Many of the HPV target mimics tested resulted in a specific
signal, with the exception of HPV types 16, 26, 35, 40, 42,
51, 52, and 82. This nonspecific hybridization signal generally
resulted from a long stretch of complementary
sequences (6–8 bases) among the HPV types due to their
close genetic relatedness. Nonspecific hybridization was
eliminated by introducing a mismatched base to the complementary
region in the signal probes for HPV types 16,
26, 35, 42, and 82 and the capture probes for HPV types
40, 42, 51, 52, and 82. For instance, the HPV 16 signal
probe hybridized with both the HPV 16 target mimic (Fig.
3, left panel) and the HPV 52 capture probe (Fig. 3, center
panel). This cross-reactivity was eliminated by changing
the second A base in the 5'-end of signal probe to a G base
(Fig. 3, right panel). In addition, we demonstrated that
one base modification of the signal probe (Fig. 3, left and
right panels) generated minimal negative impact to the
assay signal level.
Bioelectronic DNA detection involves forming an electronic circuit mediated by nucleic acid hybridization and it serves as the basis for a DNA detection system called eSensor™ [1-4]. This system uses low-density DNA chips containing electrodes coated with DNA capture probes. Target DNA present in the sample hybridizes specifically both to capture probes and ferrocene labeled signal probes in solution thereby generating an electric current. Currente Sensor DNA chips contain as many as 36 electrodes for simultaneous detection of multiple pathogens from a single sample.
Many pathogens cause both acute and chronic disease at relatively low copy number and may be difficult or impossible to propagate in culture. Thus, most pathogen detection systems rely on nucleic acid amplification by using polymerase chain reaction (PCR). One highly effective amplification strategy targets conserved sequences among the family of organisms of interest. Such broad-range PCR strategies have been used to identify and characterize several known and previously uncharacterized bacteria [5,6] and viruses [7,8]. In order to maximize the utility of these effective pathogen nucleic acid amplification systems, amplification needs to be coupled with rapid, sensitive, and specific detection. Bioelectronic DNA detection by use of the eSensor chip might fulfill this need.
Human papillomaviruses (HPV) serve as an ideal model system for determining the efficiency and feasibility of eSensor DNA detection technology since there are at least 30 distinct genital HPV types that can be effectively amplified with broad-range consensus PCR primers. We designed two eSensor chips, each containing 14 probes specific for the conserved L1 region of the HPV genome. We evaluated clinical cervical cytology samples known to contain one or more HPV types. The eSensor DNA detection platform successfully detected the correct HPV type in most of these clinical samples, demonstrating that the system provides a rapid, sensitive, specific, and economical approach for multiple-pathogen detection and identification from a single sample.Background We used human papillomaviruses (HPV) as a model system to evaluate the utility of a nucleic acid, hybridization-based bioelectronic DNA detection platform (eSensor) in identifying multiple pathogens.