACCGGCCAAGAAGTGCAGCAAAAACTA CTTGAAACCCAAAGCCCATTGGGAGTTATCTTTCTCACGGGGCACGGTGATTTGCCCATGGCATTAAGCG CCTTTCGTAAGGGTGCATGCGATTTTTTTCAAAAGCCGGTATCTGGCAAAGCCCTAGTACAAGCCATTAA AAAAGCGCATAAAGAAAGCCAAGCCAGCTTTGAGCAACAGAGTCTGCAGCATAAATTTGCCCAACTGACC GACCGTGAACAACAAGTGTTAGCCCATGTGGTTCAAGGTATGACCAACAAGCAGATCTCCGAGGCCATGT ATTTATCCTTAAGAACCATTGAAGTGCACCGCGCTAAGATCATGAAAAAGCTCGAAGTCAGTAATATGGC AGAATTAGTACAGCACTTAGCCCACCTAAATACACTCTTACCGGAGTAA TCCAATAAAC 3’
Primer 1: AAA ACC ATG TCC ACC ATG CTG C LENGTH:22 GC CONTENT:50.0 % MELT TEMP:58.7 ºC MOLECULAR WEIGHT:6648.4 g/mole EXTINCTION COEFFICIENT:207700 L/(mole·cm) nmole/OD260:4.81 µg/OD260:32.01
Primer 2: ATT GGA TTA CTC CGG TAA GAG TGT ATT TAG GT LENGTH:32 GC CONTENT:37.5 % MELT TEMP:58.6 ºC MOLECULAR WEIGHT:9924.5 g/mole EXTINCTION COEFFICIENT:320800 L/(mole·cm) nmole/OD260:3.12 µg/OD260:30.94
hlyU
ATGAAAACCA TTAATGACAATAAATATTGTTCAATAAATGGATCATCTCACGTACCTCATCACTTTTCAGTGAGTAGAAT ACAGTTTGCGCTTCTTTGCGTGTGGTCACTAAATTATCTTTGCGCAACCAAGCAAGGTGTTGTGATAGTG CCGATTGACTTAAGCCTAATTTTTTATTCATTTCGCCAACGCACATTTCTCCTTCATTCAATAAATAACA AAGGATAAATAAACGGCGTTCGTTTGCGAGTGCCTTTAATAGCACCACGGCATGATCGGCTCGCTCCTGC ATCAATTCAATATTCAT TACGCACTTT
Primer 1: ATG AAA ACC ATT AAT GAC AAT AAA TAT TGT TCA ATA AAT GG LENGTH:41 GC CONTENT:22.0 % MELT TEMP:56.6 ºC MOLECULAR WEIGHT:12655.3 g/mole EXTINCTION COEFFICIENT:432600 L/(mole·cm) nmole/OD260:2.31 µg/OD260:29.25
Primer 2: GTG CGT AAT GAA TAT TGA ATT GAT GCA GGA LENGTH:30 GC CONTENT:36.7 % MELT TEMP:57.8 ºC MOLECULAR WEIGHT:9349.1 g/mole EXTINCTION COEFFICIENT:309700 L/(mole·cm) nmole/OD260:3.23 µg/OD260:30.19
Week's (Ambitious) Goals
Wednesday 5/30
- Get all protocols
- Identify materials/prepare order
- Design Primers
- Learn about budget/POs
Thursday 5/31
- Do primer order
- Start conjugation practice
- Confirm restriction enzymes, ligases
- Order confirmed/needed materials
- Team Revew Meeting
- Draft Thank-You Letters for our Sponsors
Friday 6/1
- Evaluate/continue conjugation, practice electroporation for E. coli
- Revise proposal to include possibility of screening with alginate beads and fluorocytometer
- Meeting with Tim: Budgets/protocols, Pfizer/fundraising, iGEM registration, beads
Materials We Need
Primers: Need to Buy
Error-Prone PCR: Need to Buy
Plasmids: Need to Buy?
Restriction Enzymes: Need to Buy?
Ligases: Need to Buy?
Short-Term To-Do List
Lab Orientation: COMPLETED!
Lab Safety Training: Not Completed (Dave, Rahul, and Christian are scheduled for a training session on 5/30/07. Danny will be taking it next week)
Design of Primers: Not Completed (Dave, please send me info about the finished primers when ready)
Ordering of Primers: Not Completed
Gathering of Protocols: Not Completed (Chris, please send me the protocols when they are gathered)
Ordering of Error-Prone PCR Materials: Not completed
Thank-You Letters sent to Pfizer: COMPLETED!
Thank-You Letters sent to BU ppl: Not completed
