Glycerol Reduces Cross Hybridization on Nitrocellulose Membrane

https://doi.org/10.22146/jsv.44895

Narendra Yoga Hendarta(1), Abu Tholib Aman(2), Asmarani Kusumawati(3), Tri Wibawa(4*)

(1) Department of Medical Laboratory Politeknik Kesehatan Kementerian Kesehatan Yogyakarta
(2) Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada
(3) Department of Reproduction and Obstetrics, Faculty of Veterinary Medicine, Universitas Gadjah Mada
(4) Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada
(*) Corresponding Author

Abstract


Lateral flow assay (LFD) based nucleic acid lateral flow (NALF)  method has been developed recently. The method met point of care testing (POCT) as simple and rapid procedures, less equipment, and can be performance by less skilled technician. NALF based on nucleic acid hybridizationis  more economical then immunochromatography assay which use antibody-antigen recognition. Cross hybridization has issued while used to differentiate organism with high GC content and high homology as high similarity genome. Some techniques has applied to give high stringency condition avoid cross hybridization reaction but need more procedure to apply. We found glycerol applied to buffer assay could reduce cross hybridization on nitrocellulose membrane. The study used 2 kinds of high stringency buffer as PBS and SSC bases and high concentration of ssDNA amplicon as sample. Without glycerol ingredient gave cross hybridization signal on test line. But used glycerol could reduce those even omitted with PBS based buffer assay. Beside those, glycerol could significantly increased hybridization signal in SSC based buffer assay (p<0.05).

Keywords


cross-hybridization; nucleic acid lateral flow; nitrocellulose membrane; buffer

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References

Anderson, M.L.M. and Young. B.D. (1985) Quantitative filter hybridization. In: Nucleic Acid Hybridization, a Practical Approach. Hames, B.D. and Higgins, S.J. (Eds.), IRL Press, Oxford, pp. 73-111.

Chang, C.T., Hain, T.C., Hutton, J.R. and Wetmur, J.G. (1974) Effect of microscopic and macroscopic viscosity on the rate of renaturation of DNA. Biopolymers 13 (1974) 1847-1858.

Dave, N. and Liu., J. (2010) Fast Molecular Beacon Hybridization in Organic Solvents with Improved Target Specificity, J. Phys. Chem. B 2010, 114, 15694–15699

Farrell-Jr, R.E. 2010. A Laboratory Guide for Isolation and Characterization In Practical Nucleic Acid Hybridization in RNA Methodologies (4th Edition), Academic Press, New York. p. 287

Gao, Y., Wolf, L.K. and Georgiadis, R. M. (2006). Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison. Nucleic Acids Research, 34 (11), doi:10.1093/nar/gkl422, pp. 3370–3377.

Haslam, N.J., Whiteford, N.E., Weber, G., Prugel-Bennett, A, Essex, J.W., and Neylon, C. (2008). Optimal probe length varies for targets with high sequence variation: implications for probe library design for resequencing highly variable genes. PLoS One. 3(6):e2500

Jauset-Rubio, M, Svobodová, M., Mairal, M., Mc-Neil, C., Keegan, N., Saeed, A., Abbas, MN., El-Shahawi, MS., Bashammakh, AS, Alyoubi, AO., and O´Sullivan, CK., 2016, Ultrasensitive, rapid and inexpensive detection of DNA using paper based lateral flow assay. Sci. Rep. 6, 37732; doi: 10.1038/srep37732

Kucho, K., Yoneda, H., Harada, M. and Ishiura, M. 2004. Determinants of sensitivity and specificity in spotted DNA microarrays with unmodified oligonucleotides. Genes Genet Syst., 79:189-197.

Kusumawati, A., Tampubolon, I.D., Hendarta, N.Y., Salasia, S.I., Wanahari, T.A., Mappakaya, B.A. and Hartati, S. (2015). Use of reverse transcription loop-mediated isothermal amplification combined with lateral flow dipstick for an easy and rapid detection of Jembrana disease virus. Virusdisease., 26(3):189-95. doi: 10.1007/s13337-015-0277-5

Letowski, J., Brousseau,R., and Masson, L., 2004, Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays, Journal of Microbiological Methods, 57, pp. 269– 278

Lyberopoulou, A., Efstathopoulos, E. P. and Gazouli. M. 2016. Chap. 6. Nanotechnology‐Based Rapid Diagnostic Tests, in Proof and Concepts, in Rapid Diagnostic Tests and Technologies. Shailendra K. Saxena ed. , InTechOpen, pp. 89-105

Reinhartz, A., Alajem, S., Samson, A. and Herzberg, M., (1993) A novel rapid hybridization technique: paper chromatography hybridization assay (PACHA), Gene, 136, 221-226

Sambrook, J. and Russel, D.W. 2001. Molecular Cloning: A Laboratory Manual vol.1. 3rd ed. Cold Spring Harbor Laboratory Press, New York, p. 10.2 Wang, X., Lim, HJ., and Son, A., 2014 , Characterization of denaturation and renaturation of DNA for DNA hybridization, Environ Health Toxicol. , 29: e2014007

Weckx, S., Carlon, E., Vuyst, L.D. Hummelen, P. V. (2007) Thermodynamic behavior of short oligonucleotides in microarray hybridizations can be described using Gibbs free energy in a nearest-neighbor model. J. Phys. Chem. B, 111 (48), pp 13583–13590



DOI: https://doi.org/10.22146/jsv.44895

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