Table 2: HPV type and signal probe sequence.
6 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) TGT AGT TAC GGA TGC AC
11 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) CAG ATG CAG ATA GTG TCA T
16 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) CAG CGC ATA ATG ACA TAT TT
18 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) TAC AGG AGA CTG TGT AG
26 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) AGA TGC TGT AGA TAA TGT AC
31 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) TGT TTG CAA TTG CAG CA
35 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) CAG ACA TAT TTG TTC TAC GG
40 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) TAA GGT TAA ATT AGT GCA ACG A
42 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) CAA AGA CAT GTT AGT ACT AC
45 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) ACA GGA TTT TGT GTA GAG G
51 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) ATA GTT AAA TTT GTA CTT CTG G
52 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) CAG CAC ATA AAG TCA TG
54 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) TGG ATG CTG TAG CAC AC
56 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) ACT GTT CTG TAG CAG TAC T
58 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) TGC ATA ATG TCA TAT TAG TG
59 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) GAA TAG AAG AAG TAG TAG AA
66 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) TGT GCT TTT AGC TGC AT
68 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) CAG CTG ATT CAG TAG TAG TA
82 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) CTA ATG GTT AAA TTG GTA GTT
83 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) CTG TGT AGC AGG AGC TGA AA
84 (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) TGG TAG CAG CAC TAA TA
Globin (N6) C(N6) G(N6) C(N6) GCT TA(N6) C(N6) G(N6) C(N6) TGA CTT TTA TGC CCA GAC CTG G
Table 3: HPV type and target mimic oligonucleotide sequences
6 ACC ACA CGC AGT ACC AAC ATG ACA TTA TGT GCA TCC GTA ACT ACA TCT TCC ACA TAC ACC AAT TCT GAT TAT AAA
11 GTA CAA ATA TGA CAC TAT GTG CAT CTG TGT CTA AAT CTG CTA CAT ACA CTA ATT CAG ATT ATA AGG AAT ACA TGC G
16 ACT ACA CGC AGT ACA AAT ATG TCA TTA TGT GCT GCC ATA TCT ACT TCA GAA ACT ACA TAT AAA AAT ACT AAC TTT AA
18 ACC ACT CCC AGT ACC AAT TTA ACA ATA TGT GCT TCT ACA CAG TCT CCT GTA CCT GGG CAA TAT GAT GCT ACC AAA T
26 GTA CTA ACC TTA CCA TTA GTA CAT TAT CTG CAG CAT CTG CAT CCA CTC CAT TTA AAC CAT CTG ATT ATA AAC AAT T
31 ACC ACA CGT AGT ACC AAT ATG TCT GTT TGT GCT GCA ATT GCA AAC AGT GAT ACT ACA TTT AAA AGT AGT AAT TTT AA
35 TGT AGT TGA TAC AAC CCG TAG TAC AAA TAT GTC TGT GTG TTC TGC TGT GTC TTC TAG TGA CAG TAC ATA TAA AAA T
40 AGT TGT AGA CAC CAC TCG TAG CAC TAA TTT AAC CTT ATG TGC TGC CAC ACA GTC CCC CAC ACC AAC CCC ATA TAA T
42 ACT ACC CGT AGT ACT AAC ATG ACT TTG TGT GCC ACT GCA ACA TCT GGT GAT ACA TAT ACA GCT GCT AAT TTT AAG G
45 AAC ATT ATG TGC CTC TAC ACA AAA TCC TGT GCC AAG TAC ATA TGA CCC TAC TAA GTT TAA GCA GTA TAG TAG ACA T
51 GTT GAT ACT ACC AGA AGT ACA AAT TTA ACT ATT AGC ACT GCC ACT GCT GCG GTT TCC CCA ACA TTT ACT CCA AGT A
52 ACC ACT CGT AGC ACT AAC ATG ACT TTA TGT GCT GAG GTT AAA AAG GAA AGC ACA TAT AAA AAT GAA AAT TTT AAG
54 GTA CTA ACC TAA CAT TGT GTG CTA CAG CAT CCA CGC AGG ATA GCT TTA ATA ATT CTG ACT TTA GGG AGT ATA TTA G
56 GTA CTA ACA TGA CTA TTA GTA CTG CTA CAG AAC AGT TAA GTA AAT ATG ATG CAC GAA AAA TTA ATC AGT ACC TTA G
58 ACC ACT CGT AGC ACT AAT ATG ACA TTA TGC ACT GAA GTA ACT AAG GAA GGT ACA TAT AAA AAT GAT AAT TTT AAG
59 ACT ACT CGC AGC ACC AAT CTT TCT GTG TGT GCT TCT ACT ACT TCT TCT ATT CCT AAT GTA TAC ACA CCT ACC AGT
66 ACT ACC AGA AGC ACC AAC ATG ACT ATT AAT GCA GCT AAA AGC ACA TTA ACT AAA TAT GAT GCC CGT GAA ATC AAT
68 GTA CCA ATT TTA CTT TGT CTA CTA CTA CTG AAT CAG CTG TAC CAA ATA TTT ATG ATC CTA ATA AAT TTA AGG AAT A
82 ACT ACT AGA AGT ACC AAT TTA ACC ATT AGC ACT GCT GTT ACT CAA TCT GTT GCA CAA ACA TTT ACT CCA GCA AAC T
83 GTA CCA ATA TTA CTA TTT CAG CTG CTG CTA CAC AGG CTA ATG AAT ACA CAG CCT CTA ACT TTA AGG AAT ACC TCC G
84 ACC ACC CGC AGC ACC AAT TTT ACT ATT AGT GCT GCT ACC AAC ACC GAA TCA GAA TAT AAA CCT ACC AAT TTT AAG
globin GGG AGG GCA GGA GCC AGG GCT GGG CAT AAA AGT CAG GGC AGA GCC ATC TAT TGC TTA CAT TTG CTT CTG ACA CAA C
Tuesday, July 29, 2008
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.