Skip to main content
SpringerLink
Log in

The effect of two layers of graphene with a striped pattern on wettability parameters of the biodroplets

  • Published:
Adsorption Aims and scope Submit manuscript

Abstract

Microarrays play a determinant role in the detection and specification of biological molecules. The immobility of probe oligonucleotide with different sequences on the substrate surface is one of the main aims in designing of microarrays. In this regard, we select five different DNA single-strands to determine the best of probe single strand in the microarrays with a striped patterned double-layer graphene substrate. The results of the simulation illustrate that DNA single-strands on the substrate have distinct conformations related to each other. Thymine single strand has the maximum end to end distance and is more accessible for detecting target single strand in the microarrays. Also, the analysis of wettability results displays that the presence of a DNA single-strand in water drop decreases the amount of spreading of the droplets. Another important point is that the presence of a single strand increases the chance of water droplet pining on such surfaces.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13
Fig. 14
Fig. 15
Fig. 16
Fig. 17
Fig. 18
Fig. 19

Similar content being viewed by others

References

  • Beaucage, S.L.: Strategies in the preparation of DNA oligonucleotide arrays for diagnostic applications. Curr. Med. Chem. 8(10), 1213–1244 (2001)

    Article  CAS  PubMed  Google Scholar 

  • Beier, M., Hoheisel, J.D.: Versatile derivatisation of solid support media for covalent bonding on DNA-microchips. Nucleic Acids Res. 27(9), 1970–1977 (1999)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bier, F.F. et al.: DNA microarrays. In: Biosensing for the 21st Century, Springer, Berlin, pp. 433–453 (2007)

  • Brandon, S., Haimovich, N., Yeger, E., Marmur, A.: Partial wetting of chemically patterned surfaces: the effect of drop size. J. Colloid Interface Sci. 263(1), 237–243 (2003)

    Article  CAS  PubMed  Google Scholar 

  • Caminade, A.-M., Padié, C., Laurent, R., Maraval, A., Majoral, J.-P.: Uses of dendrimers for DNA microarrays. Sensors 6(8), 901–914 (2006)

    Article  CAS  PubMed Central  Google Scholar 

  • Campbell, C.T., Kim, G.: SPR microscopy and its applications to high-throughput analyses of biomolecular binding events and their kinetics. Biomaterials 28(15), 2380–2392 (2007)

    Article  CAS  PubMed  Google Scholar 

  • Chen, Y., He, B., Lee, J., Patankar, N.A.: Anisotropy in the wetting of rough surfaces. J. Colloid Interface Sci. 281(2), 458–464 (2005)

    Article  PubMed  CAS  Google Scholar 

  • Chen, H., Müller, M.B., Gilmore, K.J., Wallace, G.G., Li, D.: Mechanically strong, electrically conductive, and biocompatible graphene paper. Adv. Mater. 20(18), 3557–3561 (2008)

    Article  CAS  Google Scholar 

  • Choi, J., Oh, B., Kim, Y., Min, J.: Nanotechnology in biodevices. J. Microbiol. Biotechnol. 17(1), 5 (2007)

    CAS  PubMed  Google Scholar 

  • Deegan, R.D., Bakajin, O., Dupont, T.F., Huber, G., Nagel, S.R., Witten, T.A.: Contact line deposits in an evaporating drop. Phys. Rev. E 62(1), 756 (2000)

    Article  CAS  Google Scholar 

  • Dong, X., Shi, Y., Huang, W., Chen, P., Li, L.: Electrical detection of DNA hybridization with single-base specificity using transistors based on CVD-grown graphene sheets. Adv. Mater. 22(14), 1649–1653 (2010)

    Article  CAS  PubMed  Google Scholar 

  • Dugas, V., Depret, G., Chevalier, Y., Nesme, X., Souteyrand, É.: Immobilization of single-stranded DNA fragments to solid surfaces and their repeatable specific hybridization: covalent binding or adsorption? Sensors Actuators B Chem. 101(1), 112–121 (2004)

