Basic Protocol 1: Bait Construction, Transformation into Yeast Reporter Strain, and Detection by Immunoblotting Materials - cDNA encoding the bait protein
- Primers for subcloning bait cDNA into vector:
- Forward primer: 5′‐TACTCTTATggccattacggcc‐NNN NNN NNN NNN NNN NNN NNN‐3′ (where NNN denotes the gene‐specific sequence)
- Reverse primer: 5′‐TACTCTTATggccgaggcggcc‐GC NNN NNN NNN NNN NNN NNN NNN‐3′ (where NNN denotes the gene‐specific sequence)
- DNA gel extraction kit (e.g., NucleoSpin Extract II kit, Macherey‐Nagel; Wizard SV Gel and PCR Clean‐up System, Promega)
- Appropriate MbY2H bait vector: pBT3‐C, pBT3‐SUC, or pBT3‐STE (Dualsystems Biotech, see and Internet Resources)
- Sfi I restriction enzyme
- PCR DNA purification kit (e.g. MinElute PCR Purification kit, Qiagen)
- Competent E. coli cells (XL1‐Blue, DH10B, TOP10, or similar cloning strains)
- LB plates supplemented with kanamycin (see appendix 4A )
- Sequencing primers appropriate to the vector:
- pBT3‐C, pBT3‐SUC, and pBT3‐STE
- Forward primer: 5′‐TGGCATGCATGTGCTCTG‐3′
- Reverse primer: 5′‐GTAAGGTGGACTCCTTCT‐3′
- pBT3‐N
- Forward primer: 5′‐CAGAAGGAGTCCACCTTAC‐3′
- Reverse primer: 5′‐AAGCGTGACATAACTAATTAC‐3′
- pDHB1
- Forward primer: 5′‐TTTCTGCACAATATTTCAAGC‐3′
- Reverse primer: 5′‐GTAAGGTGGACTCCTTCT‐3′
- 1×YPAD liquid medium (see recipe )
- NMY51 yeast strain: MATa his3Δ200 trp1‐901 leu2‐3,112 ade2 LYS2::(lexAop) 4 ‐HIS3 ura3::(lexAop) 8 ‐lacZ ade2::(lexAop) 8 ‐ADE2 GAL4 (Dualsystems Biotech, see Internet Resources)
- 50% (w/v) PEG 4000 (see recipe )
- 1 M LiOAC (see recipe )
- Single‐stranded carrier DNA ( protocol 7 )
- Control plasmids: pCCW‐Alg5 (positive control) and pPR3‐N (negative control), Dualsystems Biotech (see Internet Resources)
- 0.9% (w/v) NaCl
- 10‐cm plates containing SD solid medium lacking leucine (SD−Leu; see recipe )
- 10‐cm plates containing SD solid medium lacking tryptophan (SD−Trp; see recipe )
- Bait‐specific antibody or mouse monoclonal antibody against LexA (Dualsystems Biotech, see Internet Resources)
- Shaking incubator, 30°C
- Parafilm
- Additional reagents and equipment for performing PCR amplification ( appendix 4J ), restriction enzyme digestion of DNA ( appendix 4I ), agarose gel electrophoresis ( appendix 4F ), and immunoblotting and immunodetection (unit 10.10 ), and for preparing minipreps of plasmid DNA ( appendix 4C )
Basic Protocol 2: Functional Assay to Determine Bait Suitability for Screening Materials - 1×YPAD liquid medium (see recipe )
- Yeast strain NMY51 (Dualsystems Biotech, see Internet Resources), growing on plates
- 50% (w/v) PEG 4000 (see recipe )
- 1 M lithium acetate (LiOAC; see recipe )
- Single‐stranded carrier DNA ( protocol 7 )
- Bait construct ( protocol 1 )
- Control plasmids: pAI‐Alg5, pDL2‐Alg5, and pPR3‐N (Dualsystems Biotech, see Internet Resources)
- 10‐cm diameter plates containing SD solid medium lacking tryptophan, leucine, histidine, or adenine (SD−Trp−Leu, SD−Trp−Leu−His, and SD−Trp−Leu−His−Ade; see recipe )
- 0.9% (w/v) NaCl
- Shaking incubator, 30°C
- 42°C water bath
- Parafilm
Basic Protocol 3: Pilot Screen to Optimize the Stringency of Selection Materials - Bait‐transformed yeast strain NMY51 ( protocol 2 ), growing on plate <2 weeks old
- SD liquid medium lacking leucine (SD−Leu; see recipe )
- 2×YPAD liquid medium (see recipe )
- Single‐stranded carrier DNA ( protocol 7 )
- 1 M lithium acetate (LiOAC; see recipe )
- 10× TE buffer, pH 7.5: 100 mM Tris·Cl, pH 7.5, 10 mM EDTA (see appendix 2E ); store up to 1 year at room temperature
- 50% (w/v) PEG 4000 (see recipe )
- Library vector pPR3‐N (Dualsystems Biotech, see Internet Resources)
- Dimethyl sulfoxide (DMSO)
- 0.9% (w/v) NaCl
- 10‐cm plates containing SD medium lacking tryptophan and leucine (SD−Trp−Leu; see recipe )
