WO2010060060A1 - Procédés électrochimiques de détection d’hybridation d’acide nucléique - Google Patents
Procédés électrochimiques de détection d’hybridation d’acide nucléique Download PDFInfo
- Publication number
- WO2010060060A1 WO2010060060A1 PCT/US2009/065580 US2009065580W WO2010060060A1 WO 2010060060 A1 WO2010060060 A1 WO 2010060060A1 US 2009065580 W US2009065580 W US 2009065580W WO 2010060060 A1 WO2010060060 A1 WO 2010060060A1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- probe
- nucleic acid
- binding
- redox
- immobilized
- Prior art date
Links
- 238000002848 electrochemical method Methods 0.000 title abstract description 5
- 238000007899 nucleic acid hybridization Methods 0.000 title description 4
- 239000000523 sample Substances 0.000 claims abstract description 146
- 150000007523 nucleic acids Chemical class 0.000 claims abstract description 119
- 108020004707 nucleic acids Proteins 0.000 claims abstract description 94
- 102000039446 nucleic acids Human genes 0.000 claims abstract description 94
- 238000000034 method Methods 0.000 claims abstract description 84
- 108020005187 Oligonucleotide Probes Proteins 0.000 claims abstract description 64
- 239000002751 oligonucleotide probe Substances 0.000 claims abstract description 64
- 230000027455 binding Effects 0.000 claims abstract description 55
- 238000009396 hybridization Methods 0.000 claims abstract description 37
- 108091028043 Nucleic acid sequence Proteins 0.000 claims abstract description 25
- 108020004414 DNA Proteins 0.000 claims description 43
- 108091093037 Peptide nucleic acid Proteins 0.000 claims description 36
- 108091034117 Oligonucleotide Proteins 0.000 claims description 34
- 239000011324 bead Substances 0.000 claims description 26
- 230000000295 complement effect Effects 0.000 claims description 16
- 230000008859 change Effects 0.000 claims description 14
- YACKEPLHDIMKIO-UHFFFAOYSA-N methylphosphonic acid Chemical compound CP(O)(O)=O YACKEPLHDIMKIO-UHFFFAOYSA-N 0.000 claims description 14
- JLCPHMBAVCMARE-UHFFFAOYSA-N [3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methyl [5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] hydrogen phosphate Polymers Cc1cn(C2CC(OP(O)(=O)OCC3OC(CC3OP(O)(=O)OCC3OC(CC3O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c3nc(N)[nH]c4=O)C(COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3CO)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cc(C)c(=O)[nH]c3=O)n3cc(C)c(=O)[nH]c3=O)n3ccc(N)nc3=O)n3cc(C)c(=O)[nH]c3=O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)O2)c(=O)[nH]c1=O JLCPHMBAVCMARE-UHFFFAOYSA-N 0.000 claims description 12
- 108010090804 Streptavidin Proteins 0.000 claims description 11
- 125000003729 nucleotide group Chemical group 0.000 claims description 11
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 claims description 10
- 230000015572 biosynthetic process Effects 0.000 claims description 9
- 239000002773 nucleotide Substances 0.000 claims description 9
- 108090000623 proteins and genes Proteins 0.000 claims description 9
- 238000003786 synthesis reaction Methods 0.000 claims description 9
- PCHJSUWPFVWCPO-UHFFFAOYSA-N gold Chemical compound [Au] PCHJSUWPFVWCPO-UHFFFAOYSA-N 0.000 claims description 8
- 229910052737 gold Inorganic materials 0.000 claims description 8
- 239000010931 gold Substances 0.000 claims description 8
- 102000004169 proteins and genes Human genes 0.000 claims description 8
- 108090001008 Avidin Proteins 0.000 claims description 7
- 108010075031 Cytochromes c Proteins 0.000 claims description 7
- 244000052769 pathogen Species 0.000 claims description 7
- 241000894006 Bacteria Species 0.000 claims description 6
- 239000002105 nanoparticle Substances 0.000 claims description 6
- 230000001717 pathogenic effect Effects 0.000 claims description 6
- 201000010099 disease Diseases 0.000 claims description 5
- 208000035475 disorder Diseases 0.000 claims description 5
- 229920000642 polymer Polymers 0.000 claims description 5
- 229920000936 Agarose Polymers 0.000 claims description 4
- OKTJSMMVPCPJKN-UHFFFAOYSA-N Carbon Chemical compound [C] OKTJSMMVPCPJKN-UHFFFAOYSA-N 0.000 claims description 4
- KJTLSVCANCCWHF-UHFFFAOYSA-N Ruthenium Chemical compound [Ru] KJTLSVCANCCWHF-UHFFFAOYSA-N 0.000 claims description 4
- 229910052799 carbon Inorganic materials 0.000 claims description 4
- 239000011859 microparticle Substances 0.000 claims description 4
- 230000027756 respiratory electron transport chain Effects 0.000 claims description 4
- 229910052707 ruthenium Inorganic materials 0.000 claims description 4
- 239000002245 particle Substances 0.000 claims description 3
- 241000233866 Fungi Species 0.000 claims description 2
- RJQXTJLFIWVMTO-TYNCELHUSA-N Methicillin Chemical compound COC1=CC=CC(OC)=C1C(=O)N[C@@H]1C(=O)N2[C@@H](C(O)=O)C(C)(C)S[C@@H]21 RJQXTJLFIWVMTO-TYNCELHUSA-N 0.000 claims description 2
- 206010028980 Neoplasm Diseases 0.000 claims description 2
- 240000004808 Saccharomyces cerevisiae Species 0.000 claims description 2
- 241000191967 Staphylococcus aureus Species 0.000 claims description 2
- 241000700605 Viruses Species 0.000 claims description 2
- 201000011510 cancer Diseases 0.000 claims description 2
- 239000003795 chemical substances by application Substances 0.000 claims description 2
- 229960003085 meticillin Drugs 0.000 claims description 2
- 230000035772 mutation Effects 0.000 claims description 2
- 244000045947 parasite Species 0.000 claims description 2
- ROFVEXUMMXZLPA-UHFFFAOYSA-N Bipyridyl Chemical compound N1=CC=CC=C1C1=CC=CC=N1 ROFVEXUMMXZLPA-UHFFFAOYSA-N 0.000 claims 12
- KTWOOEGAPBSYNW-UHFFFAOYSA-N ferrocene Chemical compound [Fe+2].C=1C=C[CH-]C=1.C=1C=C[CH-]C=1 KTWOOEGAPBSYNW-UHFFFAOYSA-N 0.000 claims 9
- AZQWKYJCGOJGHM-UHFFFAOYSA-N 1,4-benzoquinone Chemical compound O=C1C=CC(=O)C=C1 AZQWKYJCGOJGHM-UHFFFAOYSA-N 0.000 claims 6
- 102000004190 Enzymes Human genes 0.000 claims 6
- 108090000790 Enzymes Proteins 0.000 claims 6
- QIGBRXMKCJKVMJ-UHFFFAOYSA-N Hydroquinone Chemical compound OC1=CC=C(O)C=C1 QIGBRXMKCJKVMJ-UHFFFAOYSA-N 0.000 claims 6
- ISWSIDIOOBJBQZ-UHFFFAOYSA-N Phenol Chemical compound OC1=CC=CC=C1 ISWSIDIOOBJBQZ-UHFFFAOYSA-N 0.000 claims 6
- BASFCYQUMIYNBI-UHFFFAOYSA-N platinum Chemical compound [Pt] BASFCYQUMIYNBI-UHFFFAOYSA-N 0.000 claims 6
- 102000002260 Alkaline Phosphatase Human genes 0.000 claims 3
- 108020004774 Alkaline Phosphatase Proteins 0.000 claims 3
- 108010001336 Horseradish Peroxidase Proteins 0.000 claims 3
