An RNA Sensor for Detection of Circulating Tumor Cells

Project: Research project

Project Details

Description

This proposal seeks to develop an RNA Sensor to be employed for detection of circulating tumor cells.
RNA detection is based upon an hybridization "sandwich". Two target RNAs have been chosen for clinically
important cancers (prostate, breast, and melanoma), and library selection protocols will be utilized to
identify/optimize accessible sites for antisense oligonucleotide (ASO) binding. Silicon nanowires will then be
covalently derivatized with ASO to a library-selected site (ASO-,) in the target RNA. The ASOi nanowires will
then be deposited by fluidic deposition onto chips, and integrated into the underlying CMOS circuitry. Target
RNA will be purified from cellular preparations, and will then be hybridized to the ASd-nanowires. An ASO2,
targeted to a 2nd library-selected site, will be covalently attached to 12 nm gold particles (ASO2-nanoprobe).
Binding of the ASO2-nanoprobe to the target RNA-ASOi-nanowire complexes will induce a resonance
frequency shift in the nanowires, which is greatly amplified by the mass of the gold particle. This resonance
frequency shift (RXA)will be detected by direct electrical read-out, with voltage (quantitatively) related to
binding events (RX,A) will initially be detected optically). We have successfully measured RX of 300 nm
silicon nanowires (with high Quality-Factors) under ambient conditions. Theoretical calculations predict very
good Quality-Factors for silicon nanowires in H20, and detection of single binding events should be
achievable.
Preliminary data related to all aspects of RNA Sensor development have been obtained. These include:
library selection of target sites in prostatic DD3 RNA, sandwich hybridization specificity "off-chip" synthesis
and derivatization of nanowires, R>. measurements with nanowires, and fluidic deposition of nanowires on
chips. After basic developmental steps are completed, experiments will include quantitative determination of
target RNAs using the detection device compared to QPCR amplification. The Specific Aims for this funding
period are designed to develop an RNA Sensor appropriate for subsequent use in clinical validation studies
for circulating tumor cells. Successful development of this RNA Sensor would provide a major advantage
over PCR-based assays, and could form the basis for high-throughput screening tests for simultaneous
detection of many different circulating tumor cell types.
StatusFinished
Effective start/end date2/15/061/31/10

Funding

  • National Cancer Institute: $284,503.00
  • National Cancer Institute: $284,503.00
  • National Cancer Institute: $293,000.00

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