Journal: Molecular cell

Article Title: DNA Polymerase Delta Synthesizes Both Strands during Break-Induced Replication

doi: 10.1016/j.molcel.2019.07.033

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-AID-tag MBL Cat# M214-3 Anti-PSTAIR Sigma-Aldrich Cat# P7962; RRID:AB_261183 Bacterial Strains and Plasmids NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs (NEB) Cat# {"type":"entrez-nucleotide","attrs":{"text":"C29871","term_id":"2361667","term_text":"C29871"}} C29871 YIAL3-URA ( Pavlov et al., 2001 ) N/A P170-URA ( Clausen et al., 2015 ) N/A Biological Samples Genomic DNA isolated from HeLa and HEK293T cells Björn Rabe N/A Chemicals, Peptides, and Recombinant Proteins Nocodazole Sigma-Aldrich Cat# M1404 Doxycycline hyclate Sigma-Aldrich Cat# D9891 3-indoleacetic acid (IAA) Abcam Cat# ab146403 Certified low melt agarose Bio-rad Cat# 1613111 SYBR Gold Invitrogen Cat# S11494 dCTP-alpha-P32 6000Ci/mmol Perkin Elmer Cat# BLU513H250 β Agarase I NEB Cat# M0392 Shrimp Alkaline Phosphatase NEB Cat# M0371 RNase HII NEB Cat# M0288 T4 RNA Ligase I NEB Cat# M0204 T7 DNA Polymerase NEB Cat# M0274 Zymolyase 20T USBiological Cat# 37340-57-1 Proteinase K Roche Cat# 03115852001 Critical Commercial Assays MasterPure Yeast DNA Purification Kit Lucigen Cat# MPY80200 KAPA HiFi HotStart Ready Mix Kapa Biosystems Cat# KK2602 HighPrep PCR Clean-Up System MagBio Genomics Cat# AC-60050 Deposited Data Agarose gels and Southern blot data This paper https://doi.org/10.17632/44hk5n646g.3 Raw and analyzed DNA sequencing data This paper https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= {"type":"entrez-geo","attrs":{"text":"GSE133558","term_id":"133558"}} GSE133558 Experimental Models: Organisms/Strains S. cerevisiae : Strain background: W303 ( Table S1 ) R. Rothstein N/A Oligonucleotides ( Table S2 ) Software and Algorithms Flow Jo Flow Jo https://www.flowjo.com/ ImageJ ImageJ https://imagej.nih.gov/ij/ Bowtie 2 ( Langmead and Salzberg, 2012 ) http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Custom algorithm for HydEn-seq analysis This paper Other CHEF-DR II Pulsed-Field Gel Electrophoresis system Bio-rad N/A Open in a separate window KEY RESOURCES TABLE Pol δ synthesizes both strands during BIR Pol α-primase and DNA ligase I are required for BIR DNA synthesis during BIR is independent of Pol ε HydEn-seq technology is applied to DNA repair synthesis

Techniques: Isolation, Recombinant, DNA Purification, Southern Blot, DNA Sequencing, Software, Pulsed-Field Gel

Journal: Methods in enzymology

Article Title: Protein and Antibody Engineering by Phage Display

doi: 10.1016/bs.mie.2016.05.005

Figure Lengend Snippet: Kunkel mutagenesis. Single-stranded DNA with uracil incorporated (dU-ssDNA; green (gray in the print version) above) is isolated from phage produced in CJ236 cells. Degenerate primers (red (black in the print version)) are annealed (mutagenesis regions indicated by asterices) to the dU-ssDNA. T7 DNA polymerase and T4 DNA ligase and dNTPs are added to synthesize the complementary strand based on the dU-ssDNA template. This covalently closed circular double-stranded DNA (CCC-dsDNA) is then electroporated into E. coli SS320 cells, in which the uracil-containing template is deactivated and the new, mutagenic strand is preferentially replicated.

