Team:Kyoto/MaterialsMethods

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  • Design
  　　　　
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• Parts
  • Basic Parts
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Material&Methods

• 1) Parts
• 2) Primer list
• 3) Materials
• 3-1 Kit
• 3-2 Restriction Enzyme
• 3-3 Polymerase
• 3-4 DNA ligase
• 3-5 Marker
• 3-6 Organism
• 3-7 Antibiotics
• 3-8 Equipment
• 3-9 Backbone
• 3-10 Buffer
• 3-11 SDS-PAGE&Westernblotting
• 4) Methods
• 4-1 Miniprep
• 4-2 Gel Extraction and PCR purification
• 4-3 Restriction Enzyme Digestion
• 4-4 Ligation
• 4-5 Transformation
• 4-6 PCR
• 4-7 Sequencing
• 4-8 Western blotting
• 4-9 Overnight-Culture
• 4-10 Plates

1) Parts

Basic Parts

Composite Parts

2) Primer List

primer name	sequence	Length	GC%	Tm	Designer	Manufacturer
Z001	GTTAGGGCAGGGATGTAGATT	21	47.62	53.07	Shimazoe	eurofin
Z002	TGGTTAACGTATTCTCGATGTAAAG	25	36	53.19	Shimazoe	eurofin
Z003	TGGTTACAAACTACCTACAATTTG	24	33.33	51.29	Shimazoe	eurofin
Z004	GATCTTTTACCTGATTTCGACC	22	40.91	51.18	Shimazoe	eurofin
Z005	TGTTCACACTTAATTCACATTTATTTGAGGCAACAATACGTGGCCAGCGACATGGAGGCCCAGAA	65	44.62	72.86	Shimazoe	eurofin
Z006	ATGAATAAGGAAAAAGATAGGGAGCACTTAATAGGCCCTGCCCTCGTTTAAACTGGATGGCGG	63	46.03	71.92	Shimazoe	eurofin
Z007	acacgctttttcagttcgagtttat	25	36	55.89	Shimazoe	eurofin
Z008	gtttcgaataaacacacataaacaaacaaaatgcgtaaaggagaagaacttttcactgga	60	33.33	66.8	Shimazoe	eurofin
Z009	tccagtgaaaagttcttctcctttacgcattttgtttgtttatgtgtgtttattcgaaac	60	33.33	66.8	Shimazoe	eurofin
Z010	catggcatggatgaactatacaaataataaAACAGGTGGATCCCACATTGtcatgtaatt	60	35	66.71	Shimazoe	eurofin
Z011	aattacatgaCAATGTGGGATCCACCTGTTttattatttgtatagttcatccatgccatg	60	35	66.71	Shimazoe	eurofin
Z012	ggccgcaaattaaagccttcgagcg	25	56	63.35	Shimazoe	eurofin
Z013	gtttcgaataaacacacataaacaaacaaaatggcttcctccgaagacgttatcaaagag	60	36.67	67.57	Shimazoe	eurofin
Z014	ctctttgataacgtcttcggaggaagccattttgtttgtttatgtgtgtttattcgaaac	60	36.67	67.57	Shimazoe	eurofin
Z015	aataacgctgatagtgctagtgtagatcgcAACAGGTGGATCCCACATTGtcatgtaatt	60	41.67	69.94	Shimazoe	eurofin
Z016	aattacatgaCAATGTGGGATCCACCTGTTgcgatctacactagcactatcagcgttatt	60	41.67	69.94	Shimazoe	eurofin
Z017	gaattcgcggccgcttctagagaca	25	56	62.89	Shimazoe	eurofin
Z018	tgccggactgcagcggccgctacta	25	68	69.57	Shimazoe	eurofin
Z019	AAACATACTATTTAGGCTTGTTTATGTTCAGAACCTGTGACTCGTTTAAACTGGATGGCGGCGTT	65	40	70.47	Shimazoe	eurofin
Z020	atggccgctactgacagattaaacc	25	48	58.98	Shimazoe	eurofin
Z021	gagacccatcttgtaactcaatacg	25	44	55.16	Shimazoe	eurofin
Z022	gaataaacacacataaacaaacaaaatggccgctactgacagattaaacc	50	36	65.41	Shimazoe	eurofin
Z023	ggtttaatctgtcagtagcggccattttgtttgtttatgtgtgtttattc	50	36	65.41	Shimazoe	eurofin
