What is the potential of nanolock– and nanocross–nanopore technology in cancer diagnosis?

References

• Vogelstein B, Papadopoulos N, Velculescu VE, et al. Cancer genome landscapes. Science. 2013;339(6127):1546–1558.
   PubMed Web of Science ®Google Scholar
• Lee JS. Exploring cancer genomic data from the cancer genome atlas project. BMB Rep. 2016;49(11):607–611.
   PubMed Web of Science ®Google Scholar
• Couch FJ, Nathanson KL, Offit K. Two decades after BRCA: setting paradigms in personalized cancer care and prevention. Science. 2014;343(6178):1466–1470.
   PubMed Web of Science ®Google Scholar
• Lynch TJ, Bell DW, Sordella R, et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med. 2004;350(21):2129–2139.
   PubMed Web of Science ®Google Scholar
• Paez JG, Janne PA, Lee JC, et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science. 2004;304(5676):1497–1500.
   PubMed Web of Science ®Google Scholar
• Bollag G, Hirth P, Tsai J, et al. Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma. Nature. 2010;467(7315):596–599.
   PubMed Web of Science ®Google Scholar
• Flaherty KT, Puzanov I, Kim KB, et al. Inhibition of mutated, activated BRAF in metastatic melanoma. N Engl J Med. 2010;363(9):809–819.
   PubMed Web of Science ®Google Scholar
• Bollag G, Tsai J, Zhang J, et al. Vemurafenib: the first drug approved for BRAF-mutant cancer. Nat Rev Drug Discov. 2012;11(11):873–886.
   PubMed Web of Science ®Google Scholar
• Shin SH, Bode AM, Dong ZG. Addressing the challenges of applying precision oncology. Npj Precis Oncol. 2017;1:28.
   Web of Science ®Google Scholar
• Cibulskis K, Lawrence MS, Carter SL, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31(3):213–219.
   PubMed Web of Science ®Google Scholar
• Halait H, DeMartin K, Shah S, et al. Analytical performance of a real-time PCR-based assay for V600 mutations in the BRAF Gene, used as the companion diagnostic test for the Novel BRAF inhibitor vemurafenib in metastatic melanoma. Diagn Mol Pathol. 2012;21(1):1–8.
   PubMedGoogle Scholar
• Sapio MR, Posca D, Troncone G, et al. Detection of BRAF mutation in thyroid papillary carcinomas by mutant allele-specific PCR amplification (MASA). Eur J Endocrinol. 2006;154(2):341–348.
   PubMed Web of Science ®Google Scholar
• Matsuda K. PCR-based detection methods for single-nucleotide polymorphism or mutation: real-time PCR and its substantial contribution toward technological refinement. Adv Clin Chem. 2017;80:45–72.
   PubMed Web of Science ®Google Scholar
• Olmedillas-Lopez S, Garcia-Arranz M, Garcia-Olmo D. Current and emerging applications of droplet digital PCR in oncology. Mol Diagn Ther. 2017;21:493–510.
   PubMed Web of Science ®Google Scholar
• Starostik P. Clinical mutation assay of tumors: new developments. Anti-Cancer Drugs. 2017;28(1):1–10.
   PubMed Web of Science ®Google Scholar
• Kamps R, Brandao RD, Bosch BJ, et al. Next-Generation sequencing in oncology: genetic diagnosis, risk prediction and cancer classification. Int J Mol Sci. 2017;18(2):308.
   PubMed Web of Science ®Google Scholar
• Yohe S, Thyagarajan B. Review of clinical next-generation sequencing. Arch Pathol Lab Med. 2017;141(11):1544–1557.
   PubMed Web of Science ®Google Scholar
• Wu CC, Ko FH, Yang YS, et al. Label-free biosensing of a gene mutation using a silicon nanowire field-effect transistor. Biosens Bioelectron. 2009;25(4):820–825.
   PubMed Web of Science ®Google Scholar
• Fang Z, Kelley SO. Direct electrocatalytic mRNA detection using PNA-nanowire sensors. Anal Chem. 2009;81(2):612–617.
   PubMed Web of Science ®Google Scholar
• Huber F, Lang HP, Backmann N, et al. Direct detection of a BRAF mutation in total RNA from melanoma cells using cantilever arrays. Nat Nanotechnol. 2013;8(2):125–129.
   PubMed Web of Science ®Google Scholar
• Wang Y, Tian K, Shi R, et al. Nanolock-Nanopore facilitated digital diagnostics of cancer driver mutation in tumor tissue. ACS Sensors. 2017;2(7):975–981.
