SnapGene 5.3.1 – Software for everyday molecular biology


The Industry’s Most Popular Molecular Cloning Tool. SnapGene offers the fastest and easiest way to plan, visualize, and document your molecular biology procedures. The streamlined interface supports a range of cloning and PCR manipulations. SnapGene is the most popular cloning tool for a reason. It’s fast, smart and extremely user-friendly.


Improve accuracy while moving faster, so you save time and money.

  • Elegant, information-rich windows for simulating common cloning and PCR methods
  • Clear visual schematics let you see exactly how your construct will be put together
  • SnapGene helps you identify and avoid common mis-steps by keeping track of details like DNA methylation and phosphorylation


Beyond the Basics of Molecular Cloning

  • Intuitive technology identifies design flaws in cloning procedures so they can be corrected
  • Simulate standard PCR using your own primers, or allow SnapGene to design them automatically
  • Specialised cloning tools ensure fast accurate construct design for all major molecular cloning techniques


Restriction Cloning

Restriction cloning is a common cloning technique where restriction enzymes are used to prepare an insert and a vector for ligation.


Gateway Cloning

Plasmids can be constructed without restriction enzymes using Gateway cloning, which inserts DNA fragments by recombination. SnapGene simulates different variations of this method.


For standard Gateway cloning, a DNA fragment is inserted into a Donor Vector in a BP cloning reaction, creating an Entry Vector. Then the fragment is transferred to a Destination Vector in an LR cloning reaction, creating the final Expression Vector. Multisite Gateway cloning allows up to four fragments to be inserted simultaneously.


Gibson Assembly

Gibson Assembly is a popular way to insert fragments into a plasmid without using restriction enzymes. To simulate this method, SnapGene provides an intuitive interface.


For Gibson Assembly, PCR amplify the DNA segments to create overlapping ends. Then incubate the amplified products with assembly enzymes, and transform the mixture into bacteria.


In-Fusion Cloning

Clontech’s In-Fusion cloning is a remarkably versatile method for creating seamless gene fusions. SnapGene was the first software to simulate this procedure.


For the In-Fusion reaction, a linearized vector is mixed with one or more PCR products that have overlapping ends.


TA and GC Cloning

TA cloning is used to clone PCR products. It takes advantage of the 3′ A overhangs added during amplification by Taq and some other polymerases. These sticky ends enable insertion into a linearized vector with complementary 3′ T overhangs. GC cloning is similar, and is based on the finding that Taq actually adds a mixture of 3′ A and 3′ G overhangs.


TOPO Cloning

  • PCR products can be cloned at high efficiency using TOPO cloning, which is performed with linearized vectors that have vaccinia virus topoisomerase I covalently bound to the 3’ phosphates. SnapGene simulates three different variations of this method.
  • TOPO TA cloning employs linearized vectors such as pcDNA™3.4 TOPO to clone PCR products with 3’-A overhangs. These PCR products are typically generated with Taq polymerase.
  • Blunt TOPO cloning employs linearized vectors such as pCR-Blunt II-TOPO to clone PCR products with blunt overhangs. These PCR products are typically generated with high-fidelity polymerases.
  • Directional TOPO cloning employs linearized vectors such as pET200/D-TOPO to clone PCR products in a directional manner.


NEBuilder HiFi Assembly

NEBuilder HiFi DNA Assembly enables virtually error-free joining of DNA fragments, even those with 5´- and 3´-end mismatches without using restriction enzymes.


See what you’re thinking:

  • Beautiful maps
  • Zooming for chromosomes
  • Primer binding sites
  • Enzyme sites and properties
  • Sequence trace viewer
  • Intuitive sequence editing
  • Realistic agarose gels
  • Customized enzyme sets
  • Simulate in a snap:Restriction cloning
  • Conventional PCR
  • Overlap extension PCR
  • Primer-directed mutagenesis
  • Gateway cloning
  • Gibson Assembly
  • In-Fusion cloning
  • TA and GC cloningAvoid making mistakes:Restriction site overview
  • Clear methylation indicators
  • Reading frames for gene fusions
  • Sequence trace alignment
  • Alignment with other sequences
  • Manage your data:Feature and primer lists
  • Versatile file conversion
  • Automatic feature annotation
  • Customized automatic annotation
  • Import of features and primersRecord every step:Comprehensive “Undo” capability
  • History overview
  • History color-coding
  • Embedded ancestor sequences



Version 5.3.1:

  • Release notes were unavailable when this listing was updated.



  • Intel, 64-bit processor
  • macOS 10.13 or later




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Size – 44.3MB