- 108091000080 Phosphotransferase Proteins 0.000 claims 3
- 238000005411 Van der Waals force Methods 0.000 claims 3
- BFUZANWGLHWYKK-UHFFFAOYSA-N cyclopenta-1,3-diene iron(2+) 5-methylcyclopenta-1,3-dien-1-ol Chemical compound [Fe++].c1cc[cH-]c1.C[c-]1cccc1O BFUZANWGLHWYKK-UHFFFAOYSA-N 0.000 claims 3
- 229910052739 hydrogen Inorganic materials 0.000 claims 3
- 239000001257 hydrogen Substances 0.000 claims 3
- 102000020233 phosphotransferase Human genes 0.000 claims 3
- 229910052697 platinum Inorganic materials 0.000 claims 3
- 229920000767 polyaniline Polymers 0.000 claims 3
- 239000000126 substance Substances 0.000 claims 3
- 108010075027 Cytochromes a Proteins 0.000 claims 2
- 108010039918 Polylysine Proteins 0.000 claims 2
- 239000007772 electrode material Substances 0.000 claims 2
- LNQCJIZJBYZCME-UHFFFAOYSA-N iron(2+);1,10-phenanthroline Chemical compound [Fe+2].C1=CN=C2C3=NC=CC=C3C=CC2=C1.C1=CN=C2C3=NC=CC=C3C=CC2=C1.C1=CN=C2C3=NC=CC=C3C=CC2=C1 LNQCJIZJBYZCME-UHFFFAOYSA-N 0.000 claims 2
- 229920000656 polylysine Polymers 0.000 claims 2
- XFXPMWWXUTWYJX-UHFFFAOYSA-N Cyanide Chemical compound N#[C-] XFXPMWWXUTWYJX-UHFFFAOYSA-N 0.000 claims 1
- 208000026350 Inborn Genetic disease Diseases 0.000 claims 1
- 208000016361 genetic disease Diseases 0.000 claims 1
- 150000004676 glycans Chemical class 0.000 claims 1
- 229910052742 iron Inorganic materials 0.000 claims 1
- 229920001282 polysaccharide Polymers 0.000 claims 1
- 239000005017 polysaccharide Substances 0.000 claims 1
- 229910001927 ruthenium tetroxide Inorganic materials 0.000 claims 1
- 230000035945 sensitivity Effects 0.000 abstract description 3
- 210000004027 cell Anatomy 0.000 description 16
- 238000000157 electrochemical-induced impedance spectroscopy Methods 0.000 description 10
- 238000001514 detection method Methods 0.000 description 9
- UYTPUPDQBNUYGX-UHFFFAOYSA-N guanine Chemical compound O=C1NC(N)=NC2=C1N=CN2 UYTPUPDQBNUYGX-UHFFFAOYSA-N 0.000 description 7
- 238000003556 assay Methods 0.000 description 6
- 229910052751 metal Inorganic materials 0.000 description 6
- 239000002184 metal Substances 0.000 description 6
- AKIZPWSPNKVOMT-UHFFFAOYSA-N 1-sulfanylhexan-1-ol Chemical compound CCCCCC(O)S AKIZPWSPNKVOMT-UHFFFAOYSA-N 0.000 description 5
- 230000000694 effects Effects 0.000 description 5
- 238000001179 sorption measurement Methods 0.000 description 5
- 238000012360 testing method Methods 0.000 description 5
- 230000003321 amplification Effects 0.000 description 4
- 108010053098 biotin receptor Proteins 0.000 description 4
- 238000010494 dissociation reaction Methods 0.000 description 4
- 230000005593 dissociations Effects 0.000 description 4
- 239000000178 monomer Substances 0.000 description 4
- 238000003199 nucleic acid amplification method Methods 0.000 description 4
- 239000002094 self assembled monolayer Substances 0.000 description 4
- 239000013545 self-assembled monolayer Substances 0.000 description 4
- 238000012546 transfer Methods 0.000 description 4
- -1 alkane bisphosphonate Chemical class 0.000 description 3
- 239000012472 biological sample Substances 0.000 description 3
- 229960002685 biotin Drugs 0.000 description 3
- 239000011616 biotin Substances 0.000 description 3
- 238000010586 diagram Methods 0.000 description 3
- 239000012634 fragment Substances 0.000 description 3
- 230000003993 interaction Effects 0.000 description 3
- 239000010410 layer Substances 0.000 description 3
- 239000003446 ligand Substances 0.000 description 3
- 150000003573 thiols Chemical class 0.000 description 3
- 238000005406 washing Methods 0.000 description 3
- YBJHBAHKTGYVGT-ZKWXMUAHSA-N (+)-Biotin Chemical group N1C(=O)N[C@@H]2[C@H](CCCCC(=O)O)SC[C@@H]21 YBJHBAHKTGYVGT-ZKWXMUAHSA-N 0.000 description 2
- DBGIVFWFUFKIQN-UHFFFAOYSA-N (+-)-Fenfluramine Chemical compound CCNC(C)CC1=CC=CC(C(F)(F)F)=C1 DBGIVFWFUFKIQN-UHFFFAOYSA-N 0.000 description 2
- 108091032973 (ribonucleotides)n+m Proteins 0.000 description 2
- KDCGOANMDULRCW-UHFFFAOYSA-N 7H-purine Chemical compound N1=CNC2=NC=NC2=C1 KDCGOANMDULRCW-UHFFFAOYSA-N 0.000 description 2
- 241000588724 Escherichia coli Species 0.000 description 2
- KYQCOXFCLRTKLS-UHFFFAOYSA-N Pyrazine Chemical compound C1=CN=CC=N1 KYQCOXFCLRTKLS-UHFFFAOYSA-N 0.000 description 2
- CZPWVGJYEJSRLH-UHFFFAOYSA-N Pyrimidine Chemical compound C1=CN=CN=C1 CZPWVGJYEJSRLH-UHFFFAOYSA-N 0.000 description 2
- 235000001014 amino acid Nutrition 0.000 description 2
- 229940024606 amino acid Drugs 0.000 description 2
- 150000001413 amino acids Chemical class 0.000 description 2
- 210000001124 body fluid Anatomy 0.000 description 2
- 239000003153 chemical reaction reagent Substances 0.000 description 2
- 238000003745 diagnosis Methods 0.000 description 2
- 238000000835 electrochemical detection Methods 0.000 description 2
- 239000012530 fluid Substances 0.000 description 2
- 230000014509 gene expression Effects 0.000 description 2
- 239000000463 material Substances 0.000 description 2
- 239000002082 metal nanoparticle Substances 0.000 description 2
- 125000002467 phosphate group Chemical group [H]OP(=O)(O[H])O[*] 0.000 description 2
- 238000002360 preparation method Methods 0.000 description 2
- 235000018102 proteins Nutrition 0.000 description 2
- 238000011160 research Methods 0.000 description 2
- 230000004044 response Effects 0.000 description 2
- 239000002356 single layer Substances 0.000 description 2
- RYYWUUFWQRZTIU-UHFFFAOYSA-K thiophosphate Chemical class [O-]P([O-])([O-])=S RYYWUUFWQRZTIU-UHFFFAOYSA-K 0.000 description 2
- 210000001519 tissue Anatomy 0.000 description 2
- 108020004465 16S ribosomal RNA Proteins 0.000 description 1
- PIINGYXNCHTJTF-UHFFFAOYSA-N 2-(2-azaniumylethylamino)acetate Chemical group NCCNCC(O)=O PIINGYXNCHTJTF-UHFFFAOYSA-N 0.000 description 1
- RBTBFTRPCNLSDE-UHFFFAOYSA-N 3,7-bis(dimethylamino)phenothiazin-5-ium Chemical compound C1=CC(N(C)C)=CC2=[S+]C3=CC(N(C)C)=CC=C3N=C21 RBTBFTRPCNLSDE-UHFFFAOYSA-N 0.000 description 1
- AOJJSUZBOXZQNB-VTZDEGQISA-N 4'-epidoxorubicin Chemical compound O([C@H]1C[C@@](O)(CC=2C(O)=C3C(=O)C=4C=CC=C(C=4C(=O)C3=C(O)C=21)OC)C(=O)CO)[C@H]1C[C@H](N)[C@@H](O)[C@H](C)O1 AOJJSUZBOXZQNB-VTZDEGQISA-N 0.000 description 1
- 206010003445 Ascites Diseases 0.000 description 1
- 229940122361 Bisphosphonate Drugs 0.000 description 1
- 108010035563 Chloramphenicol O-acetyltransferase Proteins 0.000 description 1
- 102100030497 Cytochrome c Human genes 0.000 description 1
- 230000005778 DNA damage Effects 0.000 description 1
- 231100000277 DNA damage Toxicity 0.000 description 1