   PubMed Web of Science ®Google Scholar
• Zhang X, Price NE, Fang X, et al. Characterization of interstrand DNA-DNA cross-links using the alpha-hemolysin protein nanopore. ACS Nano. 2015;9(12):11812–11819.
   PubMed Web of Science ®Google Scholar
• Nejad MI, Shi R, Zhang X, et al. Sequence-Specific covalent capture coupled with high-contrast nanopore detection of a disease-derived nucleic acid sequence. ChemBioChem. 2017;18(14):1383–1386.
   PubMed Web of Science ®Google Scholar
• Villanueva MT. Melanoma: blocking BRAF to the BRIM. Nat Rev Clin Oncol. 2014;11(4):179.
   PubMedGoogle Scholar
• Ono A, Torigoe H, Tanaka Y, et al. Binding of metal ions by pyrimidine base pairs in DNA duplexes. Chem Soc Rev. 2011;40(12):5855–5866.
   PubMed Web of Science ®Google Scholar
• Granzhan A, Kotera N, Teulade-Fichou MP. Finding needles in a basestack: recognition of mismatched base pairs in DNA by small molecules. Chem Soc Rev. 2014;43(10):3630–3665.
   PubMed Web of Science ®Google Scholar
• Sato Y, Honjo A, Ishikawa D, et al. Fluorescent trimethyl-substituted naphthyridine as a ligand for C-C mismatch detection in CCG trinucleotide repeats. Chem Commun (Camb). 2011;47(20):5885–5887.
   PubMed Web of Science ®Google Scholar
• Zeglis BM, Barton JK. DNA base mismatch detection with bulky rhodium intercalators: synthesis and applications. Nat Protoc. 2007;2(2):357–371.
   PubMed Web of Science ®Google Scholar
• Lu CH, Willner I. Stimuli-responsive DNA-functionalized nano-/microcontainers for switchable and controlled release. Angewandte Chemie. 2015;54(42):12212–12235.
   Google Scholar
• Miyake Y, Togashi H, Tashiro M, et al. MercuryII-mediated formation of thymine-HgII-thymine base pairs in DNA duplexes. J Am Chem Soc. 2006;128(7):2172–2173.
   PubMed Web of Science ®Google Scholar
• Kumar K, Isa L, Egner A, et al. Formation of nanopore-spanning lipid bilayers through liposome fusion. Langmuir. 2011;27(17):10920–10928.
   PubMed Web of Science ®Google Scholar
• Wang G, Zhao Q, Kang X, et al. Probing mercury(II)-DNA interactions by nanopore stochastic sensing. J Phys Chem B. 2013;117(17):4763–4769.
   PubMed Web of Science ®Google Scholar
• Torigoe H, Miyakawa Y, Ono A, et al. Thermodynamic properties of the specific binding between Ag+ ions and C:C mismatched base pairs in duplex DNA. Nucleosides Nucleotides Nucleic Acids. 2011;30(2):149–167.
   PubMed Web of Science ®Google Scholar
• Price NE, Johnson KM, Wang J, et al. Interstrand DNA-DNA cross-link formation between adenine residues and abasic sites in duplex DNA. J Am Chem Soc. 2014;136(9):3483–3490.
   PubMed Web of Science ®Google Scholar
• Cherf GM, Lieberman KR, Rashid H, et al. Automated forward and reverse ratcheting of DNA in a nanopore at 5-A precision. Nat Biotechnol. 2012;30(4):344–348.
   PubMed Web of Science ®Google Scholar
• Kasianowicz JJ, Brandin E, Branton D, et al. Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci U S A. 1996;93(24):13770–13773.
   PubMed Web of Science ®Google Scholar
• Manrao EA, Derrington IM, Laszlo AH, et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol. 2012;30(4):349–U174.
   PubMed Web of Science ®Google Scholar
• An N, Fleming AM, Middleton EG, et al. Single-molecule investigation of G-quadruplex folds of the human telomere sequence in a protein nanocavity. Proc Natl Acad Sci U S A. 2014;111(40):14325–14331.
   PubMed Web of Science ®Google Scholar
• Cao C, Ying YL, Hu ZL, et al. Discrimination of oligonucleotides of different lengths with a wild-type aerolysin nanopore. Nat Nanotechnol. 2016;11(8):713–718.
   PubMed Web of Science ®Google Scholar
• An N, Fleming AM, White HS, et al. Crown ether-electrolyte interactions permit nanopore detection of individual DNA abasic sites in single molecules. Proc Natl Acad Sci U S A. 2012;109(29):11504–11509.
