NEB® Primer Design Tools

NEB Primer Design Tools

Primer design is not one-size-fits-all. There are critical application-specific parameters to consider that can vastly increase your likelihood of experimental success. Whether you are creating an assembly that incorporates multiple fragments, conducting your entire PCR at a single temperature, or incorporating intentionally mismatched nucleotides, careful primer design can set you up for success before you even pick up your pipette.

Here at NEB, we have created a variety of interactive tools to help you accurately design primers to suit your specific needs. Select the application to get started.

NEBuilder HiFi DNA Assembly & Gibson Assembly

NEBuilder^® Assembly Tool

NEBuilder Assembly Tool can be used to design primers for your NEBuilder^® HiFi DNA Assembly or Gibson^® Assembly reaction, based on the entered fragment sequences and the polymerase being used for amplification.

Loop-mediated Amplification
(LAMP)

NEB LAMP Primer Design Tool

NEB LAMP Primer Design Tool can be used to design primers for your Loop-mediated Isothermal Amplification. Fixed primers can be specified for the design of LAMP primers, and subsequent Loop primers are then designed based on LAMP primer selection.

Golden Gate Assembly

NEB Golden Gate Assembly Tool

NEBuilder Assembly Tool can be used to design primers for your Gibson Assembly reaction, based on the entered fragment sequences and the polymerase being used for amplification.

Site-directed Mutagenesis

NEBaseChanger^®

NEBaseChanger can be used to design primers specific to the mutagenesis experiment you are performing using the Q5 Site-Directed Mutagenesis Kit. This tool will also calculate a recommended custom annealing temperature based on the sequence of the primers by taking into account any mismatches.

Videos

Primer Design and Fragment Assembly Using NEBuilder HiFi DNA Assembly^® or Gibson Assembly^®

Watch an interactive tutorial on primer design to see how simple it really is to clone with either NEBuilder HiFi DNA Assembly or the Gibson Assembly Cloning Kit.
NEBUILDER^® Assembly Tool 2.0 What’s New?

NEBuilder Assembly Tool can be used to design primers for your NEBuilder HiFi or Gibson Assembly reactions based on entered fragment sequences and the polymerase being used for amplification. This video will highlight some useful updates and the main differences between the two versions.
NEBUILDER^® Assembly Tool 2.0 Restriction Enzyme Digest

This video demonstrates how to use the NEBuilder® Assembly Tool to build a construct using a restriction enzyme digested vector and two PCR-generated inserts. The tool will help to design PCR primers containing the required overlap sequences. We will also regenerate one of the restriction enzyme recognition sites.
NEBUILDER^® Assembly Tool 2.0 Fragments Amplified by PCR

This video demonstrates how the NEBuilder Assembly Tool can be used to generate overlap sequences for the assembly of two fragments into a vector. In this scenario, all fragments are amplified by PCR and the vector does not have convenient restriction sites.
Golden Gate Assembly Tool Tutorial

This video demonstrates how to use the Golden Gate Assembly Tool, we will walk through selecting insert and plasmids, primer design to make amplicon inserts.
Loop Mediated Isothermal Amplification (LAMP) Tutorial

Did you know that this isothermal amplification method can be performed in as little as 5-10 minutes with limited resources? Get a quick overview on how LAMP works in this animation.