- KCXVZYZYPLLWCC-UHFFFAOYSA-N EDTA Chemical compound OC(=O)CN(CC(O)=O)CCN(CC(O)=O)CC(O)=O KCXVZYZYPLLWCC-UHFFFAOYSA-N 0.000 description 1
- 101100050026 Enterobacteria phage T4 y01J gene Proteins 0.000 description 1
- HTIJFSOGRVMCQR-UHFFFAOYSA-N Epirubicin Natural products COc1cccc2C(=O)c3c(O)c4CC(O)(CC(OC5CC(N)C(=O)C(C)O5)c4c(O)c3C(=O)c12)C(=O)CO HTIJFSOGRVMCQR-UHFFFAOYSA-N 0.000 description 1
- 108091092584 GDNA Proteins 0.000 description 1
- 108091027874 Group I catalytic intron Proteins 0.000 description 1
- 101000976075 Homo sapiens Insulin Proteins 0.000 description 1
- CKLJMWTZIZZHCS-REOHCLBHSA-N L-aspartic acid Chemical compound OC(=O)[C@@H](N)CC(O)=O CKLJMWTZIZZHCS-REOHCLBHSA-N 0.000 description 1
- 239000004472 Lysine Substances 0.000 description 1
- KDXKERNSBIXSRK-UHFFFAOYSA-N Lysine Natural products NCCCCC(N)C(O)=O KDXKERNSBIXSRK-UHFFFAOYSA-N 0.000 description 1
- 108020004711 Nucleic Acid Probes Proteins 0.000 description 1
- PCNDJXKNXGMECE-UHFFFAOYSA-N Phenazine Natural products C1=CC=CC2=NC3=CC=CC=C3N=C21 PCNDJXKNXGMECE-UHFFFAOYSA-N 0.000 description 1
- 241000233872 Pneumocystis carinii Species 0.000 description 1
- 239000004952 Polyamide Substances 0.000 description 1
- 239000004793 Polystyrene Substances 0.000 description 1
- 206010036790 Productive cough Diseases 0.000 description 1
- 229910021607 Silver chloride Inorganic materials 0.000 description 1
- 125000000217 alkyl group Chemical group 0.000 description 1
- 125000003277 amino group Chemical group 0.000 description 1
- 238000004458 analytical method Methods 0.000 description 1
- 238000004873 anchoring Methods 0.000 description 1
- 210000004102 animal cell Anatomy 0.000 description 1
- 230000000692 anti-sense effect Effects 0.000 description 1
- 239000000074 antisense oligonucleotide Substances 0.000 description 1
- 238000012230 antisense oligonucleotides Methods 0.000 description 1
- 229940009098 aspartate Drugs 0.000 description 1
- 238000005452 bending Methods 0.000 description 1
- 230000008901 benefit Effects 0.000 description 1
- 210000000941 bile Anatomy 0.000 description 1
- 238000001574 biopsy Methods 0.000 description 1
- 235000020958 biotin Nutrition 0.000 description 1
- 108091006374 cAMP receptor proteins Proteins 0.000 description 1
- 150000001718 carbodiimides Chemical class 0.000 description 1
- 150000001732 carboxylic acid derivatives Chemical class 0.000 description 1
- 125000002843 carboxylic acid group Chemical group 0.000 description 1
- 238000005119 centrifugation Methods 0.000 description 1
- 210000001175 cerebrospinal fluid Anatomy 0.000 description 1
- 230000005591 charge neutralization Effects 0.000 description 1
- 238000006243 chemical reaction Methods 0.000 description 1
- 230000000052 comparative effect Effects 0.000 description 1
- 230000008878 coupling Effects 0.000 description 1
- 238000010168 coupling process Methods 0.000 description 1
- 238000005859 coupling reaction Methods 0.000 description 1
- 125000004122 cyclic group Chemical group 0.000 description 1
- 238000002484 cyclic voltammetry Methods 0.000 description 1
- 235000018417 cysteine Nutrition 0.000 description 1
- XUJNEKJLAYXESH-UHFFFAOYSA-N cysteine Natural products SCC(N)C(O)=O XUJNEKJLAYXESH-UHFFFAOYSA-N 0.000 description 1
- 238000000354 decomposition reaction Methods 0.000 description 1
- 238000001212 derivatisation Methods 0.000 description 1
- 238000013461 design Methods 0.000 description 1
- 229940079593 drug Drugs 0.000 description 1
- 239000003814 drug Substances 0.000 description 1
- 230000002183 duodenal effect Effects 0.000 description 1
- 229960001904 epirubicin Drugs 0.000 description 1
- 239000007850 fluorescent dye Substances 0.000 description 1
- 235000011389 fruit/vegetable juice Nutrition 0.000 description 1
- 238000011331 genomic analysis Methods 0.000 description 1
- 229910021397 glassy carbon Inorganic materials 0.000 description 1
- 125000000623 heterocyclic group Chemical group 0.000 description 1
- 230000003100 immobilizing effect Effects 0.000 description 1
- 238000002847 impedance measurement Methods 0.000 description 1
- 238000001566 impedance spectroscopy Methods 0.000 description 1
- 238000001453 impedance spectrum Methods 0.000 description 1
- 230000006872 improvement Effects 0.000 description 1
- 208000015181 infectious disease Diseases 0.000 description 1
- 230000005764 inhibitory process Effects 0.000 description 1
- PBGKTOXHQIOBKM-FHFVDXKLSA-N insulin (human) Chemical group C([C@@H](C(=O)N[C@@H](CC(C)C)C(=O)N[C@H]1CSSC[C@H]2C(=O)N[C@H](C(=O)N[C@@H](CO)C(=O)N[C@H](C(=O)N[C@H](C(N[C@@H](CO)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CC=3C=CC(O)=CC=3)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](CC(N)=O)C(=O)N[C@@H](CC=3C=CC(O)=CC=3)C(=O)N[C@@H](CSSC[C@H](NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CC=3C=CC(O)=CC=3)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](C)NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CC=3NC=NC=3)NC(=O)[C@H](CO)NC(=O)CNC1=O)C(=O)NCC(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](CCCNC(N)=N)C(=O)NCC(=O)N[C@@H](CC=1C=CC=CC=1)C(=O)N[C@@H](CC=1C=CC=CC=1)C(=O)N[C@@H](CC=1C=CC(O)=CC=1)C(=O)N[C@@H]([C@@H](C)O)C(=O)N1[C@@H](CCC1)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H]([C@@H](C)O)C(O)=O)C(=O)N[C@@H](CC(N)=O)C(O)=O)=O)CSSC[C@@H](C(N2)=O)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](C(C)C)NC(=O)[C@@H](NC(=O)CN)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)O)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CC(N)=O)NC(=O)[C@@H](NC(=O)[C@@H](N)CC=1C=CC=CC=1)C(C)C)C1=CN=CN1 PBGKTOXHQIOBKM-FHFVDXKLSA-N 0.000 description 1
- 230000002452 interceptive effect Effects 0.000 description 1
- 239000000543 intermediate Substances 0.000 description 1
- 150000002527 isonitriles Chemical class 0.000 description 1
- 238000011898 label-free detection Methods 0.000 description 1
- 238000002372 labelling Methods 0.000 description 1
- 125000005647 linker group Chemical group 0.000 description 1
- 239000007788 liquid Substances 0.000 description 1
- 230000002934 lysing effect Effects 0.000 description 1
- 239000003550 marker Substances 0.000 description 1
- 239000012528 membrane Substances 0.000 description 1
- 229960000907 methylthioninium chloride Drugs 0.000 description 1
- KKZJGLLVHKMTCM-UHFFFAOYSA-N mitoxantrone Chemical compound O=C1C2=C(O)C=CC(O)=C2C(=O)C2=C1C(NCCNCCO)=CC=C2NCCNCCO KKZJGLLVHKMTCM-UHFFFAOYSA-N 0.000 description 1
