Microchimica Acta

, 186:833 | Cite as

Sensitive and selective fluorometric determination of DNA by using layered hexagonal nanosheets of a covalent organic framework prepared from p-phenylenediamine and benzene-1,3,5-tricarboxaldehyde

  • Tapas Kumar MandalEmail author
  • Nargish Parvin
  • Kanchan Mishra
  • Sonaimuthu Mohandoss
  • Yong Rok Lee
Original Paper


A modified method is described for the preparation of amino-functionalized covalent organic framework nanosheets (COF-NSs). These consist of hexagonal layered sheets and were prepared from commercially available starting materials (p-phenylenediamine and benzene-1,3,5-tricarboxaldehyde). The interlayer stacking interactions between the ultra-thin COF-NSs became weak because the π stacking is destroyed by sonication. This result in the exfoliation of COF-NSs. As an application, the COF-NSs used for sensitive and selective fluorometric determination of DNA. To reach this goal, H1 and H2 hairpin-like DNA probes were chosen; H1 used Texas Red-labeled dye as a fluorescent probe. The addition of the COF-NSs, the hairpin probes was adsorbed onto the porous surface of the COFNSs. The π stacking and hydrogen-bond interactions between COFNSs and nucleic acid quench the fluorescence of the Texas red-labeled probe. The target DNA enables the recovery of the quenched fluorescence of the Texas red-labelled probe by triggering an inter-chain hybridization within hairpin probes. This results in a weaker interaction of double-stranded DNA (dsDNA) with the COFNSs. Consequently, the dsDNA detaches from the COFNSs, thereby recovering the dye’s fluorescence (excitation/emission maxima at 590/612 nm) with increasing target DNA concentration. The findings were applied to design a method for the determination of DNA that has a 2 pM detection limit. This is significantly lower than the limit of detection reported previously for 2D nanomaterial-based fluorometric DNA assays.

Graphical abstract

Schematic representation of 2D-covalent organic framework nanosheets (COF-NSs) probe act as a quencher allowing the highly sensitive and selective fluorescence turn-on detection for biomolecules. Here the H1 H2 are hairpin DNAs. H1 is associated with the fluorescent tag (red circle), while the "fluorescence off" state it denoted as a black circle.


Porous nanomaterials Bond Fluorescence Signal Target Biomolecules Biomarker Diseases Sensor Diagnostics 



This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2018R1A2B2004432), TKM and NP contributed equally.

Compliance with ethical standards

Conflict of interest

There are no conflicts to declare.

Supplementary material

604_2019_3944_MOESM1_ESM.docx (2.2 mb)
ESM 1 (DOCX 2286 kb)


