Izvestiya of Saratov University.

Chemistry. Biology. Ecology

ISSN 1816-9775 (Print)
ISSN 2541-8971 (Online)


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Shmakov S. L., Bayburdov T. А., Shipovskaya A. B., Suska-Malawska M., Rogachaeva S. M. Prospects for the use of polymer-containing materials and sorbents for membrane ultrafi ltration, sorption and concentration of nucleic acids from aqueous media. A review. Izvestiya of Saratov University. Chemistry. Biology. Ecology, 2022, vol. 22, iss. 2, pp. 150-160. DOI: 10.18500/1816-9775-2022-22-2-150-160

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544[723.2+725.7]:57.088.2/3

Prospects for the use of polymer-containing materials and sorbents for membrane ultrafi ltration, sorption and concentration of nucleic acids from aqueous media. A review

Autors: 
Shmakov Sergei L., Saratov State University
Bayburdov Telman А., Saratov State University
Shipovskaya Anna B., Saratov State University
Suska-Malawska Malgoshata, University of Warsaw
Rogachaeva Svetlana Michailovna, Yuri Gagarin State Technical University of Saratov
Abstract: 

Unlike antibiotics and heavy metals, nucleic acids exist in the aquatic environment as a part of prokaryotic and eukaryotic microorganisms (bacteria, fungi, etc.) rather than in a free form. In this regard, the most important primary stage of sample preparation of an object for the quantitative analysis of DNA and RNA in natural and wastewaters includes membrane ultrafi ltration of an aqueous sample, followed by its sorption preconcentration on a solid phase carrier. The effi ciency of ultrafi ltration and subsequent sorption of nucleic acids from natural and wastewaters largely depends on the material of fi lters, membranes, and sorbents. Polymeric materials are widely used due to their special properties: the affi nity of polymers for biological objects, the ability to create pores of any required size, good mechanical properties and resistance to the extraction of microorganisms captured. The paper reviews the 15-year-old scientifi c literature on fi ltering, membrane and sorption polymeric materials used to extract nucleic acids from aqueous media and preserve them. Polymeric sorbents for collecting and concentrating DNA and RNA from the liquid phase, as well as storing nucleic acids, are covered. It has been found that ultrafi ltration is used at a relatively low concentration of the analyzed object, followed by extraction of the substance using commercially available kits, including cartridges. Sorption (solid-phase concentration) is used to extract nucleic acids at their relatively high concentration in the analyte. The main polymeric materials used include cellulose and its derivatives (nitrocellulose, cellulose acetate, mixed cellulose nitrate–acetate, diethylaminoethylcellulose, polyethyleneiminocellulose), agarose, dextran, polyestersulfone, polycarbonate, fl uoroplasts, polyacrylates and polymethacrylates, polyaramids, polyamides, polyvinyl alcohol, polyaniline, polycaprolactone, polyacrylamide and polymethacrylamide, polystyrene. Chitosan, modifi ed polycaprolactone, and magnetic particles coated with polydopamine, polyethyleneimine, polyvinylpyrrolidone, polystyrene, or polyamidoamine dendrimer are considered as promising polymers for further research in this fi eld.