- 239000000203 mixture Substances 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 238000010369 molecular cloning Methods 0.000 description 1
- 230000007935 neutral effect Effects 0.000 description 1
- 238000006386 neutralization reaction Methods 0.000 description 1
- QJGQUHMNIGDVPM-UHFFFAOYSA-N nitrogen group Chemical group [N] QJGQUHMNIGDVPM-UHFFFAOYSA-N 0.000 description 1
- 238000001216 nucleic acid method Methods 0.000 description 1
- 239000002853 nucleic acid probe Substances 0.000 description 1
- 210000000056 organ Anatomy 0.000 description 1
- 230000003647 oxidation Effects 0.000 description 1
- 238000007254 oxidation reaction Methods 0.000 description 1
- 210000001819 pancreatic juice Anatomy 0.000 description 1
- 230000036961 partial effect Effects 0.000 description 1
- 230000007170 pathology Effects 0.000 description 1
- 239000013610 patient sample Substances 0.000 description 1
- OJMIONKXNSYLSR-UHFFFAOYSA-N phosphorous acid Chemical class OP(O)O OJMIONKXNSYLSR-UHFFFAOYSA-N 0.000 description 1
- 210000002381 plasma Anatomy 0.000 description 1
- 210000004910 pleural fluid Anatomy 0.000 description 1
- 229920002647 polyamide Polymers 0.000 description 1
- 102000054765 polymorphisms of proteins Human genes 0.000 description 1
- 108091033319 polynucleotide Proteins 0.000 description 1
- 102000040430 polynucleotide Human genes 0.000 description 1
- 239000002157 polynucleotide Substances 0.000 description 1
- 229920002223 polystyrene Polymers 0.000 description 1
- 238000001524 potential step chrono-amperometry Methods 0.000 description 1
- 230000008569 process Effects 0.000 description 1
- 108090000765 processed proteins & peptides Proteins 0.000 description 1
- 230000002062 proliferating effect Effects 0.000 description 1
- PBMFSQRYOILNGV-UHFFFAOYSA-N pyridazine Chemical compound C1=CC=NN=C1 PBMFSQRYOILNGV-UHFFFAOYSA-N 0.000 description 1
- JUJWROOIHBZHMG-UHFFFAOYSA-N pyridine Substances C1=CC=NC=C1 JUJWROOIHBZHMG-UHFFFAOYSA-N 0.000 description 1
- UMJSCPRVCHMLSP-UHFFFAOYSA-N pyridine Natural products COC1=CC=CN=C1 UMJSCPRVCHMLSP-UHFFFAOYSA-N 0.000 description 1
- 150000003222 pyridines Chemical class 0.000 description 1
- 230000035484 reaction time Effects 0.000 description 1
- 230000009257 reactivity Effects 0.000 description 1
- 230000002829 reductive effect Effects 0.000 description 1
- 230000002441 reversible effect Effects 0.000 description 1
- 210000003296 saliva Anatomy 0.000 description 1
- 238000000926 separation method Methods 0.000 description 1
- 210000002966 serum Anatomy 0.000 description 1
- HKZLPVFGJNLROG-UHFFFAOYSA-M silver monochloride Chemical compound [Cl-].[Ag+] HKZLPVFGJNLROG-UHFFFAOYSA-M 0.000 description 1
- 150000003384 small molecules Chemical class 0.000 description 1
- 238000010532 solid phase synthesis reaction Methods 0.000 description 1
- 239000002904 solvent Substances 0.000 description 1
- 238000011895 specific detection Methods 0.000 description 1
- 210000003802 sputum Anatomy 0.000 description 1
- 208000024794 sputum Diseases 0.000 description 1
- 230000000707 stereoselective effect Effects 0.000 description 1
- 230000008685 targeting Effects 0.000 description 1
- 210000001138 tear Anatomy 0.000 description 1
- 229910052723 transition metal Inorganic materials 0.000 description 1
- 150000003624 transition metals Chemical class 0.000 description 1
- 230000001960 triggered effect Effects 0.000 description 1
- 210000002700 urine Anatomy 0.000 description 1
- 238000004832 voltammetry Methods 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6816—Hybridisation assays characterised by the detection means
- C12Q1/6825—Nucleic acid detection involving sensors
Definitions
- the present invention relates generally to electrochemical methods of detecting nucleic acid hybridization, and more specifically to methods of detecting hybridization by measuring changes in impedance.
- DNA hybridization assays are used routinely in genomic analysis, gene expression studies, and, diagnostic assays.
- the most widely used detection methods rely on labeling of target DNA, usually by fluorescent dyes.
- electrochemical techniques for detection of DNA hybridization have been reported in which hybridization is detected using redox- active metal complexes. Such electrochemical methodologies have been demonstrated to provide sequence-specific detection of DNA that is rapid and label-free.
- Rates of guanine oxidation catalyzed by electrochemically oxidized transition- metal complexes have been used to evaluate the solvent accessibility of bases for the detection of mismatches in solution.
- Electrochemical signals triggered by the association of small molecules with DNA have also been applied in the design of other novel biosensors.
- oligonucleotides have been immobilized on electrode surfaces by a variety of linkages for use in hybridization assays. These include thiols on gold, carbodiimide coupling of guanine residues on glassy carbon, and alkane bisphosphonate films on Al 3+ - treated gold.
- Hybridization can be detected by redox-active metal complexes and drugs that associate selectively and reversibly with DNA.
- redox-active metal complexes and drugs that associate selectively and reversibly with DNA.
- methylene blue, epirubicin. and mitoxantron have been used as redox-active indicators for the electrochemical detection of hybridization.
- Label-free detection of hybridization by using the electrochemical signal of guanine has been studied in detail, because guanine is the most redox active nitrogenous base in nucleic acid.
- systems for detecting hybridization of nucleic acids using electrochemical methods having improved sensitivity include an electrode having a variably charged oligonucleotide probe and a redox probe.
- the systems may further include a binding nexus or particle having immobilized oligonucleotide probes attached.
- the purpose of the binding nexus is to amplify a charge effect associated with the target hybridized at the electrode.
- the specificity of this effect is provided by the oligonucleotide sequence immobilized to the binding nexus.
- the charge effect may be a result of the charge of the oligonucleotide or of charge directly associated with the binding nexus.
- the oligonucleotide probe immobilized on the binding nexus is designed to hybridize to a first region of a target nucleic acid molecule and the oligonucleotide probe immobilized on the electrode is designed to hybridize to a second region of the target nucleic acid molecule.
