Single cell HaloChip assay on paper for point-of-care diagnosis


This article describes a paper-based low cost single cell HaloChip assay that can be used to assess drug- and radiation-induced DNA damage at point-of-care. Printing ink on paper effectively blocks fluorescence of paper materials, provides high affinity to charged polyelectrolytes, and prevents penetration of water in paper. After exposure to drug or ionizing radiation, cells are patterned on paper to create discrete and ordered single cell arrays, embedded inside an agarose gel, lysed with alkaline solution to allow damaged DNA fragments to diffuse out of nucleus cores, and form diffusing halos in the gel matrix. After staining DNA with a fluorescent dye, characteristic halos formed around cells, and the level of DNA damage can be quantified by determining sizes of halos and nucleus with an image processing program based on MATLAB. With its low fabrication cost and easy operation, this HaloChip on paper platform will be attractive to rapidly and accurately determine DNA damage for point-of-care evaluation of drug efficacy and radiation condition.

Single cell HaloChip on paper

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6


  1. 1.

    Fedier A, Fink D. Mutations in DNA mismatch repair genes: implications for DNA damage signaling and drug sensitivity (review). Int J Oncol. 2004;24(4):1039–47.

    CAS  Google Scholar 

  2. 2.

    Frankenberg-Schwager M. Review of repair kinetics for DNA damage induced in eukaryotic cells in vitro by ionizing radiation. Radiother Oncol J Eur Soc Ther Radiol Oncol. 1989;14(4):307–20.

    CAS  Article  Google Scholar 

  3. 3.

    Zhang P, Qiao Y, Wang C, Ma L, Su M. Enhanced radiation therapy with internalized polyelectrolyte modified nanoparticles. Nanoscale. 2014;6(17):10095–9.

    CAS  Article  Google Scholar 

  4. 4.

    Wan J, Johnson M, Schilz J, Djordjevic MV, Rice JR, Shields PG. Evaluation of in vitro assays for assessing the toxicity of cigarette smoke and smokeless tobacco. Cancer Epidemiol Biomarkers Prev. 2009;18(12):3263–304.

    Article  Google Scholar 

  5. 5.

    Fenech M. The advantages and disadvantages of the cytokinesis-block micronucleus method. Mutat Res. 1997;392(1–2):11–8.

    CAS  Article  Google Scholar 

  6. 6.

    Watanabe M, Hitomi M, van der Wee K, Rothenberg F, Fisher SA, Zucker R, et al. The pros and cons of apoptosis assays for use in the study of cells, tissues, and organs. Microsc Microanal. 2002;8(5):375–91.

    CAS  Article  Google Scholar 

  7. 7.

    Nusse M, Marx K. Flow cytometric analysis of micronuclei in cell cultures and human lymphocytes: advantages and disadvantages. Mutat Res. 1997;392(1–2):109–15.

    CAS  Article  Google Scholar 

  8. 8.

    Slamenova D, Gabelova A, Ruzekova L, Chalupa I, Horvathova E, Farkasova T, et al. Detection of MNNG-induced DNA lesions in mammalian cells; validation of comet assay against DNA unwinding technique, alkaline elution of DNA and chromosomal aberrations. Mutat Res. 1997;383(3):243–52.

    CAS  Article  Google Scholar 

  9. 9.

    Wood DK, Weingeistb DM, Bhatia SN, Engelwardb BP. Single cell trapping and DNA damage analysis using microwell arrays. Proc Natl Acad Sci U S A. 2010;107:10008–13.

    CAS  Article  Google Scholar 

  10. 10.

    Gichner T, Mukherjee A, Wagner ED, Plewa MJ. Evaluation of the nuclear DNA diffusion assay to detect apoptosis and necrosis. Mutat Res. 2005;586(1):38–46.

    CAS  Article  Google Scholar 

  11. 11.

    Sestili P, Martinelli C, Stocchi V. The fast halo assay: an improved method to quantify genomic DNA strand breakage at the single-cell level. Mutat Res. 2006;607(2):205–14.

    CAS  Article  Google Scholar 

  12. 12.

    Yu WW, White IM. Inkjet-printed paper-based SERS dipsticks and swabs for trace chemical detection. Analyst. 2013;138(4):1020–5.

    CAS  Article  Google Scholar 

  13. 13.

