Primerize
Primerize (previously named NA_thermo) is a Python package for primer design and nucleic acid thermodynamics, developed by the Das Lab at Stanford University for high-throughput RNA synthesis and design.
Given a desired DNA template sequence, Primerize uses a dynamic programming-based algorithm to design primers optimized for PCR assembly into templates for high-throughput RNA synthesis. The algorithm minimizes mispriming during PCR by avoiding primer boundaries that might anneal to incorrect sequences.
The algorithm has been tested in the synthesis and rapid purification of numerous RNA sequences from our lab with lengths up to 300 nucleotides. Although developed independently, Primerize is a special case of the general 'Gapped Oligo Design' algorithm described by Thachuk and Condon.
Design Primers with Claude Code or another AI assistant
Paste this prompt into Claude Code or another AI coding assistant to design primers for your sequence:
Help me design PCR assembly primers for my RNA construct using the Primerize Python package (https://github.com/ribokit/Primerize), and produce the IDT ordering block.
1. Install: pip install git+https://github.com/ribokit/Primerize.git
2. Run:
import primerize
sequence = "PASTE_YOUR_SEQUENCE_HERE" # RNA or DNA, any case
result = primerize.Primerize_1D.design(sequence, prefix="my_rna")
if result.is_success:
print(result)
result.save() # writes my_rna.txt
3. Open my_rna.txt — scroll to the bottom for the IDT block (between START/END markers),
formatted for direct paste into IDT Bulk Input:
https://www.idtdna.com/site/order/oligoentry
Use "Lab Ready" for Normalization when ordering.
My sequence is: PASTE_YOUR_SEQUENCE_HERE
Citation
Tian, S., and Das, R. (2017)
Primerize-2D: automated primer design for RNA multidimensional chemical mapping.
Bioinformatics 33(9): 1405-1406.
Publications of mutate-map-rescue pipeline:Tian, S., Yesselman, J.D., Cordero, P., and Das, R. (2015)
Primerize: automated primer assembly for transcribing interesting RNAs.
Nucleic Acid Research 43(W1): W522-W526.
Tian, S., and Das, R. (2016)
RNA structure through multidimensional chemical mapping.
Quarterly Review of Biophysics 49(e7): 1-30.Tian, S., Cordero, P., Kladwang, W., and Das, R. (2014)
High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states.
RNA 20(11): 1815-1826.Kladwang, W., VanLang, C.C., Cordero P., and Das, R. (2011)
A two-dimensional mutate-and-map strategy for non-coding RNA structure.
Nature Chemistry 3: 954-962.