- methods for detecting hybridization of nucleic acids include contacting an electrode having an uncharged or slightly charged oligonucleotide probe with a solution containing a target nucleic acid and a redox probe; and detecting a change in impedance or current generated by electrostatic repulsion or attraction of the redox probe from the electrode, when the target nucleic acid hybridizes to the probe.
- methods for detecting the presence of a nucleic acid sequence of interest in a sample include contacting an electrode having an uncharged or slightly charged oligonucleotide probe, wherein the probe contains a nucleotide sequence that is complementary to a target nucleic acid sequence of interest, with a sample containing nucleic acids; allowing hybridization to occur between the probe and nucleic acids of the sample containing nucleic acids; further contacting the electrode with a redox probe and detecting a change in impedance or current generated by electrostatic repulsion or attractionof the redox probe relative to the electrode, when the capture oligo hybridizes with a nucleic acid comprising the sequence of interest, thereby identifying the presence of the nucleic acid sequence of interest.
- kits for conducting an assay include an electrode having an uncharged or slightly charged oligonucleotide probe attached thereto, and an appropriate redox probe.
- the oligonucleotide probe is designed to hybridize to a target nucleic acid molecule of interest.
- the kit may further contain a binding nexus containing an oligonucleotide probe that hybridizes to a second region of the target nucleic acid molecule, and the binding nexus with the olionucleotide capable of affecting the charge of the surface of the electrode.
- Figure 1 shows a schematic diagram of a system of the invention with a negative redux probe.
- Figure 2 shows a graph with ssPNA versus dsPNA:DNA.
- Figure 3 shows a schematic diagram of a system of the invention with a positive redux probe.
- Figure 4 shows a schematic diagram of a system of the invention.
- Figure 5 shows a graph with data from MRSA specific oligonucleotide probes using the methods of the invention.
- Figure 6 shows a comparison between a short oligonucleotide that has hybridized and a long genomic strand of target.
- the present invention is based on the discovery that the hybridization of nucleic acid molecules to variably charged oligonucleotides of a self-assembled monolayer (SAM) on the surface of an electrode, can modulate the charge of the monolayer.
- SAM self-assembled monolayer
- This change in the charge of the monolayer, and therefore the hybridization of nucleic acid molecules can be detected by the changes in current or impedance produced by attraction or repulsion of a redox probe.
- the redox probe acts to transfer electrons between electrode in an electrochemical cell, the redistribution of redox probe solution density acts to modulate the electrical characteristics of the cell.
- such systems may be used in, for example, methods of detecting nucleic acid hybridization or methods for detecting the presence of a target nucleic acid sequence of interest in a nucleic acid-containing sample.
- EIS electrochemical impedance spectroscopy
- CV cyclic voltametry
- Electrochemical techniques may be used to determine the presence of a target DNA in sample.
- the optimal method may depend on several factors including the dimension of the electrodes, the type(s) and concentration(s) of the redox probes, the solution components of the cell and other parameters one skilled in the art would recognize to be influential.
- systems containing an electrode, having an uncharged oligonucleotide probe immobilized thereon, and a redox probe.
- the uncharged oligonucleotide probe is designed to hybridize to a target nucleic acid of interest.
- the term "variably charged oligonucleotide probe” refers to a nucleic acid oligomer or analog thereof which carries a net charge that is different from natural DNA and wherein the variably charged oligonucleotide probe is capable of hybridization to DNA or RNA molecules. Probes may contain about 4 to 100 monomer units, or about 10-50 monomer units, or about 15 to 30 monomer units. In some embodiments, the variably charged oligonucleotide probe is a peptide nucleic acid (PNA). In other embodiments, the uncharged nucleic acid probes are constructed from nucleotide analogs known in the art such as methylphosphonates or phosphotriesters.
- PNA peptide nucleic acid
- the variably charged oligonucleotide probe may be modified to contain at least one positive or negative charge.
- the oligonucleotide probe may be constructed such that it contains one or more charged nucleotides in combination with uncharged nucleotide analogs.
- the uncharged oligonucleotide probe is modified to contain a single positive or negative charge.
- a variably charged oligonucleotide probe will not contribute, to the attraction of a redox probe compared to a probe made of natural DNA.
- the variably charged oligonucleotide will affect the redox probe in a manner opposite to the effect of the natural DNA target of interest.
- the electrical characteristics of the cell with unhybridized variably charged oligonucleotides may be maximally differentiated from the electrical characteristics of the cell with target DNA hybridized to the variably charged oligonucleotides.
- the target nucleic acid will typically contain a natural phosphate backbone having negatively charged groups which attract positively charged redox probes or repel negatively charged redox probes, thus allowing detection of the hybridized target nucleic acid.
- PNAs Peptide nucleic acids
- the monomer units of PNAs contain a nucleobase, which allows the PNA molecule to hybridize to complementary nucleic acid strands, via Watson-Crick base pairing, with high affinity and specificity.
- the various purine and pyrimidine nucleobases are linked to the backbone by methylene carbonyl bonds.
- PNA includes an achiral polyamide as the backbone.
- the N-(2-aminoethyl)glycine forms the backbone.
- the PNA contains at least one positive or negative charge.
- the capture probe may attract or repulse the redox probe thereby affecting the electrochemical characteristics of the cell to alter the impedance and or current.
- Positive charge may be added to a PNA oligonucleotide with the addition of an ionic amino acid such as lysine.
- Negative charge may be added by the addition of aspartate.
- Other methods of altering the charge of the PNA oligonucleotide will be known to one practiced in the art of chemistry.and may include addition of amine groups or carboxylic acid groups.
- Methylphosphonates are discussed in: U.S. Pat. No. 4,469,863 (Ts'o et al.); Lin et al., "Use of EDTA derivatization to characterize interactions between oligodeoxyribonucleoside methylphophonates and nucleic acids," Biochemistry, 1989, Feb.
- Phophotriesters are discussed in: Sung et al., "Synthesis of the human insulin gene. Part II. Further improvements in the modified phosphotriester method and the synthesis of seventeen deoxyribooligonucleotide fragments constituting human insulin chains B and mini- CDNA," Nucleic Acids Res, 1979 Dec.
- Electrodes on which the uncharged oligonucleotide probe may be immobilized are known in the art and include those electrodes use for immobilization of nucleic acids.
- the electrode is other than a carbon electrode.
- the electrode is a gold electrode.
- Uncharged oligonucleotide probes may be immobilized on the surface of the electrode by methods known in the art for nucleic acid immobilization.
- PNA probes may be immobilized on the electrode by methods known in the art (e.g., Liu et al., Chem. Commun. 23:2969-71, 2005).
- various strategies used for immobilizing DNA molecules on an electrode by specific covalent adsorption utilizing a reaction between the metal surface of an electrode and an anchoring group of the nucleic acid molecules may also be used.
- One exemplary method employs a PNA molecule having a terminal thiol, molecular linker group, which binds a metal surface via a sulfur— metal bond (Tornow et al., NanoBioTechnology Biolnspired Devices and Materials of the Future, Shoseyov and Levy, Eds., pp. 187-214, Humana Press, 2008).
- the thiol may be present in an amino acid as cysteine.
- an electrode having a layer of variably charged oligonucleotide probe molecules may be further treated by co-adsorption of short alkanol- thiol molecules, particularly mercaptohexanol (MCH).
- MCH mercaptohexanol
- Such MCH co-adsorption can be employed to control the structure of the PNA layers on the surface.
- the process of co- adsorption removes and replaces the loosely bound nucleic acids, and changes the specifically bound PNA conformation to an upright position, preventing nonspecific interaction of the specifically bound PNA with the metal surface.
- any remaining areas of uncovered electrode between bound PNA molecules can be passivated electrochemically and physically by co-adsorption of MCH. Agents as MCH may added alone, after oligonucleotide immobilization has taken place.