    Article  CAS  Google Scholar 

  • Dupuis, A., Yeomans, J.M.: Lattice Boltzmann modelling of droplets on chemically heterogeneous surfaces. Futur. Gener. Comput. Syst. 20(6), 993–1001 (2004)

    Article  Google Scholar 

  • Erbil, H.Y., McHale, G., Newton, M.I.: Drop evaporation on solid surfaces: constant contact angle mode. Langmuir 18(7), 2636–2641 (2002)

    Article  CAS  Google Scholar 

  • Fixe, F., Dufva, M., Telleman, P., Christensen, C.B.V.: Functionalization of poly (methyl methacrylate)(PMMA) as a substrate for DNA microarrays. Nucleic Acids Res. 32(1), e9 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hoover, W.G.: Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A 31(3), 1695 (1985)

    Article  CAS  Google Scholar 

  • Humphrey, W., Dalke, A., Schulten, K.: VMD: visual molecular dynamics. J. Mol. Graph. 14(1), 33–38 (1996)

    Article  CAS  PubMed  Google Scholar 

  • Hurst, S.J., Lytton-Jean, A.K.R., Mirkin, C.A.: Maximizing DNA loading on a range of gold nanoparticle sizes. Anal. Chem. 78(24), 8313–8318 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L.: Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79(2), 926–935 (1983)

    Article  CAS  Google Scholar 

  • Kerr, M.K., Churchill, G.A.: Statistical design and the analysis of gene expression microarray data. Genet. Res. (Camb.) 77(2), 123–128 (2001)

    Article  CAS  Google Scholar 

  • Kerr, M.K., Martin, M., Churchill, G.A.: Analysis of variance for gene expression microarray data. J. Comput. Biol. 7(6), 819–837 (2000)

    Article  CAS  PubMed  Google Scholar 

  • Kim, Y.S., Kim, B.C., Lee, J.H., Kim, J., Gu, M.B.: Specific detection of DNA using quantum dots and magnetic beads for large volume samples. Biotechnol. Bioprocess. Eng. 11(5), 449–454 (2006)

    Article  CAS  Google Scholar 

  • Kimura, N.: One-step immobilization of poly (dT)-modified DNA onto non-modified plastic substrates by UV irradiation for microarrays. Biochem. Biophys. Res. Commun. 347(2), 477–484 (2006)

    Article  CAS  PubMed  Google Scholar 

  • Le Berre, V., et al.: Dendrimeric coating of glass slides for sensitive DNA microarrays analysis. Nucleic Acids Res. 31(16), e88–e88 (2003)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lee, H.H., Yager, P.: Microfluidic lab-on-a-chip for microbial identification on a DNA microarray. Biotechnol. Bioprocess. Eng. 12(6), 634 (2007)

    Article  CAS  Google Scholar 

  • Lee, S.W., Chang, W.-J., Bashir, R., Koo, Y.-M.: ‘Bottom-up’ approach for implementing nano/microstructure using biological and chemical interactions. Biotechnol. Bioprocess. Eng. 12(3), 185 (2007)

    Article  CAS  Google Scholar 

  • Lennard-Jones, J.E.: Cohesion. Proc. Phys. Soc. 43(5), 461 (1931)

    Article  CAS  Google Scholar 

  • Li, F., Bao, Y., Chai, J., Zhang, Q., Han, D., Niu, L.: Synthesis and application of widely soluble graphene sheets. Langmuir 26(14), 12314–12320 (2010)

    Article  CAS  PubMed  Google Scholar 

  • Liu, Z., Robinson, J.T., Sun, X., Dai, H.: PEGylated nanographene oxide for delivery of water-insoluble cancer drugs. J. Am. Chem. Soc. 130(33), 10876–10877 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu, Y., Yu, D., Zeng, C., Miao, Z., Dai, L.: Biocompatible graphene oxide-based glucose biosensors. Langmuir 26(9), 6158–6160 (2010)

    Article  CAS  PubMed  Google Scholar 

  • Lu, C., Yang, H., Zhu, C., Chen, X., Chen, G.: A graphene platform for sensing biomolecules. Angew. Chem. Ind. Ed. Engl. 121(26), 4879–4881 (2009)

