Programmable Molecular Technology Center

Niles Pierce, PI
Dr. Harry M. T. Choi, Molecular Instruments Director

The Programmable Molecular Technology Center (PMTC) develops and supports two major resources serving the biological sciences and engineering communities at Caltech.

The Molecular Instruments resource applies concepts from the emerging discipline of molecular programming to develop and support programmable molecular technologies for reading out and regulating cell state. Molecular Instruments currently supports:

  • In situ HCR. Multiplexed in situ hybridization based on the mechanism of hybridization chain reaction (HCR) enables simultaneous mapping of up to five target mRNAs within intact biological organisms, including whole-mount vertebrate embryos.
  • Shielded covalent probes. Shielded covalent probes eliminate the longstanding tradeoff between sequence selectivity and durable target capture, enabling covalent capture of complementary DNA or RNA targets and efficient discrimination of mismatched targets.

The Molecular Instruments Team synthesizes kits and provides unlimited technical support and training to Caltech labs. []

The NUPACK resource is a growing software suite for the analysis and design of nucleic acid molecules, devices, and systems. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. The NUPACK web application currently enables:

  • Analysis: thermodynamic analysis of dilute solutions of an arbitrary number of interacting nucleic acid strands (e.g., a test tube).
  • Design: single-state and multi-state sequence design for an arbitrary number of interacting nucleic acid strands.
  • Utilities: analysis, display, and annotation of nucleic acid complexes.

The NUPACK web interface facilitates rapid job submission and result inspection. Core algorithms run in parallel on the 256-core NUPACK cluster, enabling interactive use for most jobs. The NUPACK Team provides unlimited technical support to Caltech labs. []


Niles Pierce
Room 165 Broad Center
Mail Code 114-96
Phone: 626-375-4562
Dr. Harry M. T. Choi
171 Broad
Mail Code 114-96