- Redox probes for use in the present systems and methods may be any of those known to those in the art of electrochemical techniques.
- Redox probes may be positively or negatively charged, either of which may be paired with variably charged oligonucleotide probe in the present systems.
- redox probes may be paired with an oligonucleotide probe having a single charge, so that the redox probe and oligonucleotide probe have the same or opposite charge.
- the skilled artisan will recognize how to pair a positively or negatively charged redox probe with an oligonucleotide probe depending on whether attraction or repulsion of the redox probe is desired. Exemplary redox probes are shown in Table 1 below.
- the redox probe is a ruthenium (Ru) complex, wherein the Ru complex is not Ru(NH 3 ) 5 R when R is an electron withdrawing ligand.
- the electron withdrawing ligand is a heterocyclic moiety, such as a nitrogen- containing heterocycle including substituted or unsubstituted pyridine, pyrimidine, pyridazine, or pyrazine.
- Other ligands include phosphite derivatives and isonitrile derivatives.
- the redox probe is Ru(NH 3 ) 6 3+ .
- the redox probe is Fe(CN) 6 3"74" .
- the redox probe is cytochrome c.
- methods for detecting hybridization of nucleic acids include contacting an electrode having an uncharged oligonucleotide probe, with a solution containing a single stranded nucleic acid and a negatively charged redox probe; and detecting a change in impedance generated by pWtrn Q tatir r p rmision of the redox probe from the electrode, when the single stranded nucleic acid hybridizes to the probe.
- the redox probe is positively charged and a change in current generated by the attraction of the redox probe to the hybridized nucleic acid is detected.
- the probe contains at least one positive or negative charge.
- the oligonucleotide probe is a PNA molecule having at least one positive or negative charge.
- the oligonucleotide probe comprises methylphosphonates .
- a target molecule may be assayed by more than one system in series.
- the method comprises a first step in which a target nucleic acid is contacted with a system comprising an electrode comprising a variably charged oligonucleotide probe having a single positive or negative charge and a redox probe having the same charge.
- the target nucleic acid molecule is with a system comprising an electrode comprising a probe having a single positive or negative charge and a redox probe having the opposite charge.
- the steps could also be performed in the reverse order.
- Electrochemical detection techniques include potential step chronoamperometry, DC cyclic voltammetry, and electrochemical impedance spectroscopy (EIS).
- EIS is used to detect differences in impedances between electrochemical cells with variably charged oligonucleotides that are unhybridized relative to those cells that contain target DNA hybridized to the variably charged oligos.
- the binding of the target molecule to electrode surface-immobilized probe may be indicated by a shift in the impedance spectrum of the electrode (Katz and Willner, Electroanalysis 15:913-947, 2003).
- a conventional three-electrode cell may be used in EIS. Such cells may be enclosed in a grounded Faraday cage. Impedance spectroscopy may be measured with a 1025 frequency response analyzer interfaced to an EG&G 283 potentiostat/galvanostat via GPIB on a PC running Power Suite (Princeton Applied Research). Impedance may be measured at the potential of 250 mV versus Ag/ AgCl, and be superimposed on a sinusoidal potential modulation of ⁇ 5 mV. The frequencies used for impedance measurements can range from 100 kHz to 100 mHz. The impedance data may be analyzed using the ZSimpWin software (Princeton Applied Research).
- impedance data are plotted as a Nyquist plot (i.e., the imaginary impedance (Z") versus the real impedance (Z'), recorded as a function of the applied frequency).
- R ct can be determined by fitting the Nyquist plot using the normal Randies equivalent circuit (Patolsky et al., JAm Chem Soc 123:5194, 2001). By plotting the Rct values versus the corresponding reaction time, the association and dissociation kinetics of the fully matched DNA/PNA duplex can be obtained.
- the sensors of the present invention may be used in methods for detecting single nucleotide polymorphisms in target nucleic acid molecules.
- Such methods involve varying the hybridization conditions (e.g., hybridization temperature, ionic strength, pH, or components of the buffer used in hybridization or washing) under which a test target nucleic acid (i.e., a target nucleic acid molecule whose polymorphism status is unknown) is allowed to hybridize to the probe on the surface of the electrode.
- a test target nucleic acid i.e., a target nucleic acid molecule whose polymorphism status is unknown
- the association or dissociation of the test target nucleic acid can be detected using the systems of the invention.
- association or dissociation kinetic parameters can be compared to the kinetic parameters of a target nucleic acid molecule that is fully complemetary to the probe, as well as to a target sequence having a single mismatch to identify a mismatch in the test target nucleic acid molecule.
- methods for detecting the presence of a nucleic acid sequence of interest in a sample include contacting an electrode having a variably charged oligonucleotide , wherein the oligo contains a nucleotide sequence that is complementary to a nucleic acid sequence of interest, with a sample containing nucleic acids; allowing hybridization to occur between the variably charged oligo and nucleic acids of the sample containing nucleic acids should the complement be present; further contacting the SAM exposed to the sample with negatively charged oligo and detecting a change in electrochemical characteristics generated by electrostatic repulsion of the redox probe from the electrode, when the probe hybridizes to a nucleic acid comprising the sequence of interest, thereby identifying the presence of the nucleic acid sequence of interest.
- the redox probe is positively charged and a change in current generated by the attraction of the redox probe to the hybridized nucleic acid is detected.
- the variably charged oligo contains at least one positive or negative charge.
- the oligonucleotide probe is a PNA molecule having at least one positive or negative charge.
- the method for detecting the presence of a nucleic acid sequence of interest in a sample includes contacting an electrode having a peptide nucleic acid (PNA) probe, wherein the PNA probe contains a nucleotide sequence that is complementary to a nucleic acid sequence of interest, and wherein further the probe contains at least one positive charge, with a sample containing nucleic acids. Hybridization is allowed to occur between the probe and nucleic acids of the sample containing nucleic acids.
- PNA peptide nucleic acid
- the electrode is further contacted with a redox probe having a negative charge and a change in impedance generated by electrostatic repulsion of the redox probe from the electrode is detected when the probe hybridizes to a nucleic acid comprising the sequence of interest, thereby identifying the presence of the nucleic acid sequence of interest.
- the target nucleic acid sequence of interest can be essentially any nucleic acid sequence.
- the nucleic acid sequence of interest is a sequence associated with a particular disease.
- the sequence of interest comprises a mutation.
- the sequence of interest is associated with a cell proliferative disorder or cancer. Accordingly, detection of a sequence associated with a disease or disorder in a sample from a subject can be used in the diagnosis of the disease or disorder.
- the nucleic acid sequence of interest is from a pathogen. Accordingly, the detection of a sequence from a pathogen can be used in the diagnosis of an infection.
- Pathogens may be a bacterium, a yeast, a fungus, a parasite, or a virus.
- the pathogen is a bacterium.
- the bacterium is methicillin-resistant Staphylococcus aureus (MRSA).
- the systems or methods of the invention further include a binding nexus having immobilized oligonucleotide probes.
- the oligonucleotide Drobe immobilized on the binding nexus is designed to hybridize to a first region of a target nucleic acid molecule and the electrode used in the system or method comprises a variably charged oligonucleotide probe designed to hybridize to a second region of the target nucleic acid molecule.
- the probes should be designed so that each probe is able to bind to the target nucleic acid molecule simultaneously, without the binding of one probe interfering with the binding of the other.
- the binding nexus and electrode are used together in essentially a sandwich format. While not wishing to be bound to any particular theory, it is believed that the use of a binding nexus, to which a multiplicity of target molecules may bind simultaneously, increases the charged nucleic acid molecules at the surface of the electrode, and thereby increases the signal generated by the hybridization of a target molecule (simultaneously hybridized to a binding nexus) to the electrode.
- the format described above may be used in methods of detecting a target nucleic acid molecule in a sample.
