New England Biolabs, R3539S, BbsI-HF®

Learn about Ligase Fidelity and Push the Limits of Related Categories High-Fidelity (HF®) Restriction Endonucleases,, Restriction Endonucleases B,, Time-Saver Qualified Restriction Enzymes Applications High-throughput cloning and automation solutions,, NEBridge® Golden Gate Assembly ,, Restriction Enzyme Digestion Specification Unit Definition One unit is defined as the amount of enzyme required to digest 1 µg of λ DNA in 1 hour at 37°C in a total reaction volume of 50 μl. Reaction Conditions 1X rCutSmart™ Buffer Incubate at 37°C 1X rCutSmart™ Buffer 50 mM Potassium Acetate 20 mM Tris-acetate 10 mM Magnesium Acetate 100 µg/ml Recombinant Albumin (pH 7.9 @ 25°C) Activity in NEBuffers NEBuffer™ r1.1: 10% NEBuffer™ r2.1: 10% NEBuffer™ r3.1: 10% rCutSmart™ Buffer: 100% Diluent Compatibility Diluent B Storage Buffer 10 mM Tris-HCl 300 mM NaCl 1 mM DTT 0.1 mM EDTA 500 µg/ml Recombinant Albumin 50% Glycerol pH 7.4 @ 25°C Heat Inactivation 65°C for 20 minutes Methylation Sensitivity dam methylation: Not Sensitive dcm methylation: Not Sensitive CpG Methylation: Not Sensitive FAQ Q: What does the HF® refer to following the name of a restriction enzyme? A: HF stands for high fidelity. Many restriction endonucleases are capable of cleaving sequences which are similar but not identical to their defined recognition sequence. This altered or relaxed specificity has been termed star activity. HF restriction endonucleases have been engineered to cleave with higher fidelity than the wild type enzyme, hence exhibiting less star activity. Screens using increased glycerol concentration, increased reaction time and high enzyme concentration were used to identify enzymes that would offer the highest fidelity over a wide range of conditions. In addition, all HF enzymes are supplied with rCutSmart Buffer as well as a free vial of Purple Loading Dye. Q: Do I have to set-up digests with Time-Saver™ qualified enzymes for 5-15 minutes? Can I digest longer? A: NEB's Time-Saver™ enzymes have the benefit of working fast (5-15 minutes), but are also designed and qualified to withstand overnight digestions without degradation of DNA. Q: Which NEB restriction enzymes are supplied with Gel Loading Dye, Purple (6X)? A: All HF-restriction enzymes and most NEB non-HF restriction enzymes are supplied with Gel Loading Dye, Purple (6X). The non-HF restriction enzymes that come supplied with purple dye are: AatII AsiSI BsmBI-v2 EagI MboI NlaIII PvuI SmaI Acil AvrII BspHI EcoRI MboII NotI RsaI SpeI AfeI BamHI BsrGI EcoRV MluI NspI SacI StuI AflII BbsI ClaI Esp3I FseI MseI PacI SacII AgeI BglII DdeI HaeIII MspI PciI SalI XbaI AluI BsaI DpnI HindIII NcoI PmeI SapI XhoI ApaI BseYI DpnII HpaI NdeI PsiI-v2 SfaNI XmaI ApeKI BsiWI DraI KpnI NheI PstI SfiI XmnI AscI * All HF restriction enzymes are also supplied with Gel Loading Dye, Purple (6X) Q: Which restriction enzymes are used in GoldenBraid Assembly? A: BsaI is one Type IIS enzyme used in this method. NEB also offers an engineered high-fidelity version of this enzyme, BsaI-HF®v2, which has the added benefit of being Time-Saver™ qualified (can digest DNA in 5-15 mins and can be digested safely overnight) and exhibits reduced star activity. BsaI-HFv2 works in CutSmart® Buffer, as does T4 DNA Ligase (also part of the GoldenBraid workflow) which is 100% functionally active in this buffer, when the reaction is supplemented with 1 mM ATP. Other Type IIS enzymes used in GoldenBraid include BsmBI-v2/Esp3I, BtgZI, BbsI/BbsI-HF and PaqCI (AarI isoschizomer with 7 bp recognition sequence). Reference: GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology Q: Which restriction enzymes are used in Golden Gate Assembly? A: Golden Gate Assembly is a one-tube efficient cloning method based on Type IIS restriction enzymes that cleave outside their recognition sites and leave 3 or 4-base overhangs. BsaI is the most commonly used Type IIS enzyme for Golden Gate Assembly. NEB also offers an engineered high-fidelity version of this enzyme, BsaI-HF®v2, which has the added benefit of being Time-Saver™ qualified (can digest DNA in 5-15 mins or overnight without degradation to DNA) and exhibits dramatically reduced star activity. Other Type IIS enzymes used in Golden Gate Assembly include BsmBI-v2/Esp3I, BbsI/BbsI-HF, PaqCI (AarI isoschizomer with 7 bp recognition sequence), and SapI/BspQI/BspQI-HF (with 7bp recognition sequence and 3bp overhangs). Q: Is this enzyme sensitive to dam, dcm or mammalian CpG methylation? A: No. This enzyme is not sensitive to dam, dcm, or mammalian CpG methylation. For up-to-date information about methylation sensitivities, please visit Dam-Dcm and CpG Methylation or REBASE. Q: Does NEB offer any BSA-free and/or animal origin-free restriction enzymes for linearization of plasmids for mRNA vaccine development? A: Yes, NEB has formulated some restriction enzymes (including BspQI, an SapI isoschizomer) without animal-derived components and no BSA appears in their final formulation. In addition, we have several restriction enzymes available without BSA nor other animal-derived components in their final formulation. This list includes: BbsI-HF BsaI-HFv2 BspQI, isoschizomer of LguI, GMP-grade* now available BspQI-HF ClaI HindIII-HF PacI SapI SpeI SwaI XbaI XhoI XmnI Other enzymes can be formulated upon request. Please inquire here. * “GMP Grade” and “GMP-grade” are branding terms NEB uses to describe products manufactured or finished at NEB’s Rowley facility. The Rowley facility was designed to manufacture products under more rigorous infrastructure and process controls to achieve more stringent product specifications and customer requirements. Products manufactured at NEB’s Rowley facility are manufactured in compliance with ISO 9001 and ISO 13485 quality management system standards. However, at this time, NEB does not manufacture or sell products known as Active Pharmaceutical Ingredients (APIs), nor does NEB manufacture its products in compliance with all of the Current Good Manufacturing Practice regulations. Q: Can you tell me more about the switch from BSA to Recombinant Albumin (rAlbumin) in NEBuffers? A: NEB is excited to announce that we have switched BSA-containing reaction buffers (NEBuffer 1.1, 2.1, 3.1 and CutSmart® Buffer) to Recombinant Albumin-containing buffers (NEBuffer r1.1, r2.1, r3.1 and rCutSmart™ Buffer). We are also in the process of moving all restriction enzyme formulations to contain rAlbumin. We feel that moving away from animal-containing products is a step in the right direction and are able to offer this enhancement at the same price. Q: Can Gel Loading Dye, Purple 6X (B7024) be stored in cold temperatures? A: The recommended storage temperature for Gel Loading Dye, Purple 6X, is room temperature (25°C). Commonly, the SDS may precipitate out of solution when the dye is stored on cold temperatures. This slight precipitate can be dissipated by letting the vial sit at room temperature for an hour, or warming gently for 10 minutes. Mix the vial a few times before use, to bring the solution back to homogeneity.