Boston UniversityStatus

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 ==What We've Accomplished==
-===Primer Design===
+[[Boston_UniversityPlasmidChoice | Plasmid Choice]]
-SO1415
+[[Boston_UniversityRestrictionChoice | Restriction Enzyme Choice]]
-Gene sequence: '''overhang''' of the actual gene
+[[Boston_UniversityPrimerDesign | Primer Design]]
-This sequence was found on http://www.ncbi.nlm.nih.gov/
+[[Boston_UniversityCompTransf | Making Shewanella Competent and Transforming Plasmid]]
-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:
-’
-'''GAATGAATAA'''
-ATGAAATGTCCTTCGGACTCCCTGTCCATTTTACGTTGTAATCAAATATTGGATGCGGCTGAAAAGCTCA
-TTGAGTCACAAGGTGTTGTATCTTTTAAGTTTTCTCAGCTTGCGCATGAGGTGGGATGCTCTACGGGTAC
-TTTATATAAATTTTTTGAACGTAAAGAAGATGTGTTGGTTTGTTTATTTTTAAGAAGCGCAACCTCAAAT
-CACTTACCGATATTTATCCATAAAAATCCAGAGTTAACTGCGCAAGAGAAGGTGCTGTTACCCATTTTAT
-TTACCTTTGAAACCATTAAGCGCAGTAGTAGCTTTTTTACGCTGCGTTCGGTGTCGGTCAATACCATGGT
-GTGGAAACTGGCCAGTGACGAAAAAGTGGAGCGGTTTAAAAAACGCATTAATGCTTTTTGGAGTTGGTTT
-ACAGACTCACTGCATTTAGCTGTTGAAAACGGCGAATTAGTGGCAACACCATTACAAATTAAAGAATTGG
-TCCAAGGGATAACGTTTTATTTAACAGGGTCTTTGACACAATTTGAAAGTCAATTGATTGCCCCAGAGTT
-TTTGTCTGATCGCCGTGAAACCTGTTATCGACATTTAGCAAACCTGATGGAGCGATACGAGTGGAAAAAG
-CCTTTAACTCTTGCGCTGTTTGATTCGTTAGAGGCGAGAACTATTAAGTTTTTTGACCAACATTATCGTG
-ACCATATGACCTGCGCGGCTTGTAGTGCGCTGTCAAATACCGACACTAAGACATCATCTCCCTGTACTCG
-TCAGTGTGGTTAG
-‘’’GGCGTCCTGC’’’
-’
-Primer 1:
-'''TGA ATA A'''AT 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
-’
-'''AAGGAAAACC'''
-ATGTCCACCATGCTGCCACTGTATTTAGTCGATGATGATGAAGCGATTCTCGACTCCTTAGGGTTTATGC
-TCAGGCAATTTGGTTACCAAGTACAAACCTTTAGCAGTGGACGGGATTTTTTAGCCCAATGTCCGTTAAC
-ACAGGCTGGCTGCGTGATTTTAGATAGCCGAATGCCGGAGATCACCGGCCAAGAAGTGCAGCAAAAACTA
-CTTGAAACCCAAAGCCCATTGGGAGTTATCTTTCTCACGGGGCACGGTGATTTGCCCATGGCATTAAGCG
-CCTTTCGTAAGGGTGCATGCGATTTTTTTCAAAAGCCGGTATCTGGCAAAGCCCTAGTACAAGCCATTAA
-AAAAGCGCATAAAGAAAGCCAAGCCAGCTTTGAGCAACAGAGTCTGCAGCATAAATTTGCCCAACTGACC
-GACCGTGAACAACAAGTGTTAGCCCATGTGGTTCAAGGTATGACCAACAAGCAGATCTCCGAGGCCATGT
-ATTTATCCTTAAGAACCATTGAAGTGCACCGCGCTAAGATCATGAAAAAGCTCGAAGTCAGTAATATGGC
-AGAATTAGTACAGCACTTAGCCCACCTAAATACACTCTTACCGGAGTAA
-'''TCCAATAAAC'''
-’
-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 A'''TT 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 A'''AT 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:  From CAB(?)
-Error-Prone PCR:  Need to Buy
+Ligases:  Need to Buy
-Plasmids:  Need to Buy?
-Restriction Enzymes:  Need to Buy?
-Ligases:  Need to Buy?
 == Short-Term To-Do List ==
+EDIT THE WIIIIKIIII
-Lab Orientation: COMPLETED!
+== Protocols ==
-*[[Lab Orientation Checklist]]
+[[Boston_UniversityHeatShockProtocol | Calcium Chloride/Heat Shock Plasmid Transformations Protocol]]
-Lab Safety Training: COMPLETED!
-Design of Primers:  COMPLETED!
+[[Boston_UniversityFilterConjugationProtocol | Filter Cojugation Protocol]]
-Ordering of Primers:  Not Completed
+[[Boston_UniversityTOPO | pTrcHis TOPO TA Expression Kit Cloning Protocol]]
-Gathering of Protocols:  Not Completed (Chris, please send me the protocols when they are gathered)
+[[Boston_UniversityNEBCutter| Using NEBCutter for checking specific restriction enzymes against a sequence]]
-Ordering of Error-Prone PCR Materials:  Not completed
+[[Boston_UniversityGel | Making an Electrophoresis Gel]]
-Thank-You Letters sent to Pfizer:  Not Completed
+[[Boston_UniversityZymo/SOB | Procedure for 50 mL E. Coli mixture in Zymo Broth or SOB
+]]
-Thank-You Letters sent to BU ppl:  Not completed
+== Question and Answer ==
-== Relevant Publications and Links==
-http://www.shewybase.bu.edu
 [https://2007.igem.org/Boston_University Back]