- the binding nexus acts to capture the target nucleic acid molecule on the surface of the bead via hybridization to a first oligonucleotide probe contained on the surface of the bead.
- the binding nexuses having the target nucleic acid bound thereto may then be separated from the biological sample by methods known the those of skill in the art. Washing steps may further be incorporated.
- the presence of the target nucleic acid on the bead may then be detected upon hybridization to a second oligonucleotide probe on the surface of the electrode.
- the bead is a magnetic bead and a magnetic field may be applied to facilitate separation of the bead from the sample.
- a novel advantage of this method is that the target sequence does not need to be eluted from the binding nexus in order to be analyzed. This saves a step in sample preparation thereby increasing the value of the invention.
- the amplifying repulsive effect of the binding nexus attachment to the target immobilized on the electrode surface may be further enhanced.
- a target is first hybridized to variably charged oligonucleotides immobilized on the electrode.
- a reporter oligonucleotide containing sequence complementary to a second region of the target and containing a biotin moiety is then contacted with the electrode.
- the reporter hybridizes with the target.
- a binding nexus having a biotin receptor bound to it is then contacted with the electrode.
- the biotin receptor may be for example streptavidin and the binding nexus itself may be a streptavidin molecule.
- the binding nexus is placed in contact with the nucleic acid complex immobilized on the surface of the electrode. After washing away unbound binding nexus entities, the electrode is contacted with a primary biotinylated amplifying oligonucleotide that has no sequence complementarity to any of the previously incorporated oligonucleotides. Therefore, the amplifying oligonucleotide will only bind to biotin receptor sites on the immobilized binding nexus.
- This system shall further contain an amplifying target oligonucleotide with a first region complementary to the primary biotinylated amplifying oligonucleotide.
- the amplifying target sequence shall contain a second region that is complementary to a secondary biotinylated amplifying oligo.
- a secondary biotinylated oligo is further contacted to the immobilized nucleic acid complex on the electrode. In this way a self-assembling charge amplification network or complex is formed.
- the self-assembling charge amplification network or complex is a composition including an electrode having a source of electrons, a variably charged oligonucleotide immobilized on the electrode, target DNA hybridized to the variably charged oligonucleotide through a first nucleotide sequence, biotinylated reporter oligo hybridized to a second nucleotide sequence, binding nexus containing a biotin receptor bound to the biotinylated reporter oligo, primary biotinylated amplifying oligo bound to the binding nexus, amplifying target oligo hybridized to the primary biotinylated amplifying oligo through a first amplifying target oligo sequence, secondary amplifying oligonucleotide hybridized to a second amplifying target oligo sequence.
- Samples which may be assayed by the invention methods include any sample containing nucleic acid.
- the sample is a biological sample.
- samples include but are not limited to any bodily fluid, such as a serum, urine, saliva, plasma, blood, cerebrospinal fluid, tears, pleural fluid, ascites fluid, sputum, stool, pancreatic juice, bile duodenal juice, and any bodily fluid that drains a body cavity or organ.
- Further examples include cell-containing samples, tissue samples or biopsy samples.
- Samples may be treated prior to use in the invention methods with a reagent effective for lysing the cells contained in the fluids, tissues, or animal cell membranes of the sample, and for exposing the nucleic acid(s) contained therein.
- a reagent effective for lysing the cells contained in the fluids, tissues, or animal cell membranes of the sample, and for exposing the nucleic acid(s) contained therein.
- Methods for purifying or partially purifying nucleic acid from a sample may also be employed and are well known in the art (e.g., Sambrook et al., Molecular Cloning: a Laboratory Manual, Cold Spring Harbor Press, 1989, herein incorporated by reference). [0041]
- the skilled artisan will recognize that the binding nexus used in these embodiments can take many forms, but require that an oligonucleotide probe is able to be immobilized thereon.
- Examples include, but are not limited, to magnetic beads, agarose beads, polymer beads, microparticles, nanoparticles, proteins with a positive or negative charge, brush DNA, avidin, streptavidin, nuetravidin or combinations thereof.
- an avidin, streptavidin, or nuetravidin molecule comprises immobilized charged oligonucleotide probes. Biotinylated probe molecules may be attached to the avidin, streptavidin, or nuetravidin molecule via the avidin-biotin interation.
- the oligonucleotide probe immobilized on the avidin, streptavidin, or nuetravidin molecule is designed to hybridize to a first region of a target nucleic acid molecule and the oligonucleotide probe immobilized on the electrode is designed to hybridize to a second region of the target nucleic acid molecule.
- the binding nexus may itself carry a repulsive or attractive charge relative to the redox molecule.
- a polystyrene bead having attached both streptavidin and carboxylic acid may be employed, resulting in a negatively charged entity at physiological pH values of solution.
- Biotinylated reporter oligo may be attached to the charged binding nexus and then reacted with the immobilized target. Alternatively, reporter oligo may first be reacted with the immobilized target and then the charged binding nexus may be put in contact with the immobilized nucleic acid complex.
- the biotinylated reporter oligonucleotide used may be variably charged or native.
- the systems and methods for detecting nucleic acid hybridization may further comprise the use of metal nanoparticles to amplify the signal generated upon hybridization of the target nucleic acid molecule to the probe on the surface of the electrode.
- the target nucleic acid molecule is biotinylated and hybridized to the probe on the surface of the probe. Hybridization can be confirmed by, for example, the change of interfacial charge transfer resistance (i? ct ), experimented by the redox marker.
- Streptavidin-coated metal nanoparticles e.g., gold nanoparticles are added to the system after hybridization of the target.
- streptavidin-nanoparticles binding to the target due to the strong streptavidin-biotin interaction, leads to a further increment of i? ct , thus obtaining significant signal amplification (see e.g., Bonanni et ah, Electrochimica Acta 53:4022-9, 2008).
- kits for conducting an assay include an electrode having an uncharged or slightly charged oligonucleotide probe attached thereto, and an appropriate redox probe.
- the oligonucleotide probe is designed to hybridize to a target nucleic acid molecule of interest, hi certain embodiments, the uncharged oligonucleotide probe will be modified to contain at least one positive or negative charge.
- the probe is a PNA molecule carrying a single charge.
- the kit may further contain a bead or particle containing an uncharged or slightly charged oligonucleotide probe that hybridizes to a second region of the target nucleic acid molecule.
- kits according to the present invention can include other reagents and/or devices which are useful in preparing or using any biological samples, electrodes, probe sequences, target sequences, liquid media, counterions, or detection apparatus, for various techniques described herein or already known in the art.
- the present invention detects the amount of charge present on the surface of an electrode. Therefore, longer strands of DNA, with concomitant greater negative charge, will give a greater signal response.
- the complementary sequence of the uncharged PNA capture probe immobilized on the electrode contains relatively few nucleotides, from about 8 to 20. Therefore a target molecule could hybridize with only a few bases, yet have a very wide range of variable charge and therefore signal output. If the genomic DNA is not intentionally fragmented into small uniformly sized fragments, the targets could be thousands of bases long.
- FIGURE 6 shows a comparison between a short oligonucleotide that has hybridized and a long genomic strand of target.
- genomic DNA unfragmented or partially fragmented nucleic acid, e.g., genomic DNA
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Organic Chemistry (AREA)
- Analytical Chemistry (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Microbiology (AREA)
- Immunology (AREA)
- Molecular Biology (AREA)
- Biotechnology (AREA)
- Biophysics (AREA)
- Physics & Mathematics (AREA)
- Biochemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
La présente invention concerne des systèmes pour détecter l’hybridation d’acides nucléiques en utilisant des procédés électrochimiques ayant une sensibilité améliorée. De tels systèmes comprennent une électrode ayant une sonde oligonucléotidique à charge variable et une sonde redox. Dans certains modes de réalisation, les systèmes peuvent comprendre en outre une nexus de liaison comportant une sonde oligonucléotidique immobilisée de rapporteur, qui s’hybride avec une séquence d’acide nucléique cible. La sonde oligonucléotidique de rapporteur peut être naturellement chargée, non chargée ou partiellement chargée négativement ou positivement. La présente invention concerne en outre des procédés pour détecter la présence d’une séquence d’acide nucléique d’intérêt dans un échantillon.
