The proposed Phase I project will transfer gammaPNA miniprobe technology developed at Carnegie Mellon University and the University of Pittsburgh to PNA Innovations, Inc, a small business located in Pittsburgh. The basis of gammaPNA miniprobes is the high affinity with which gammaPNA hybridizes to complementary DNA. The specific application addressed in this proposal is telomere analysis, which is currently done using fluorescent PNA probes 18 bases in length, which hybridize to 3 consecutive repeats of the human telomere sequence 5'-AATGGG- 3'. The higher affinity of gammaPNA allows shorter 12 base probes to be used, resulting in more fluorescent dyes being delivered to a telomere of a given length. This will allow more reliable analysis of the shortest (i.e. criticaly short) telomeres, which are implicated in a variety of conditions including aging-related diseases and cancer. The proposed research will have three specific aims.
The first aim concerns optimization of an existing 12mer miniprobe to minimize the number of gamma-modified monomers needed for effective telomere labeling. This will help to drive down the cost of the miniprobe to approximately one half the cost of commercially available PNA probes (ca. $1000probe from Panagene Inc).
The second aim i s directed toward development of FRET pairs of miniprobes. The short length of the miniprobes will translate into efficient FRET. The significance of this aim will be the elimination of washing steps to remove unhybridized probes prior to imaging, since FRET will only occur between hybridized probes.
The final aim will result in development of miniprobes having dyes attached at multiple internal positions. This will further increase the brightness of the miniprobes, up to a factor of 6 over current fluorescent PNA telomere probes. The synthesis of the gammaPNA monomers and oligomers will be done at PNA Innovations. Biophysical characterization and telomere staining will be done at academic laboratories at Carnegie Mellon and the University of Pittsburgh where the gammaPNA miniprobe technology was invented. Optimize miniprobes will then be sent to four independent beta-testing laboratories that currently use conventional PNA probes for telomere analysis.
The goal of this project is to develop a new class of fluorescent in situ hybridization probes for telomere analysis. The technology is based on work done in two academic laboratories and is well suited to commercial development, as is the goal of PA-11-335, Lab to Marketplace: Tools for Biomedical and Behavioral Research. The probes will be based on gammaPNA, an analogue of peptide nucleic acid that exhibits superior affinity and solubility. The higher affinity of gammaPNA allows shorter miniprobes to be used. The ability to hybridize shorter probes means that more probes can hybridize to a given telomere, resulting in brighter fluorescence. This will significantly improve the analysis of critically shor telomeres, which are correlated with a variety of aging-related diseases, cancer and other conditions. The miniprobes will be synthesized at PNA Innovations Inc, then tested at Carnegie Mellon University and the University of Pittsburgh. Optimized miniprobes will then be delivered to beta testing laboratories for independent testing and feedback.
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| Fouquerel, Elise; Parikh, Dhvani; Opresko, Patricia (2016) DNA damage processing at telomeres: The ends justify the means. DNA Repair (Amst) 44:159-168 |
| Pham, Ha H; Murphy, Connor T; Sureshkumar, Gopalsamy et al. (2014) Cooperative hybridization of ?PNA miniprobes to a repeating sequence motif and application to telomere analysis. Org Biomol Chem 12:7345-7354 |