Reference: 
  1. 1. Martinez J. L., Coque T. M., Baquero F. What is a resistance gene? Ranking risk in resistomes. Nature Reviews Microbiology, 2015, vol. 13, no. 2, pp. 116–123. https:// doi.org/10.1038/nrmicro3399
  2. 2. Manaia C. M., Rocha J., Scaccia N., Marano R., Radud E., Biancullo F., Cerqueira F., Fortunato G., Iakovides I. C., Zammit I., Kampouris I., Vaz-Moreira I., Nunes O. C. Antibiotic resistance in wastewater treatment plants: Tackling the black box. Environment International, 2018, vol. 115, pp. 312–324. https://doi.org/10.1016/j.envint.2018.03.044
  3. 3. Karkman A., Do T. T., Walsh F., Virta M. P. J. AntibioticResistance Genes in Waste Water. Trends in Microbiology, 2018, vol. 26, no. 3, pp. 220–228. https://doi. org/10.1016/j.tim.2017.09.005
  4. 4. Volkmann H., Schwartz T., Bischoff P., Kirchen S., Obst U. Detection of clinically relevant antibioticresistance genes in municipal wastewater using real-time PCR (TaqMan). Journal of Microbiological Methods, 2004, vol. 56, pp. 277–286. https://doi.org/10.1016/j. mimet.2003.10.014
  5. 5. Guo J., Li J., Chen H., Bond P., Yuan Z. Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements. Water Research, 2017, vol. 123, pp. 468–478. https://doi.org/10.1016/j.watres.2017.07.002
  6. 6. Schill W. B. Capture of Environmental DNA (eDNA) from Water Samples by Flocculation. JoVE (Journal of Visualized Experiments), 2020, no. 159, pp. e60967. https://doi.org/10.3791/60967
  7. 7. Calderуn-Franco D., Loosdrecht M. C. M. van, Abeel T., Weissbro D. G. A novel method to isolate free-fl oating extracellular DNA from wastewater for quantitation and metagenomic profi ling of mobile genetic elements and antibiotic resistance genes. bioRxiv, 2020. https://doi. org/10.1101/2020.05.01.072397
  8. 8. Kumar G., Eble J. E., Gaither M. R. A practical guide to sample preservation and pre-PCR processing of aquatic environmental DNA. Mol Ecol Resour., 2020, vol. 20, pp. 29–39. https://doi.org/10.1111/1755-0998.13107
  9. 9. Sanches T. M., Schreier A. D. Optimizing an eDNA protocol for estuarine environments: Balancing sensitivity, cost and time. PLoS ONE, 2020, vol. 15, no. 5, pp. e0233522. https://doi.org/10.1371/journal.pone.0233522
  10. 10. Djurhuus A., Port J., Closek C. J., Yamahara K. M., Romero-Maraccini O., Walz K. R., Goldsmith D. B., Michisaki R., Breitbart M., Boehm A. B., Chavez F. P. Evaluation of Filtration and DNA Extraction Methods for Environmental DNA Biodiversity Assessments across Multiple Trophic Levels. Front. Mar. Sci., 2017, vol. 4, pp. 314. https://doi.org/10.3389/fmars.2017.00314
  11. 11. Eichmiller J. J., Miller L. M., Sorensen P. W. Optimizing techniques to capture and extract environmental DNA for detection and quantifi cation of fi sh. Molecular Ecology Resources, 2016, vol. 16, no. 1, pp. 56–68. https://doi. org/10.1111/1755-0998.12421
  12. 12. Majaneva M., Diserud O.H., Eagle S. H. C., Bostrцm E., Hajibabaei M., Ekrem T. Environmental DNA fi ltration techniques affect recovered biodiversity. Scientifi c Reports, 2018, vol. 8, pp. 4682. https://doi.org/10.1038/ s42598-018-23052-8
  13. 13. Minamoto T., Naka T., Moji K., Maruyama A. Techniques for the practical collection of environmental DNA: Filter selection, preservation, and extraction. Limnology, 2016, vol. 17, pp. 23–32. https://doi.org/10.1007/s10201-015- 0457-4
  14. 14. Spens J., Evans A. R., Halfmaerten D., Knudsen S.W., Sengupta M. E., Mak S. S. T., Sigsgaard E. E., Hellstro€m M. Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol: advantage of enclosed fi lter. Methods in Ecology and Evolution, 2017, vol. 8, no. 5, pp. 635–645. https://doi.org/10.1111/2041-210X.12683
  15. 15. Boom R., Sol C. J., Salimans M. M. Rapid and Simple Method for Purification of Nucleic Acids. J. Clin. Microbiol., 1990, vol. 28, pp. 495–503. https:// doi.org/10.1128/JCM.28.3.495-503.1990
  16. 16. Antonova O. S., Korneva N. A., Belov Yu. V., Kurochkin V. E. Effective methods for isolating nucleic acids for analysis in molecular biology (review). Nauchnoe Priborostroenie, 2010, vol. 20, no. 1, pp. 3–9 (in Russian).
  17. 17. Sposob vydeleniya nukleinovykh kislot [Nucleic acid isolation method]. Pat. 2272072 Russ. Federation, No. 2004126133/13; filed 26 August 2004; publ. 20.03.2006 (in Russian).
  18. 18. Li J., Handley L.-J.L., Read D.S., Hдnfl ing B. The effect of fi ltration method on the effi ciency of environmental DNA capture and quantifi cation via metabarcoding. Molecular Ecology Resources, 2018, vol. 18, no. 5, pp. 1102–1114. https://doi.org/10.1111/1755-0998.12899
  19. 19. Sun L., Shi P., Zhang Q., Lv J., Zhang Y. Effects of using different ultrafi ltration membranes on the removal effi ciency of antibiotic resistance genes from secondary effl uent. Desalination and Water Treatment, 2019, vol. 156, pp. 52–58. https://doi.org/10.5004/dwt.2019.24255