- 15‐cm selective plates (six total) containing SD medium lacking tryptophan, leucine and histidine (SD−Trp−Leu−His) and (six total) containing SD−Trp−Leu−His−Ade (adenine; see recipe ), both supplemented with 0, 1, 2.5, 5, 7.5 and 10 mM 3‐amino‐1,2,4‐triazole (3‐AT; see recipe )
- Shaking incubator, 30°C
- 50‐ml conical tube
- 1‐liter shaker flask
- 99°C heating block
- 42°C water bath
- Plastic bags with tape or Parafilm
Basic Protocol 4: Screening of a cDNA Library to Identify Novel Interactors Materials - Bait‐transformed yeast strain NMY51 ( protocol 1 ), growing on plate for no longer than 2 weeks
- SD liquid medium lacking leucine (SD−Leu; see recipe )
- 2× YPAD liquid medium (see recipe )
- Single‐stranded carrier DNA ( protocol 7 )
- 1 M lithium acetate (LiOAc; see recipe )
- 10× TE buffer: 100 mM Tris·Cl, pH 7.5, 10 mM EDTA (see appendix 2E ); store up to 1 year at room temperature
- 50% (w/v) PEG 4000 (see recipe )
- Appropriate cDNA library (see Internet Resources)
- Dimethyl sulfoxide (DMSO)
- 0.9% (w/v) NaCl
- Sixteen 15‐cm diameter selective plates with appropriate selection medium (determined in protocol 3 )
- 10‐cm plates containing solid SD medium lacking tryptophan and leucine (SD−Trp−Leu; see recipe )
- Shaking incubator, 30°C
- 50‐ml conical tube
- 1‐liter shaker flask
- 42°C water bath
- Plastic bags with tape or Parafilm
Basic Protocol 5: Plasmid Recovery from Yeast Materials - Yeast colonies positive for bait/prey interaction ( protocol 4 )
- Selection plates (same stringency as protocol 4 )
- SD liquid medium lacking tryptophan and leucine (SD−Trp−Leu; see recipe )
- Plasmid miniprep kit (e.g., Wizard Plasmid Purification System, Promega), including resuspension buffer, nuclease removal buffer, wash buffer, elution buffer, and spin columns
- 425 to 600‐µm (30 to 40 U.S. sieve) acid‐washed glass beads (Sigma)
- E. coli XL‐1 Blue chemically competent cells (Stratagene)
- SOC medium (see appendix 2E ), 37°C
- Sfi I restriction enzyme
- LB plates supplemented with 100 µg/ml ampicillin (see appendix 2E )
- Plastic bags or Parafilm
- 96‐well deep‐well master block (e.g., Greiner Bio‐One GmbH)
- Breathable plate seal (e.g., EasySeal film, Hampton Research)
- Shaking incubator, 30°C
- Centrifuge with rotor adapted for 96‐well plates
- 42°C water bath
- Additional reagents and equipment for performing restriction enzyme digestion of DNA ( appendix 4I ) and agarose gel electrophoresis ( appendix 4F )
Basic Protocol 6: Confirmation of Positive Bait‐Prey Interactors Materials - Bait‐transformed yeast strain NMY51 ( protocol 1 ), growing on plate
- SD liquid medium lacking leucine (SD−Leu; see recipe )
- Prey plasmids derived from the library screen (see protocol 5 )
- 50% (w/v) PEG 4000 (see recipe )
- 1 M lithium acetate (LiOAc; see recipe )
- Single‐stranded carrier DNA ( protocol 7 )
- 0.9% (w/v) NaCl
- 10‐cm plates containing SD solid medium lacking tryptophan and leucine (SD−Trp−Leu plates; see recipe )
- 10‐cm selective plates of the same stringency as used in the original screen ( protocol 4 )
- Appropriate sequencing primers:
- Forward primer for pPR3‐N, pDSL‐Nx, and pNubG‐X library plasmids: 5′‐GTCGAAAATTCAAGACAAGG‐3′
- Reverse primer for pPR3‐N and pDSL‐Nx library plasmids: 5′‐AAGCGTGACATAACTAATTAC‐3′
- Reverse primer for pNubG‐X library plasmids: 5′‐GTTACTCAAGAACAAGAATTTTCG‐3′
- Forward primer for pPR3‐C, pDL2xN, and pX‐NubG library plasmids: 5′‐TTTCTGCACAATATTTCAAGC‐3′
- Reverse primer for pPR3‐C, pDL2xN and pX‐NubG library plasmids: 5′‐CTTGACGAAAATCTGCATGG‐3′
- Shaking incubator, 30°C
- 96‐well master block (e.g., Greiner Bio‐One GmbH) and plate sealers
- 42°C water bath
- Centrifuge with rotor adapted for 96‐well plates
- Parafilm
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