Z024	cgtattgagttacaagatgggtctcCACCACCACCACCATCACtagAACAGGTGGATCCCACATTGtcatg	71	49.3	73.64	Shimazoe	eurofin
Z025	catgaCAATGTGGGATCCACCTGTTctaGTGATGGTGGTGGTGGTGgagacccatcttgtaactcaatacg	71	49.3	73.64	Shimazoe	eurofin
Z026	gaattcgcggccgcttctagagacacgctttttcagttcgagtttat	47	46.81	69.83	Shimazoe	eurofin
Z027	tgccggactgcagcggccgctactagtaggccgcaaattaaagccttcgagcg	53	60.38	77.31	Shimazoe	eurofin
Z028	TGAAAACTCATTACCTAAATTTGTTTATGTTCGGTAGCCCCTCGTTTAAACTGGATGGCGGCGTT	65	41.54	71.34	Shimazoe	eurofin
Z029	GTATCCTTTTCAAGTACTTCCACCACCACCACCATCACta	40	45	65.52	Shimazoe	eurofin
Z030	taGTGATGGTGGTGGTGGTGGAAGTACTTGAAAAGGATAC	40	45	65.52	Shimazoe	eurofin
Z031	caacctcaatggagtgatgcaacc	24	50	58.35	Shimazoe	eurofin
Z032	AACAGGTGGATCCCACATTGtc	22	50	56.65	Shimazoe	eurofin
Z033	CCTTTGCTCTGACCGATCCATA	22	50	56.03	Shimazoe	eurofin
Z034	ACCCAGCACCATCAGAATTTAGCG	24	50	59.41	Shimazoe	eurofin
Z035	CGGTGATTATCTAATCGAGGAAGAGG	26	46.15	56.42	Shimazoe	eurofin
Z036	GCTCATCAGTTCAATGGGAATCTTG	25	44	56.33	Shimazoe	eurofin
Z037	CAGCTTTGCTGCTATGTATGGTG	23	47.83	56.35	Shimazoe	eurofin
Z038	GGAACCGCAAAACCAGACTAC	21	52.38	55.81	Shimazoe	eurofin
Z039	tttgtttgtttatgtgtgtttattcgaaac	30	26.67	54.96	Shimazoe	eurofin
Z040	AACAGGTGGATCCCACATTGtcatgtaatt	30	40	60.27	Shimazoe	eurofin
Z041	gtttcgaataaacacacataaacaaacaaa	30	26.67	54.96	Shimazoe	eurofin
Z042	aattacatgaCAATGTGGGATCCACCTGTT	30	40	60.27	Shimazoe	eurofin
Z043	GAAATTGCACTACCACCGGCGGCAAAATAT	30	46.67	63.65	Shimazoe	eurofin
Z044	cctatgaactgatggttggtg	21	47.62	52.62	Shimazoe	eurofin
Z045	ATACTGATGCTTCTGTAGAGGGTGA	25	44.00	56.62	Shimazoe	eurofin
Z046	GATAGCTTGGAGTTCATCGCGAGT	24	50.00	58.77	Shimazoe	eurofin
Z047	ggaagaggaggaagtgacatcgg	23	56.52	58.33	Shimazoe	eurofin
Z048	ggcCAAACATCCTCACCCTCTAC	23	56.52	58.81	Shimazoe	eurofin
Z049	ggacagttccatcgaggatc	20	55.00	53.93	Shimazoe	eurofin
Z050	agcttcttttcttctgcgcc	20	50.00	55.58	Shimazoe	eurofin
Z051	caggacgatggagtccaatg	20	55.00	54.50	Shimazoe	eurofin
Z052	atatcggcaccttcgacctg	20	55.00	56.03	Shimazoe	eurofin
Z053	GATGGACATAGGATCCTTAG	20	45.00	48.06	Shimazoe	eurofin
Z054	GCCACATTGTCTTTTGTTGC	20	45.00	53.22	Shimazoe	eurofin
Z055	CAGGACAGCGAGGCCGACTT	20	65.00	61.01	Shimazoe	eurofin
Z056	GCAGTTGCCACTGGTTCCGA	20	60.00	59.69	Shimazoe	eurofin
Z057	cgtatcgttgctcaaatgaa	20	40.00	51.00	Shimazoe	eurofin
Z058	tcaccacctgttccggtggt	20	60.00	59.82	Shimazoe	eurofin
Z059	GTAGAGTACAAGACGGCACT	20	50.00	53.16	Shimazoe	eurofin
Z060	CAGCGTCCTACGATAATACG	20	50.00	52.27	Shimazoe	eurofin
Z061	CCGGTTCTTCGTCCACTAAA	20	50.00	54.01	Shimazoe	eurofin
Z062	CTATTTCCAGTGGAGAAACG	20	45.00	50.25	Shimazoe	eurofin
Z063	ACAACAACCAGTTCGGAATC	20	45.00	52.73	Shimazoe	eurofin
Z064	TAGATCCCACCACCAACACGGCC	23	60.87	62.47	Shimazoe	eurofin
Z065	AGGCTATTACTGGTTATGGTCTTGG	25	44.00	55.94	Shimazoe	eurofin
