AI-powered end-to-end solution for antibody discovery—from molecular modeling to wet lab, data analysis, and registration.
Geneious Prime supports in silico simulation of all three standard TOPO™ cloning methods: TA Cloning (using vectors with 3′-T overhangs), Blunt TOPO™ Cloning (using custom-annotated TOPO™ sites), and Directional TOPO™ Cloning (using 4-bp extensions for defined insert orientation). All three are available through the same cloning interface and can be selected based on the vector system and directionality requirement of the experiment.
Geneious Prime supports batch TOPO™ cloning by selecting multiple compatible vectors or inserts simultaneously. This is useful for screening multiple PCR products against the same TOPO™ vector, or for validating the same insert across different vector systems, without repeating the workflow setup for each combination individually.
In Geneious Prime, TA and Blunt TOPO™ cloning simulate non-directional insertion — the insert is equally likely to ligate in either orientation, and reverse complements must be manually created to test both possibilities. Directional TOPO™ cloning uses 4-bp primer extensions complementary to vector overhangs, ensuring the insert clones in a single defined orientation. Researchers choosing between methods can simulate both scenarios in Geneious Prime before committing to a protocol.
Geneious Prime simulates TA TOPO™ cloning by first annotating the TOPO™ site on the vector using the motif CCCTTAAGGG (used by pCRII-TOPO™). The tool then performs the cloning operation, producing forward and reverse-complement construct variants to account for the non-directional insertion mechanism. Researchers can review both orientations before selecting clones to validate experimentally.
Geneious Prime designs primers for Directional TOPO™ cloning with the specific 4-bp extensions required for directional insertion. For example, the CACC sequence used with pENTR/D-TOPO™ vectors. The tool annotates primer_bind sites, calculates Tm across the extension and gene-specific regions, and validates the primer set against the target sequence before synthesis.
TOPO™ cloning simulation (including Blunt, TA, and Directional methods) is available in all Geneious Prime subscription plans. A free trial is available with no purchase commitment required. TOPO™ and Life Technologies™ are trademarks of Thermo Fisher Scientific and its subsidiaries.
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