NP-Sticky: Model-Guided Ligation Calculator

Linear Ligation Calculator

You can download this Excel worksheet to facilitate concentration conversion and ligation reaction setup: ligation_worksheet.xlsx

Product Distribution Prediction

This linear ligation calculator can predict product distribution given the input concentrations of all species in the ligation reaction. For library assembly applications, the identity of the library-containing fragment can be specified in order to calculate how much of the input library is incorporated into full-length product.

Please enter reaction conditions for 2-piece linear ligation reaction.

DNA 1	Valuable fragment	Molar concentration	nM
		Mass concentration	ng/μl    Size:bp   Volume:μl
DNA 2	Valuable fragment	Molar concentration	nM
		Mass concentration	ng/μl    Size:bp   Volume:μl
		Total volume of reaction:μl (only needed when using mass concentrations)
Sticky end free energy		Between DNA 1 and 2	kcal/mol
Sticky end overhang bases		Between DNA 1 and 2	AT CG AT CG 5' overhang 3' overhang

Please enter reaction conditions for 3-piece linear ligation reaction.

DNA 1	Valuable fragment	Molar concentration	nM
		Mass concentration	ng/μl    Size:bp   Volume:μl
DNA 2	Valuable fragment	Molar concentration	nM
		Mass concentration	ng/μl    Size:bp   Volume:μl
DNA 3	Valuable fragment	Molar concentration	nM
		Mass concentration	ng/μl    Size:bp   Volume:μl
		Total volume of reaction:μl (only needed when using mass concentrations)
Sticky end free energy		Between DNA 1 and 2	kcal/mol
		Between DNA 2 and 3	kcal/mol
Sticky end overhang bases		Between DNA 1 and 2	AT CG AT CG 5' overhang 3' overhang
		Between DNA 2 and 3	AT CG AT CG 5' overhang 3' overhang

Ligation Recommendation

Ligation incorporation and efficiency will be calculated over a range of concentrations and molar ratios to allow selection of optimal ligation conditions for specific applications.

Please enter reaction conditions for 2-piece linear ligation reaction.

Valuable fragment: DNA 1 DNA 2	Molar concentration	nM
	Mass concentration	ng/μl    Size:bp
Sticky end free energy	Between DNA 1 and 2	kcal/mol
Sticky end overhang bases	Between DNA 1 and 2	AT CG AT CG 5' overhang 3' overhang

Please enter reaction conditions for 3-piece linear ligation reaction.

Valuable fragment: DNA 1 DNA 2 DNA 3	Molar concentration	nM
	Mass concentration	ng/μl    Size:bp
Sticky end free energy	Between DNA 1 and 2	kcal/mol
	Between DNA 2 and 3	kcal/mol
Sticky end overhang bases	Between DNA 1 and 2	AT CG AT CG 5' overhang 3' overhang
	Between DNA 2 and 3	AT CG AT CG 5' overhang 3' overhang