    Martinez AW, Phillips ST, Wiley BJ, Gupta M, Whitesides GM. FLASH: a rapid method for prototyping paper-based microfluidic devices. Lab Chip. 2008;8(12):2146–50.

    CAS  Article  Google Scholar 

  14. 14.

    Zhou M, Yang M, Zhou F. Paper based colorimetric biosensing platform utilizing cross-linked siloxane as probe. Biosens Bioelectron. 2014;55:39–43.

    CAS  Article  Google Scholar 

  15. 15.

    Jokerst JC, Adkins JA, Bisha B, Mentele MM, Goodridge LD, Henry CS. Development of a paper-based analytical device for colorimetric detection of select foodborne pathogens. Anal Chem. 2012;84(6):2900–7.

    CAS  Article  Google Scholar 

  16. 16.

    Yang X, Forouzan O, Brown TP, Shevkoplyas SS. Integrated separation of blood plasma from whole blood for microfluidic paper-based analytical devices. Lab Chip. 2012;12(2):274–80.

    CAS  Article  Google Scholar 

  17. 17.

    Miranda BS, Linares EM, Thalhammer S, Kubota LT. Development of a disposable and highly sensitive paper-based immunosensor for early diagnosis of Asian soybean rust. Biosens Bioelectron. 2013;45:123–8.

    CAS  Article  Google Scholar 

  18. 18.

    Pelton R. Bioactive paper provides a low-cost platform for diagnostics. Trends Anal Chem. 2009;28(8):925–42.

    CAS  Article  Google Scholar 

  19. 19.

    Hu J, Wang S, Wang L, Li F, Pingguan-Murphy B, Lu TJ, et al. Advances in paper-based point-of-care diagnostics. Biosens Bioelectron. 2014;54:585–97.

    CAS  Article  Google Scholar 

  20. 20.

    Jefferies R, Ryan UM, Irwin PJ. PCR-RFLP for the detection and differentiation of the canine piroplasm species and its use with filter paper-based technologies. Vet Parasitol. 2007;144(1–2):20–7.

    CAS  Article  Google Scholar 

  21. 21.

    Cheng CM, Martinez AW, Gong J, Mace CR, Phillips ST, Carrilho E, et al. Paper-based ELISA. Angew Chem. 2010;49(28):4771–4.

    CAS  Article  Google Scholar 

  22. 22.

    Juvonen H, Maattanen A, Lauren P, Ihalainen P, Urtti A, Yliperttula M, et al. Biocompatibility of printed paper-based arrays for 2-D cell cultures. Acta Biomater. 2013;9(5):6704–10.

    CAS  Article  Google Scholar 

  23. 23.

    Derda R, Tang SKY, Laromaine A, Mosadegh B, Hong E, Mwangi M, et al. Multizone paper platform for 3D cell cultures. PLoS One. 2011;6(5):1–14.

    Article  Google Scholar 

  24. 24.

    Qiao Y, Wang C, Su M, Ma L. Single cell DNA damage/repair assay using HaloChip. Anal Chem. 2012;84(2):1112–6.

    CAS  Article  Google Scholar 

  25. 25.

    Hossain M, Luo Y, Sun Z, Wang C, Zhang M, Fu H, et al. X-ray enabled detection and eradication of circulating tumor cells with nanoparticles. Biosens Bioelectron. 2012;38:348–54.

    CAS  Article  Google Scholar 

  26. 26.

    Otsu N. A threshold selection method from gray-level histograms. IEEE Trans Syst Man Cybern B Cybern. 1979;9:62–6.

    Article  Google Scholar 

Download references


This work has been supported by a New Investigator Award from Bankhead-Copley Cancer Research Program and a seed grant from Kennedy Space Center to Liyuan Ma. This work is partially supported by a Director’s New Innovator Award from National Institute of Health (NIH) to Ming Su (1DP2EB016572).

Author information



Corresponding author

Correspondence to Ming Su.

Ethics declarations

Conflict of interest

The authors declare that there is no potential conflict of interest.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ma, L., Qiao, Y., Jones, R. et al. Single cell HaloChip assay on paper for point-of-care diagnosis. Anal Bioanal Chem 408, 7753–7759 (2016).

Download citation


  • Point-of-care diagnosis
  • Paper-based assay
  • DNA damage
  • Single cell array