Benchling Bulk DNA Assembly for High-Throughput, In Silico Combinatorial Cloning

BY Prem Mohanty
June 19, 2019

Molecular biology research in the life sciences industry has transformed in the past couple of decades. Research workflows are now more complex and diverse, often requiring several steps. Companies have embraced this challenge by building large specialized teams that have more needs for collaboration and productivity. These teams urgently need automated sequence design and analysis tools to handle high-volume research and manage the increasing complexity of molecular biology.

Benchling’s Molecular Biology application is designed with these high-throughput and automation needs in mind. With our Bulk DNA Assembly Tool, Benchling facilitates high-throughput combinatorial cloning in silico. This tool allows users to generate multiple complex plasmid maps from DNA backbones and inserts with just a few clicks.


Key features of Bulk DNA Assembly include:

  • Batch assemble plasmids with several cloning options including homology and restriction digest
  • Specify multiple backbones and inserts across several “slots”
  • Select fragment size and direction
  • Validate sequence integrity in real-time during assembly
  • Receive automatic error notification when adding enzyme / homology sites
  • Generate multiple plasmids from the backbone and fragment combinations selected


Bulk DNA Assembly is a powerful combinatorial cloning tool with unparalleled benefits:

  • Speed and throughput
    Generate hundreds or thousands of complex plasmid maps in a single workflow without the need for excel or repetitive manual steps
  • Quality output
    Minimize erroneousoutput with real-time error checks and visual cues during assembly
  • Ease of use
    Get your team up and running in a matter of minutes with the simple intuitive wizard


Bulk DNA Assembly is useful for a multitude of R&D applications, some of which are listed here:

Published by Prem Mohanty
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