  1. 1.
    Côté AP, Benin AI, Ockwig NM, O’Keeffe M, Matzger AJ, Yaghi OM (2005) Porous, crystalline, covalent organic frameworks. Science 310:1166–1170CrossRefGoogle Scholar
  2. 2.
    Huang N, Wang P, Jiang D (2016) Covalent organic frameworks: a materials platform for structural and functional designs. Nat Rev Mater 1:16068. CrossRefGoogle Scholar
  3. 3.
    Biswal BP, Chaudhari HD, Banerjee R, Kharul UK (2016) Chemically stable covalent organic framework (COF)-Polyben -zimidazole hybrid membranes: enhanced gas separation through pore modulation. Chem Eur J 22:4695. CrossRefPubMedGoogle Scholar
  4. 4.
    Kandambeth S, Biswal BP, Chaudhari HD, Rout KC, Kunjattu HS, Mitra S, Karak S, Das A, Mukherjee R, Kharul UK, Banerjee R (2016) Selective molecular sieving in self-standing porous covalent-organic-framework membranes. Adv Mater 29:1603945–1603954CrossRefGoogle Scholar
  5. 5.
    Vazquez-Molina DA, Mohammad-Pour GS, Lee C, Logan MW, Duan X, Harper JK, Uribe-Romo F (2016) Mechanically shaped 2-dimensional covalent organic frameworks reveal crystallographic alignment and fast Li-ion conductivity. J Am Chem Soc 138:9767–9770. CrossRefPubMedGoogle Scholar
  6. 6.
    Ding SY, Gao J, Wang Q, Zhang Y, Song WG, Su SY, Wang W (2011) Construction of covalent organic framework for catalysis:Pd/COF-LZU1 in SuzukiMiyaura coupling reaction. J Am Chem Soc 133:19816CrossRefGoogle Scholar
  7. 7.
    Zeng Y, Zou R, Zhao Y (2016) Covalent organic frameworks for CO 2 capture. Adv Mater 28:2855–2873CrossRefGoogle Scholar
  8. 8.
    Chandra S, Roy Chowdhury D, Addicoat M, Heine T, Paul A, Banerjee R (2017) Molecular level control of the capacitance of two-dimensional covalent organic frameworks: role of hydrogen bonding in energy storage materials. Chem Mater 29:2074CrossRefGoogle Scholar
  9. 9.
    Das G, Biswal B, Kandambeth S, Venkatesh V, Kaur G, Addicoat M, Heine T, Verma S, Banerjee R (2015) Chemical sensing in two di mensional porous covalent organic nanosheets. Chem Sci 6:3931–3939CrossRefGoogle Scholar
  10. 10.
    Zhang CL, Zhang SM, Yan YH, Xia F, Huang AN, Xian YZ (2017) Highly fluorescent polyimide covalent organic Nanosheets as sensing probes for the detection of 2,4,6-TrinitrophenolACS Appl mater. Interfaces 9:13415Google Scholar
  11. 11.
    Li ZP, Zhang YW, Xia H, Mu Y, Liu XM (2016) A versatile covalent organic framework-based platform for sensing biomolecules. Chem Commun 52:6613CrossRefGoogle Scholar
  12. 12.
    Ding SY, Dong M, Wang Y, Chen YT, Wang HZ, Su CY, Wang W (2016) Thioether-based fluorescent covalent organic framework for selective detection and facile removal of mercury(II). J Am Chem Soc 138:3031CrossRefGoogle Scholar
  13. 13.
    Mitra S, Kandambeth S, Biswal BP, Khayum MA, Choudhury CK, Mehta M, Kaur G, Banerjee S, Prabhune A, Verma S, Roy S, Kharul UK, Banerjee R (2016) Self-exfoliated Guanidinium-based ionic covalent organic Nanosheets (iCONs). J Am Chem Soc 138:2823–2828CrossRefGoogle Scholar
  14. 14.
    Wang S, Wang Q, Shao P, Han Y, Gao X, Ma L, Yuan S, Ma X, Zhou J, Feng X, Wang B (2017) Exfoliation of covalent organic frameworks into few-layer redox-active Nanosheets as cathode materials for lithium-ion batteries. J Am Chem Soc 139:4258–4261CrossRefGoogle Scholar
  15. 15.
    Chandra S, Kandambeth S, Biswal BP, Lukose L, Kunjir SM, Chaudhary M, Babarao R, Heine T, Banerjee R (2013) Chemically stable multilayered covalent organic nanosheets from covalent organic frameworks via mechanical delamination. J Am Chem Soc 135:17853–17861CrossRefGoogle Scholar
  16. 16.
    Mitra S, Sasmal HS, Kundu T, Kandambeth S, Illath K, Díaz DD, Banerjee R (2017) Targeted drug delivery in covalent organic Nanosheets (CONs) via sequential Postsynthetic modification. J Am Chem Soc 139:4513–4520CrossRefGoogle Scholar
  17. 17.
    Khayum MA, Kandambeth S, Mitra S, Nair SB, Das A, Nagane MR, Banerjee R (2016) Chemically delaminated free-standing ultrathin covalent organic Nanosheets. Angew Chem Int Ed 55:15604–15608CrossRefGoogle Scholar
  18. 18.
    Lustig WP, Mukherjee S, Rudd ND, Desai AV, Li J, Ghosh SK (2017) Metal-organic frameworks: functional luminescent and photonic materials for sensing applications. Chem Soc Rev 46:3242CrossRefGoogle Scholar
  19. 19.