    Article  Google Scholar 

  • Lu, C.-H., Zhu, C.-L., Li, J., Liu, J.-J., Chen, X., Yang, H.-H.: Using graphene to protect DNA from cleavage during cellular delivery. Chem. Commun. 46(18), 3116–3118 (2010a)

    Article  CAS  Google Scholar 

  • Lu, C., Li, J., Liu, J., Yang, H., Chen, X., Chen, G.: Increasing the sensitivity and single-base mismatch selectivity of the molecular beacon using graphene oxide as the ‘nanoquencher’. Chem. Eur. J. 16(16), 4889–4894 (2010b)

    Article  CAS  PubMed  Google Scholar 

  • MacKerell Jr., A.D., et al.: All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102(18), 3586–3616 (1998)

    Article  CAS  PubMed  Google Scholar 

  • McQuain, M.K., Seale, K., Peek, J., Levy, S., Haselton, F.R.: Effects of relative humidity and buffer additives on the contact printing of microarrays by quill pins. Anal. Biochem. 320(2), 281–291 (2003)

    Article  CAS  PubMed  Google Scholar 

  • Oh, S.J., Hong, B.J., Choi, K.Y., Park, J.W.: Surface modification for DNA and protein microarrays. Omics 10(3), 327–343 (2006)

    Article  CAS  PubMed  Google Scholar 

  • Pal, S., Maiti, P.K., Bagchi, B.: Exploring DNA groove water dynamics through hydrogen bond lifetime and orientational relaxation. J. Chem. Phys. 125(23), 234903 (2006)

    Article  PubMed  CAS  Google Scholar 

  • Plimpton, S.: Fast parallel algorithms for short-range molecular dynamics. J. Comput. Phys. 117(1), 1–19 (1995)

    Article  CAS  Google Scholar 

  • Rickman, D.S., Herbert, C.J., Aggerbeck, L.P.: Optimizing spotting solutions for increased reproducibility of cDNA microarrays. Nucleic Acids Res. 31(18), e109 (2003)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shchepinov, M.S., Case-Green, S.C., Southern, E.M.: Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 25(6), 1155–1161 (1997)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang, L.A.L., Wang, J., Loh, K.P.: Graphene-based SELDI probe with ultrahigh extraction and sensitivity for DNA oligomer. J. Am. Chem. Soc. 132(32), 10976–10977 (2010)

    Article  CAS  PubMed  Google Scholar 

  • Tseng, G.C., Oh, M.-K., Rohlin, L., Liao, J.C., Wong, W.H.: Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res. 29(12), 2549–2557 (2001)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wolfinger, R.D., et al.: Assessing gene significance from cDNA microarray expression data via mixed models. J. Comput. Biol. 8(6), 625–637 (2001)

    Article  CAS  PubMed  Google Scholar 

  • Yang, Y.H., et al.: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30(4), e15 (2002)

    Article  PubMed  PubMed Central  Google Scholar 

  • Yang, H., et al.: Covalent functionalization of chemically converted graphene sheets via silane and its reinforcement. J. Mater. Chem. 19(26), 4632–4638 (2009)

    Article  CAS  Google Scholar 

  • Yang, H., Shan, C., Li, F., Han, D., Zhang, Q., Niu, L.: Covalent functionalization of polydisperse chemically-converted graphene sheets with amine-terminated ionic liquid. Chem. Commun. 26, 3880–3882 (2009)

    Article  CAS  Google Scholar 

  • Yeomans, J.M., Kusumaatmaja, H.: Modelling drop dynamics on patterned surfaces. Tech. Sci. 55(2), 203–210 (2007)

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran

    Fahimeh Akbari & Masumeh Foroutan

Authors
  1. Fahimeh Akbari
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Masumeh Foroutan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Fahimeh Akbari.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 2831 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Akbari, F., Foroutan, M. The effect of two layers of graphene with a striped pattern on wettability parameters of the biodroplets. Adsorption 26, 407–427 (2020). https://doi.org/10.1007/s10450-020-00211-w

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10450-020-00211-w

Keywords

Search

Navigation