Programmable Molecular Technology Center

Niles Pierce – Principal Investigator
Dr. Maayan Schwarzkopf – Director, Molecular Technologies

Molecular Technologies

The Molecular Technologies resource applies concepts from the emerging disciplines of molecular programming and nucleic acid nanotechnology to develop and support programmable molecular technologies for reading out and regulating the state of endogenous biological circuitry, serving the needs of researchers across the life sciences.

In situ hybridization chain reaction (HCR) enables state-of-the-art mRNA imaging: multiplexed, quantitative, sensitive, versatile, robust. The Molecular Technologies Team synthesizes HCR kits and provides unlimited technical support to Caltech labs [].

Resource development focuses on engineering programmable molecular technologies that enable increasingly incisive interrogation of biological circuits within intact organisms.


The NUPACK resource is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems serving the needs of researchers in the fields of molecular programming, nucleic acid nanotechnology, synthetic biology, and across the life sciences more broadly.

NUPACK algorithms are unique in treating test tube ensembles containing arbitrary numbers of molecular and complex species, providing state-of-the-art tools for nucleic acid analysis and design:

• Analysis: equilibrium analysis of test tubes of interacting nucleic acid strands.
• Design: reaction pathway engineering via constrained multistate test tube design.

The NUPACK web application facilitates rapid job submission and result inspection, with core algorithms running in parallel on the 240-core NUPACK cluster. The NUPACK Team provides unlimited technical support to Caltech labs [].

Resource development focuses on developing physically sound, mathematically rigorous, computationally efficient analysis and design tools that enable increasingly reliable and sophisticated molecular engineering.


Niles Pierce

Principlal Investigator

  • (626) 395-8086

Dr. Maayan Schwwarzkopf

Director, Molecular Technologies

  • (626) 395-8875