Article Snippet: 3,3′,5,5′-Tetramethylbenzidine (TMB) (Sigma, St. Louis, MO, catalog #: T0440) 0.5 M H 2 SO 4 Anti-M13-HRP conjugated antibody (GE Healthcare, Marlborough, MA, catalog #: GE27-9421-01) T7 DNA Polymerase (NEB, Ipswich, MA, catalog #: M0274L) T4 DNA Ligase (Invitrogen, Carlsbad, CA, catalog #: 15224-017) 25 m M dNTPs (Fisher, Hampton, NH, catalog #: FERR1121) 25 mg/mL Uridine (Sigma, St. Louis, MO, catalog #: U3750-100G) BugBuster 10X Protein Extraction Reagent (Millipore, Billerica, MA, catalog #: 70921) QIAquick PCR Purification Kit (Qiagen, Hilden, Germany, catalog #: 28104) QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany, catalog #: 28704) QIAprep Spin Miniprep Kit (Qiagen, Hilden, Germany, catalog #: 27104) NucleoBond Xtra Maxi Plus (Macherey-Nagel, Düren, Germany, catalog #: 740416.50) Ni-NTA Agarose (Qiagen, Hilden, Germany, catalog #: 30210) DNaseI (Invitrogen, Carlsbad, CA, catalog #: 18047-019) SIGMAFast EDTA-free protease cocktail inhibitor (Sigma, St. Louis, MO, catalog #: S8830) Precision Plus Protein Dual Color Standards (BioRad, Hercules, CA, catalog #: 161-03741) Anti-His (C-term)-HRP antibody (Invitrogen, Carlsbad, CA, catalog #: 46-0707) Protein A Agarose (Pierce, Thermo Fisher Scientific, Waltham, MA, catalog #: 15918-014) Phusion High Fidelity PCR Master Mix with HF Buffer (NEB, Ipswich, MA, catalog #: M0531S) Restriction enzymes: BssHII, BsiWI, NheI, NsiI, FseI (NEB, Ipswich, MA, catalog #s: R0199S, R0553S, R0131S, R0127S, R0558S, respectively) Alkaline Phosphatase, Calf Intestinal (NEB, Ipswich, MA, catalog #: M0290S) Quick Ligation Kit (NEB, Ipswich, MA, catalog #: M2200S) Polyethylenimine (PEI) Linear, 25,000 MW (Polysciences, Warrington, PA, catalog #: 23966) FreeStyle™ 293 Expression Medium (ThermoFisher; Invitrogen, Carlsbad, CA, catalog #: 12338-018) M2 antibody (Sigma-Aldrich, St. Louis, MO, catalog #: F1804) Protein A-HRP conjugate (Invitrogen, Carlsbad, CA, catalog #: 101023)

Techniques: Mutagenesis, Isolation, Produced

Journal: Methods in enzymology

Article Title: Protein and Antibody Engineering by Phage Display

doi: 10.1016/bs.mie.2016.05.005

Figure Lengend Snippet:

Article Snippet: 3,3′,5,5′-Tetramethylbenzidine (TMB) (Sigma, St. Louis, MO, catalog #: T0440) 0.5 M H 2 SO 4 Anti-M13-HRP conjugated antibody (GE Healthcare, Marlborough, MA, catalog #: GE27-9421-01) T7 DNA Polymerase (NEB, Ipswich, MA, catalog #: M0274L) T4 DNA Ligase (Invitrogen, Carlsbad, CA, catalog #: 15224-017) 25 m M dNTPs (Fisher, Hampton, NH, catalog #: FERR1121) 25 mg/mL Uridine (Sigma, St. Louis, MO, catalog #: U3750-100G) BugBuster 10X Protein Extraction Reagent (Millipore, Billerica, MA, catalog #: 70921) QIAquick PCR Purification Kit (Qiagen, Hilden, Germany, catalog #: 28104) QIAquick Gel Extraction Kit (Qiagen, Hilden, Germany, catalog #: 28704) QIAprep Spin Miniprep Kit (Qiagen, Hilden, Germany, catalog #: 27104) NucleoBond Xtra Maxi Plus (Macherey-Nagel, Düren, Germany, catalog #: 740416.50) Ni-NTA Agarose (Qiagen, Hilden, Germany, catalog #: 30210) DNaseI (Invitrogen, Carlsbad, CA, catalog #: 18047-019) SIGMAFast EDTA-free protease cocktail inhibitor (Sigma, St. Louis, MO, catalog #: S8830) Precision Plus Protein Dual Color Standards (BioRad, Hercules, CA, catalog #: 161-03741) Anti-His (C-term)-HRP antibody (Invitrogen, Carlsbad, CA, catalog #: 46-0707) Protein A Agarose (Pierce, Thermo Fisher Scientific, Waltham, MA, catalog #: 15918-014) Phusion High Fidelity PCR Master Mix with HF Buffer (NEB, Ipswich, MA, catalog #: M0531S) Restriction enzymes: BssHII, BsiWI, NheI, NsiI, FseI (NEB, Ipswich, MA, catalog #s: R0199S, R0553S, R0131S, R0127S, R0558S, respectively) Alkaline Phosphatase, Calf Intestinal (NEB, Ipswich, MA, catalog #: M0290S) Quick Ligation Kit (NEB, Ipswich, MA, catalog #: M2200S) Polyethylenimine (PEI) Linear, 25,000 MW (Polysciences, Warrington, PA, catalog #: 23966) FreeStyle™ 293 Expression Medium (ThermoFisher; Invitrogen, Carlsbad, CA, catalog #: 12338-018) M2 antibody (Sigma-Aldrich, St. Louis, MO, catalog #: F1804) Protein A-HRP conjugate (Invitrogen, Carlsbad, CA, catalog #: 101023)

Techniques: