DPC Technology - Overview
DNA-Programmed Chemistry™ ( DPC™) is a patented method employing DNA to control chemical reactions. Originally developed by Professor David Liu at Harvard University, DPC reactions occur between pairs of chemical building blocks attached to complementary DNA strands. Under mild aqueous conditions, specific hybridization of the DNA strands brings the building blocks into close proximity, increasing their relative concentration by a factor of >10,000. This hybridization also controls reaction stoichiometry and lowers energies of activation, thus driving highly specific reactions. The specificity achieved by DPC is analogous to single turnover enzyme catalysis. Applications of DPC include synthesis of diverse chemical libraries, discovery of new chemical reactions, and in situ generation of signal-emitting compounds for use in biodetection applications.
DNA-Programmed Chemistry
The value of DPC is the ability to program chemical reactions:
DNA strand sequence identifies every reactant and product
Hybridization ensures selectivity of reaction
Advances in characterizing disease at the molecular level are increasingly recognized as central to the future of health care. The diagnostics industry has developed powerful methods to locate, quantify, and identify metabolites, nucleic acids, and proteins. There is currently no general diagnostics strategy, however, to determine protein functional status, especially in cells or intact tissue. Ensemble has developed assays, based on DNA-Programmed Chemistry that demonstrate this capability.
Protein functionality is frequently modulated by formation of dimeric complexes, post-translational modification, or inherited and somatic mutations of structure. Each of these types of modulation has been shown to be important in the pathology of particular diseases and responses to therapy. Ensemble’s Programmed Bioassays™ have the ability to monitor each of these types of modulation in intact cells and tissues.
Biodetection
Technology
Ensemble’s detection platform is based on the use of DPC to control individual chemical reactions in response to the presence of a biological analyte, forming a new compound with signaling capability which is then detected. These Programmed Bioassays will be valuable in both research and clinical diagnostic settings, and can be flexibly configured for a variety of formats including solution assays, fluorescence-activated cell sorting (FACS), and immunohistochemistry (IHC).
Programs
Our lead protein complex program for use in tissues is focused on detection of dimers of the ERBB family in human epithelial cells, the function of which is important for many cancers, including breast cancer. Our lead program to detect protein mutation in intact blood cells is focused on the abnormal fusion protein BCR/ABL, responsible for the generation of the blood cancer Chronic Myelogenous Leukemia (CML).
The altered structure of proteins or multimeric protein complexes underlies the mechanism of many diseases and is the focus of intense activity in medicine and drug discovery. Currently, there are no assay platforms that can easily detect and measure modified proteins and protein complexes, particularly in intact cells and tissues such as tumor biopsies. Such assessment is critical because understanding protein function in the cellular or tissue environment is the most direct means of insight into health and disease.
Ensemble's Biodetection Programs are aimed at cancer diagnosis and treatment prediction:
The BCR/ABL Program, sponsored by The Leukemia and Lymphoma Society, is developing reagents to detect and isolate cells carrying the abnormal fusion protein BCR/ABL, which is the cause of the cancer Chronic Myelogenous Leukemia (CML).
The ERBB Detection Program is developing reagents to distinguish between different protein dimers of the ERBB family of receptor tyrosine kinases, both homodimers and heterodimers. This family of receptors is important in breast cancer and other cancers such as colon, prostate, lung, ovary and brain. It is one of the most actively targeted families of receptors in modern oncology practice.
A DPC™-Enabled Detection System for Nucleic Acids and Proteins
An important application of Ensemble Discovery’s technology is for in situ generation of chemical signals and development of bioassays that use those signals as research tools, diagnostic products, and molecular imaging agents. Ensemble is developing methods for the sensitive detection of both nucleic acids and proteins. Analyte-recognition elements can be DNA-based (for nucleic acid detection) or antibodies, aptamers or small molecules for protein detection.
DPC™ probes are unique in that they do not generate a signal until two complementary probes, each recognizing a different target element, bind to their targets. This is based on a single DPC reaction as shown below.
For recognition of a biological analyte, the DPC signal generation strands are linked to elements that recognize that analyte specifically. These target elements can be, for example, adjacent regions on a DNA target (nucleic acid probe), or different proteins in a protein complex (protein probe). Nucleic acid DPC probes can be used for detection of specific genomes or genomic variations and are useful in homogeneous detection assays. Protein DPC probes are useful for detection of “functional” information about cell signaling events by detecting key changes in individual proteins, such as how they are modified (post-translational modification) or how they interact with other proteins in complexes. Detecting such cell signaling changes in diseases such as cancer, Alzheimer’s Disease, and inflammatory diseases will provide critical information of value to researchers and physicians.