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US11752808P | 2008-11-24 | 2008-11-24 | |
US61/117,528 | 2008-11-24 |
Publications (1)
Publication Number | Publication Date |
---|---|
WO2010060060A1 true WO2010060060A1 (fr) | 2010-05-27 |
Family
ID=42198542
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/US2009/065580 WO2010060060A1 (fr) | 2008-11-24 | 2009-11-23 | Procédés électrochimiques de détection d’hybridation d’acide nucléique |
Country Status (2)
Country | Link |
---|---|
US (1) | US20100133118A1 (fr) |
WO (1) | WO2010060060A1 (fr) |
Cited By (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
GB2496932A (en) * | 2011-11-22 | 2013-05-29 | Iti Scotland Ltd | Nucleic acid detection using electrochemical impedance spectroscopy |
WO2017007826A1 (fr) * | 2015-07-06 | 2017-01-12 | Georgia State University Research Foundation, Inc. | Systèmes de détection et de quantification d'acides nucléiques |
Families Citing this family (4)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO2012141605A1 (fr) * | 2011-02-16 | 2012-10-18 | Centrul International De Biodinamica | Systèmes et procédé de détection et d'analyse quantitative de substances à analyser au moyen d'une activation périodique |
CN102680456B (zh) * | 2011-03-16 | 2015-07-08 | 北京联众泰克科技有限公司 | 一种电化学发光免疫测定方法 |
EP3030678A4 (fr) * | 2013-08-07 | 2017-05-10 | Xagenic, Inc. | Systèmes, procédés et dispositifs de détection électrochimique au moyen d'oligonucléotides auxiliaires |
TWI527905B (zh) * | 2013-11-06 | 2016-04-01 | 國立台灣大學 | 透過利用基因檢測技術與微珠微流道結合進行單核苷酸多態性檢測之方法 |
Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5702895A (en) * | 1995-01-19 | 1997-12-30 | Wakunaga Seiyaku Kabushiki Kaisha | Method and kit for detecting methicillin-resistant Staphylococcus aureus |
US20040209252A1 (en) * | 2000-04-21 | 2004-10-21 | Francis Garnier | Electroactive complex, electroactive probe and preparation method |
US20050186590A1 (en) * | 2003-11-10 | 2005-08-25 | Crothers Donald M. | Nucleic acid detection method having increased sensitivity |
-
2009
- 2009-11-23 WO PCT/US2009/065580 patent/WO2010060060A1/fr active Application Filing
- 2009-11-23 US US12/624,321 patent/US20100133118A1/en not_active Abandoned
Patent Citations (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5702895A (en) * | 1995-01-19 | 1997-12-30 | Wakunaga Seiyaku Kabushiki Kaisha | Method and kit for detecting methicillin-resistant Staphylococcus aureus |
US20040209252A1 (en) * | 2000-04-21 | 2004-10-21 | Francis Garnier | Electroactive complex, electroactive probe and preparation method |
US20050186590A1 (en) * | 2003-11-10 | 2005-08-25 | Crothers Donald M. | Nucleic acid detection method having increased sensitivity |
Cited By (6)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
GB2496932A (en) * | 2011-11-22 | 2013-05-29 | Iti Scotland Ltd | Nucleic acid detection using electrochemical impedance spectroscopy |
CN104145026A (zh) * | 2011-11-22 | 2014-11-12 | Iti苏格兰有限公司 | 分析物的检测 |
US9777337B2 (en) | 2011-11-22 | 2017-10-03 | Iti Scotland Limited | Detecting analytes |
WO2017007826A1 (fr) * | 2015-07-06 | 2017-01-12 | Georgia State University Research Foundation, Inc. | Systèmes de détection et de quantification d'acides nucléiques |
CN107735498A (zh) * | 2015-07-06 | 2018-02-23 | 佐治亚州立大学研究基金会公司 | 用于检测并定量核酸的系统 |
US11156582B2 (en) | 2015-07-06 | 2021-10-26 | Georgia State Research Foundation, Inc. | Systems for detecting and quantifying nucleic acids |
Also Published As
Publication number | Publication date |
---|---|
US20100133118A1 (en) | 2010-06-03 |
Similar Documents
Publication | Publication Date | Title |
---|---|---|
Paleček et al. | Electrochemistry of nucleic acids and development of DNA sensors | |
Erdem et al. | Novel hybridization indicator methylene blue for the electrochemical detection of short DNA sequences related to the hepatitis B virus | |
Gooding | Electrochemical DNA hybridization biosensors | |
Ozkan et al. | DNA and PNA sensing on mercury and carbon electrodes by using methylene blue as an electrochemical label | |
Erdem et al. | DNA electrochemical biosensor for the detection of short DNA sequences related to the hepatitis B virus | |
US20150247843A1 (en) | Method of detecting target substance | |
US20040023258A1 (en) | Method and system or detecting nucleic acids | |
US11807893B2 (en) | Method and electronic device for determining the concentration of an analyte | |
EP1687406A2 (fr) | Procede de detection d'acides nucleiques avec sensibilite accrue | |
EP3030678A2 (fr) | Systèmes, procédés et dispositifs de détection électrochimique au moyen d'oligonucléotides auxiliaires | |
US20100133118A1 (en) | Electrochemical methods of detecting nucleic acid hybridization | |
Fojta et al. | Electrochemical stripping techniques in analysis of nucleic acids and their constituents | |
WO2004099433A2 (fr) | Procede electromecanique destine a mesurer la fixation de l'adn a une surface d'electrode en presence d'oxygene moleculaire | |
Xu et al. | Microfabricated disposable DNA sensors based on enzymatic amplification electrochemical detection | |
JP4625547B2 (ja) | 生体分子検出のための方法と装置 | |
TW200936767A (en) | Method and device for detection of nucleic acids and/or polypeptides | |
US20120058472A1 (en) | Method and system for nucleic acid detection using electroconductive or electrochemically active labels | |
JP2009517690A (ja) | 分析物を検出する電気化学的方法 | |
WO2002073183A1 (fr) | Procede permettant la detection electrochimique de la complementarite de bases d'acides nucleiques | |
JP2002000299A (ja) | 複数の電位を用いる遺伝子の発現解析 | |
JP4666525B2 (ja) | 電極表面に対するdna結合を分子酸素の存在下で測定するための電気化学的方法 | |
US20040096859A1 (en) | Method for detecting and/or quantifying an analyte | |
JP4040834B2 (ja) | 2本鎖dnaの分析方法 | |
Takenaka | Genosensors Based on Metal Complexes | |
US20050214764A1 (en) | Method for identifying, quantifying and/or characterizing an analyte |
Legal Events
Date | Code | Title | Description |
---|---|---|---|
121 | Ep: the epo has been informed by wipo that ep was designated in this application |
Ref document number: 09828366 Country of ref document: EP Kind code of ref document: A1 |
|
NENP | Non-entry into the national phase |
Ref country code: DE |
|
32PN | Ep: public notification in the ep bulletin as address of the adressee cannot be established |
Free format text: NOTING OF LOSS OF RIGHTS PURSUANT TO RULE 112(1) EPC (FORM 1205A DATED 13.09.11) |
|
122 | Ep: pct application non-entry in european phase |
Ref document number: 09828366 Country of ref document: EP Kind code of ref document: A1 |