   PubMed Web of Science ®Google Scholar
• Wallace EV, Stoddart D, Heron AJ, et al. Identification of epigenetic DNA modifications with a protein nanopore. Chem Commun (Camb). 2010;46(43):8195–8197.
   PubMed Web of Science ®Google Scholar
• Wang Y, Zheng D, Tan Q, et al. Nanopore-based detection of circulating microRNAs in lung cancer patients. Nat Nanotechnol. 2011;6(10):668–674.
   PubMed Web of Science ®Google Scholar
• Wang Y, Luan BQ, Yang Z, et al. Single molecule investigation of Ag+ interactions with single cytosine-, methylcytosine- and hydroxymethylcytosine-cytosine mismatches in a nanopore. Sci Rep. 2014;4:5883.
   PubMed Web of Science ®Google Scholar
• Rosen CB, Rodriguez-Larrea D, Bayley H. Single-molecule site-specific detection of protein phosphorylation with a nanopore. Nat Biotechnol. 2014;32(2):179–181.
   PubMed Web of Science ®Google Scholar
• Wolfe AJ, Mohammad MM, Cheley S, et al. Catalyzing the translocation of polypeptides through attractive interactions. J Am Chem Soc. 2007;129(45):14034–14041.
   PubMed Web of Science ®Google Scholar
• Wang S, Haque F, Rychahou PG, et al. Engineered nanopore of Phi29 DNA-packaging motor for real-time detection of single colon cancer specific antibody in serum. ACS Nano. 2013;7(11):9814–9822.
   PubMed Web of Science ®Google Scholar
• Hornblower B, Coombs A, Whitaker RD, et al. Single-molecule analysis of DNA-protein complexes using nanopores. Nat Methods. 2007;4(4):315–317.
   PubMed Web of Science ®Google Scholar
• Purnell RF, Schmidt JJ. Discrimination of single base substitutions in a DNA strand immobilized in a biological nanopore. ACS Nano. 2009;3(9):2533–2538.
   PubMed Web of Science ®Google Scholar
• Kong J, Zhu J, Keyser UF. Single molecule based SNP detection using designed DNA carriers and solid-state nanopores. Chem Commun (Camb). 2016;53(2):436–439.
   PubMed Web of Science ®Google Scholar
• Vercoutere W, Winters-Hilt S, Olsen H, et al. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat Biotechnol. 2001;19(3):248–252.
   PubMed Web of Science ®Google Scholar
• Ang YS, Yung LY. Rapid and label-free single-nucleotide discrimination via an integrative nanoparticle-nanopore approach. ACS Nano. 2012;6(10):8815–8823.
   PubMed Web of Science ®Google Scholar
• Cornelis S, Gansemans Y, Deleye L, et al. Forensic SNP genotyping using nanopore MinION sequencing. Sci Rep. 2017;7:41759.
   PubMed Web of Science ®Google Scholar
• Zhao Q, Sigalov G, Dimitrov V, et al. Detecting SNPs using a synthetic nanopore. Nano Lett. 2007;7(6):1680–1685.
   PubMed Web of Science ®Google Scholar
• Torigoe H, Miyakawa Y, Kozasa T, et al. The specific interaction between two T:T mismatch base pairs and mercury (II) cation. Nucleic Acids Symp Ser. 2007;51(1):185–186.
   Google Scholar
• Schmidt K, Mwaigwisya S, Crossman LC, et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother. 2017;72(1):104–114.
   Web of Science ®Google Scholar
• Schmidt K, Mwaigwisya S, Crossman LC, et al. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother. 2017;72(1):104–114.
   PubMed Web of Science ®Google Scholar
• Greninger AL, Naccache SN, Federman S, et al. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 2015;7:99.
   PubMed Web of Science ®Google Scholar
• Jain M, Olsen HE, Paten B, et al. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 2016;17(1):239.
   PubMedGoogle Scholar
• Speicher MR, Pantel K. Tumor signatures in the blood. Nat Biotechnol. 2014;32(5):441–443.
   PubMed Web of Science ®Google Scholar
• Chu D, Park BH. Liquid biopsy: unlocking the potentials of cell-free DNA. Virchows Arch. 2017;471:147–154.
   Web of Science ®Google Scholar
• Pi C, Zhang MF, Peng XX, et al. Liquid biopsy in non-small cell lung cancer: a key role in the future of personalized medicine? Expert Rev Mol Diagn. 2017;17:1089–1096.
   PubMed Web of Science ®Google Scholar