Z066	agttgataatttcatcttaatagagc	26	26.92	49.61	Shimazoe	eurofin
Z067	acttcctcctcttccatc	18	50.00	49.02	Shimazoe	eurofin
Z068	GGATGATTTGCGTTATTGTTCTTAT	25	32.00	52.46	Shimazoe	eurofin
Z069	TTTCTCAAGCATGGGAAACAAGAGA	25	40.00	56.71	Shimazoe	eurofin
Z070	GCCATGGAAGACCCACCAAGA	21	57.14	58.53	Shimazoe	eurofin
Z071	ACGGCCAAAGAGAGCCATGG	20	60.00	59.19	Shimazoe	eurofin
Z072	GTCTTGGTGGGTCTTCCATG	20	55.00	54.58	Shimazoe	eurofin
Z073	GCGTTTCGAGGTCTTTGTAGCT	22	50.00	57.40	Shimazoe	eurofin
Z074	TCTACAGAAGCATCAGTATC	20	40.00	48.01	Shimazoe	eurofin
Z075	tcaatgtggttggttcagtgac	22	45.45	55.22	Shimazoe	eurofin
Z076	agatccatcccttctcgatgtc	22	50.00	55.22	Shimazoe	eurofin
Z077	GATGAAGTCGCTCTAGGTTGGG	22	54.55	56.66	Shimazoe	eurofin
Z078	ACACACGAATTCGCGGCCGCTTCTAGATGGAGCAAGGTAGTAATGTGAATCACCTG	56	50.00	72.76	Nambu	eurofin
Z079	CCCCACCTGCAGCGGCCGCTACTAGTATTATTATGTTTTTTCCGGTGGTAAATCTCCCTG	60	50.00	72.70	Nambu	eurofin
Z080	CACACAGAATTCGCGGCCGCTTCTAGATGAATGAAGAGGGCTTTTTTTTCAGTGCCAGAGGCCACCGTCCT	71	52.11	76.39	Nambu	eurofin
Z081	AAAATCACTGCAGCGGCCGCTACTAGTATTATTAGTCCAGAGGACGGTGGCCTCTGGCACTG	62	53.23	74.83	Nambu	eurofin
Z082	GAAAAAGAATTCGCGGCCGCTTCTAGATGCAAACATCCTCACCCTCTACAGAAGC	55	49.09	71.86	Nambu	eurofin
Z083	AGGGGGCTGCAGCGGCCGCTACTAGTATTATTACTTTGTACTAGGTGATGATGCAACAC	59	49.15	72.50	Nambu	eurofin
Z084	GAACTCCAAGCTATCTGATC	20	45.00	49.40	Nambu	eurofin
Z085	TGCCGACAGGAGAACagttgataatttcatcttaatagagc	41	39.02	63.55	Nambu	eurofin
Z086	GTTCTCCTGTCGGCAggtttagcctcgactacttt	35	51.43	66.58	Shimazoe	eurofin
Z087	TGCTGAAGTTGAATTggaaaattgggccaaagtag	35	40.00	63.03	Shimazoe	eurofin
Z088	AATTCAACTTCAGCAtcttccaccgatgtcacttc	35	42.86	63.62	Shimazoe	eurofin
Z089	GGATCCTAATACGACTCACTATAGGGAACAGCCACCATGGGAACGAATGAAGAGGGCTTTTTTTTCAGTG	70	45.71	72.07	Shimazoe	eurofin
Z090	TTCTGTAGAGGGTGAGGATGTTTGTTAGGCTAGCTTACTCGCGATGA	47	46.81	69.00	Shimazoe	eurofin
Z091	GGATCCTAATACGACTCACTATAGGGAACAGCCACCATGGGCACAGAGCAAGGTAGTAATG	61	49.18	71.68	Shimazoe	eurofin
Z092	CTGAAAAAGTACTTCTAGGCTCCCTTAGTGATGATGGTGATGGTGTCTGGA	51	45.10	68.47	Shimazoe	eurofin
Z093	ccGGCTAGCTTACTCGCGATGAA	23	56.52	60.84	Shimazoe	eurofin
Z094	ATGCATGAATTCGCGGCCGCTTCTAGAGACACGCTTTTTCAGTTCGAGTT	50	48.00	72.04	Nambu	eurofin
Z095	TCCCCCCTGCAGCGGCCGCTACTAGTAGGCCGCAAATTA	39	61.54	74.13	Nambu	eurofin
Z096	ATGGCTATCTGGGAGCAACT	20	50.00	54.79	Tong	eurofin
Z097	ATCTACTGTCTGCAGAGTCAG	21	47.62	52.87	Tong	eurofin
Z098	TACGTAGGATCCCTGCAGTC	20	55.00	54.71	Tong	eurofin
Z099	GACTAGCAGGAGGTGAAGAT	20	50.00	52.43	Tong	eurofin
Z100	TGAAAGCGAAGACGAGATGG	20	50.00	54.49	Tong	eurofin
Z101	AGAGCTTTAACAGCAGTAGG	20	45.00	51.22	Tong	eurofin
VR	attaccgcctttgagtgagc	20	50.00	54.70	Tong	eurofin
VF2	tgccacctgacgtctaagaa	20	50.00	55.05	Tong	eurofin
Y001	ctaacggtacttctactgaag	21	42.86	49.31	Tong	eurofin