    Wang Y, Chen JT, Yan XP (2013) Fabrication of transferrin functionalized gold nanoclusters/graphene oxide nanocomposite for turn-on near-infrared fluorescent bioimaging of cancer cells and small animals. Anal Chem 85:2529CrossRefGoogle Scholar
  20. 20.
    Liu Y, Le P, Lim SJ, Ma L, Sarkar S, Han Z, Murphy SJ, Kosari F, Vasmatzis G, Cheville JC, Smith AM (2018) Enhanced mRNA FISH with compact quantum dots. Nature Comm 9:4461. CrossRefGoogle Scholar
  21. 21.
    Parvin N, Jin Q, Wei Y, Yu R, Zheng B, Huang L, Zhang Y, Wang L, Zhang H, Gao MY, Zhao H, Hu W, Li Y, Wang D (2017) Few-layer Graphdiyne Nanosheets applied for multiplexed real-time DNA detection. Adv Mater 29:1606755. CrossRefGoogle Scholar
  22. 22.
    Accelrys Materials Studio Release Notes (2010) 5.5; Accelrys Software, Inc.: San Diego, CA,Google Scholar
  23. 23.
    Mandal TK, Hou Y, Gao Z, Ning H, Yang Y, Gao M (2016) Graphene oxide-based sensor for ultrasensitive visual detection of fluoride. Adv Sci 3:1600217CrossRefGoogle Scholar
  24. 24.
    He S, Song B, Li D, Zhu C, Qi W, Wen Y, Wang L, Song S, Fang H, Fan C (2010) A graphene Nanoprobe for rapid, sensitive, and multicolor fluorescent DNA analysis. Adv Funct Mater 20:453–459CrossRefGoogle Scholar
  25. 25.
    Liu X, Aizen R, Freeman R, Yehezkeli O, Willner I (2012) Highly tunable Aptasensing microarrays with graphene oxide multilayers. ACS Nano 6:3553–3563CrossRefGoogle Scholar
  26. 26.
    Liu X, Wang F, Aizen R, Yehezkeli O, Willner I (2013) Graphene oxide/nucleic-acid-stabilized silver nanoclusters: functional hybrid materials for optical Aptamer sensing and multiplexed analysis of pathogenic DNAs. J Am Chem Soc 135:11832–11839. CrossRefPubMedGoogle Scholar
  27. 27.
    Qian Z, Shan X, Chai L, Ma J, Chen J, Feng H (2014) A universal fluorescence sensing strategy based on biocompatible graphene quantum dots and graphene oxide for the detection of DNA. Nanoscale 6:5671–5674. CrossRefPubMedGoogle Scholar
  28. 28.
    Wang Q, Wang W, Lei J, Xu N, Gao F, Ju H (2013) Fluorescence quenching of carbon nitride Nanosheet through its interaction with DNA for versatile fluorescence sensing. Anal Chem 85:12182–12188. CrossRefPubMedGoogle Scholar
  29. 29.
    Zhu C, Zeng Z, Li H, Li F, Fan C, Zhang H (2013) Single-layer MoS2-based Nanoprobes for homogeneous detection of biomolecules. J Am Chem Soc 135:5998–6001. CrossRefPubMedGoogle Scholar
  30. 30.
    Huang J, Ye L, Gao X, Li H, Xu J, Li ZJ (2015) Molybdenum disulfide-based amplified fluorescent DNA detection using hybridization chain reactions. J Mater Chem B 3:2395–2401. CrossRefGoogle Scholar
  31. 31.
    Yuan Y, Li R, Liu Z (2014) Establishing water-soluble layered WS2 nanosheet as a platform for biosensing. Anal Chem 86:3610–3615. CrossRefPubMedGoogle Scholar
  32. 32.
    Zhang Y, Zheng B, Zhu C, Zhang X, Tan C, Li H, Chen B, Yang J, Chen J, Huang Y, Wang L, Zhang H (2015) Single-layer transition metal dichalcogenide nanosheet-based nanosensors for rapid, sensitive, and multiplexed detection of DNA. Adv Mater 27:935–939. CrossRefPubMedGoogle Scholar
  33. 33.
    Peng Y, Huang Y, Zhu Y, Chen B, Wang L, Lai Z, Zhang Z, Zhao M, Tan C, Yang N, Shao N, Han Y, Zhang H (2017) Ultrathin two-dimensional covalent organic framework Nanosheets: preparation and application in highly sensitive and selective DNA detection. J Am Chem Soc 139:8698–8704CrossRefGoogle Scholar
  34. 34.
    Zhao M, Wang Y, Ma Q, Huang Y, Zhang X, Ping J, Zhang Z, Lu Q, Yu Y, Xu H, Zhao Y, Zhang H (2015) Ultrathin 2D metal–organic framework Nanosheets. Adv Mater 27:7372–7378. CrossRefPubMedGoogle Scholar
  35. 35.
    Dirks RM, Pierce NA (2004) Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci U SA 101:15275–15278. CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  • Tapas Kumar Mandal
    • 1
    Email author
  • Nargish Parvin
    • 2
  • Kanchan Mishra
    • 1
  • Sonaimuthu Mohandoss
    • 1
  • Yong Rok Lee
    • 1
  1. 1.School of Chemical EngineeringYeungnam UniversityGyeongsanRepublic of Korea
  2. 2.State Key Laboratory of Biochemical Engineering, CAS Center for Excellence in Nanoscience, Institute of Process EngineeringChinese Academy of SciencesBeijingPeople’s Republic of China

Personalised recommendations