3) Materials

3-1 Kit

Name	Supplier
FastGene™Plasmid Mini Kit	NIPPON Genetics Co., Ltd
FastGene™Gel/PCR Extraction Kit	NIPPON Genetics Co.,Ltd

3-2 Restriction Enzyme

Name	Supplier
EcoRI	TaKaRa, Promega
PstI	TaKaRa, Promega
SpeI	TaKaRa, Promega

3-3 Polymerase

Name	Supplier
Q5 High-Fidelity 2x master mix	New England Biolabs Japan Inc.

3-4 DNA ligase

Name	Supplier
T4 DNA ligase	TaKaRa

3-5 Marker

Name	Supplier
1kb DNA Ladder	NIPPON Genetics Co., Ltd

3-6 Organism

Name	Supplier
E.coli DH5α Genotype	TaKaRa

3-7 Antibiotics

Name	Supplier
Chloramphenicol	Wako
Ampicillin	Wako

3-8 Equipment

Name	Supplier
BioPhotometer	eppendorf
LABO SHAKER	BIO CRAFT
CO2 INCUBATOR	SANYO
Pipette Controller	Biohit Midi Plus
MiniCentrifuge Model GMC-060	LMS CO.,LTD.
HIGH-SPEED REFRIGERATED CENTRIFUGE	TOMY
HIGH-PRESSURE STEAM STERILIZER	TOMY
VOTEX-GENE2	Scientific Industryes
Scanning Electron Miniscope TM1000s	HITACHI
Fluorescence Microscope BX61N-34-FL-1-D	OLYMPUS
SCIECE IMAGING SYSTEM LAS-3000	Fuji film

3-9 Backbone

Name	Supplier
pRS421	National BioResource Project http://yeast.nig.ac.jp/yeast/
pRS423	National BioResource Project
pRS424	National BioResource Project
pRS425	National BioResource Project
pRS426	National BioResource Project
pGK421	National BioResource Project
pRS316	National BioResource Project

3-10 Buffer

Name	Supplier
Sodium Carbonate	Wako
Sodium Bicarbonate	Wako
Methanol(99.5%)	Wako
Sodium Chloride	Wako
SDS	nacalai tesque
Trisaminomethane	nacalai tesque
Potassium dihydrogenphosphste	SIGAMA-ALDRICH
Potassium Chloride	Wako
Glycine	Wako
Agar, Powder	Wako
Agarose XP	Wako
10% Hydrochloric Acid	Wako

3-11 SDS-PAGE&Westernblotting

Name	Supplier
REAL GEL PLATE (10%)	BIO CRAFT
BE-210(SDS-PAGE)	BIO CRAFT
BE-330	BIO CRAFT
Amersham ECL Anti-Mouse IgG	GE healthcare
Amersham ECL Anti-rabbit IgG	GE healthcare
Amersham ECL Prime Blocking Reagent	GE healthcare
Amersham ECL Prime WB Detection Reagent	GE healthcare

4) Methods

4-1 Miniprep

Minipreps were performed using FastGene™Plasmid Mini Kit according to the manufacturer's protocols.

4-2 Gel Extraction and PCR purification

Gel Extraction was performed using FastGene™Gel/PCR Extraction Kit according to the manufacturer's protocols.

4-3 Restriction Enzyme Digestion

Restriction enzyme treatment was performed using Q5 High-Fidelity 2x master mix according to the respective manufacturer's protocols.

4-4 Ligation

Ligation was performed using Takara Bio's Ligation High Ver.2 according to the manufacturer's.

4-5 Transformation

1.Thaw competent cells on ice
2.Add DNA sample (2.5μl) to competent cells. leave them on ice for 15 minutes
3.Keep them in heating block for 45 seconds, then cool on ice for 2 minutes
4.Add 90μl SOC liquid culture medium, then incubate for 45 minutes at 37℃
5.Seed cells onto LB+antibiotics agar plate. Incubate for 24 hours at 37℃

4-6 PCR

PCR was performed using Q5 High-Fidelity 2x master mix according to the manufacturer's protocols.

4-7 Sequencing

We outsourced the sequencing to Macrogen

http://www.macrogen-japan.co.jp/cap_seq_0203.php

4-8 Western blotting

1.Apply sample to SDS-PAGE minigel (BIOCRAFT 15%).
2.Soak the gel in transfer buffer.
3.Soak PVDF membrane in 100% methanol for 30 sec.
4.Soak PVDF membrane and filter paper in transfer buffer, leave for 5 min.
5.Set filter paper, membrane, gels, filter paper in this order to semidry transfer from anode to cathode.
6.Transfer the proteins from the gel to the membrane with 100 mA for 1 h.
7.Soak membrane in blocking buffer (dilution of 5 g ECL Blocking reagent by 100ml of TBST) for 1 h.
8.Wash for 5 min 3 times with TBST.
9.Apply 1' antibody (dilution of 10 μl of 1’antibody by 10ml of Blocking buffer) and shake for 1 h.
10.Wash for 5 min 3 times with TBST.
11.Apply 2' antibody (dilution of 4μl of 2’antibody by 10ml of Blocking buffer) and shake for 1 h.
12.Wash for 5 min 3 times with TBST.
13.Drain excess wash buffer from the washed membrane and place on flat surface, protein side up.
14.Add detection reagent onto the membrane, covering all of the membrane.
15.Incubate for 5 minutes at room temperature.
16.Drain off excess detection reagent by dabbing with Kimwipe.
17.Place the sample in the CCD camera compartment and record the images.

4-9 Overnight-Culture

1.Prepare LB media by resolving 5g Bacto Tryptone, 1.25g Bacto-yeast extract and 1.25g NaCl in 500ml of milliQ and autoclave it.
2.Transfer 7ml of LB into a culture tube and add the respective antibiotic stock solutions.
3.Inoculate the culture by picking a single colony with a pipet tip and tipping it into the medium.
4.Shake the culture at 37℃ at 180 rpm for 14-16h.
5.Isolate plasmids or use the culture for further experiments.

Concentrations of antibiotics:

Antibiotics	Stock concentration	Final concentration
Ampicillin	100mg/ml	100μg/ml
Chloramphenicol	10mg/l	30μg/ml

4-10 Plates

1.Rinse the graduated cylinder with distilled water and add 500 ml of milliQ.
2. Transfer 1. to the flask.
3. Place the following in the flask of 2.
・Bacto Tryptone 5 g
・Bacto yeast extract 2.5 g
・NaCl 2.5g
・Agar 7.5 g
4. After mixing thoroughly, autoclave it after covering with aluminum foil.
5. Add the respective antibiotics.
6. Cool until it gets moderately warm to the touch.
7. Put in a container and fix the lid with the tape after the medium solidifies.

Concentrations of antibiotics:

Antibiotics	Stock concentration	Final concentration
Ampicillin	100mg/ml	100μg/ml
Chloramphenicol	10mg/ml	30μg/ml