  20. 20. Nunes J. C., Amorim M. T. P. de, Escobar I. C., Queiroz J. A., Morгo A. M. Plasmid DNA/RNA separation by ultrafi ltration: Modeling and application study. Journal of Membrane Science, 2014, vol. 463, pp. 1–10. https://doi.org/10.1016/j.memsci.2014.03.036
  21. 21. Thomas A. C., Nguyen P. L., Howard J., Goldberg C. S., Jentoft S. A self-preserving, partially biodegradable eDNA fi lter. Methods Ecol. Evol., 2019, vol. 10, pp. 1136–1141. https://doi.org/10.1111/2041-210X.13212
  22. 22. Yang Y., Xu C., Cao X., Lin H., Wang J. Antibiotic resistance genes in surface water of eutrophic urban lakes are related to heavy metals, antibiotics, lake morphology and anthropic impact. Ecotoxicology, 2017, vol. 26, no. 6, pp. 831–840. https://doi.org/10.1007/s10646-017- 1814-3
  23. 23. Ushio M. Use of a filter cartridge combined with intra-cartridge bead-beating improves detection of microbial DNA from water samples. Methods Ecol. Evol., 2019, vol. 10, no. 8, pp. 1142–1156. https://doi. org/10.1111/2041-210X.13204
  24. 24. Smennyi mikrofl uidnyi modul’ dlya avtomatizirovannogo vydeleniya i ochistki nukleinovykh kislot iz biologicheskikh obraztsov i sposob vydeleniya i ochistki nukleinovykh kislot s ego ispol’zovaniem [Rechargeable microfl uid module for automatic isolation and purifi cation of nucleic acids from biological samples and method of isolating and purifi cation of nucleic acids with the use of thereof] : pat. 2380418 Russ. Federation, fi led 01 October 2008; publ. 27 January 2010 (in Russian).
  25. 25. Sposob vydeleniya DNK [Method to isolate DNA] : pat. 2485178 Russ. Federation, fi led 12 July 2011; publ. 20 June 2013 (in Russian).
  26. 26. Stable protein storage and stable nucleic acid storage in recoverable form: pat. US 8,431,384 B2. Appl. 12/499,031; fi led: 7.07.2009; date of patent: 30.04.2013.
  27. 27. Method and device for the collection and isolation of nucleic acid : Pat. US 2008/0280290 A1. Appl. 10599248; fi led 18.08.2006; publication date 13.11.2008.
  28. 28. Kendall D., Lye G. J., Levy M. S. Purifi cation of Plasmid DNA by an Integrated Operation Comprising Tangential Flow Filtration and Nitrocellulose Adsorption. Biotechnology and Bioengineering, 2002, vol. 79, no. 7, pp. 816–822. https://doi.org/10.1002/bit.10325
  29. 29. Nur M. N., Ulayya N., Azis M., Maryanto A. E., Andayani N. Methods to maximize environmental DNA (eDNA) for detection the presence of Alligator Gar (Atractosteus spatula). IOP Conf. Series: Earth and Environmental Science, 2020, no. 538, pp. 012018. https:// doi.org/10.1088/1755-1315/538/1/012018
  30. 30. Hinlo R., Gleeson D., Lintermans M., Furlan E. Methods to maximize recovery of environmental DNA from water samples. PLoS ONE, 2017, vol. 12, no. 6, pp. 179–251. https://doi.org/10.1371/journal.pone.0179251
  31. 31. Bockelmann U., Dorries H.-H., Ayuso-Gabella M. N., de Marçay M. S., Tandoi V., Levantesi C., Masciopinto C., Van Houtte E., Szewzyk U., Wintgens T., Grohmann E. Quantitative PCR Monitoring of Antibiotic Resistance Genes and Bacterial Pathogens in Three European Artifi cial Groundwater Recharge Systems. Applied and Environmental Microbiology, 2009, vol. 75, no. 1, pp. 154–163. https://doi.org/10.1128/AEM.01649-08
  32. 32. Kumar G., Farrell E., Reaume A. M., Eble J. A., Gaither M. R. One size does not fi t all: Tuning eDNA protocols for high- and low-turbidity water sampling. Environmental DNA, 2022, vol. 4, no. 1, pp. 167–180. https://doi.org/10.1002/edn3.235
  33. 33. Liang Z., Keeley A. Filtration Recovery of Extracellular DNA from Environmental Water Samples. Environmental Science & Technology, 2013, vol. 47, no. 16, pp. 9324–9331. https://doi.org/10.1021/es401342b
  34. 34. Günal G., Kip Ç., Eda Öğüt S., Ilhan H., Kibar G., Tuncel A. Comparative DNA isolation behaviours of silica and polymer based sorbents in batch fashion: Monodisperse silica microspheres with bimodal poresize distribution as a new sorbent for DNA isolation. Artifi cial Cells, Nanomedicine, and Biotechnology, 2018, vol. 46, no. 1, pp. 178–184. https://doi.org/10.1080/ 21691401.2017.1304404
  35. 35. Sorbent material for separating bio-macromolecules : pat. 2017/0053635A KR, fi led 8 July 2016; publication date 17.03.2016 (in Korean).
  36. 36. Zhang M., Li L., Li B., Tian N., Yang M., Zhang H., You C., Zhang J. Adsorption of DNA by using polydopamine modifi ed magnetic nanoparticles based on solid-phase extraction. Analytical Biochemistry, 2019, no. 579, pp. 9–17. https://doi.org/10.1016/j.ab.2019.05.004
  37. 37. Pan X., Cheng S., Su T., Zuo G., Zhang C., Wu L., Jiao Y., Dong W. Poly (2-hydroxypropylene imines) functionalized magnetic polydopamine nanoparticles for high-effi ciency DNA isolation. Applied Surface Science, 2019, vol. 498, pp. 143888. https://doi.org/10.1016/j. apsusc.2019.143888
  38. 38. Magnitnyi sorbent, sposob ego polucheniya i sposob vydeleniya molekul nukleinovykh kislot [Magnetic sorbent, method of its obtaining, and method of isolating molecules of nucleic acids]: Pat. 2653130 Russ. Federation, no. 2017121208; fi led 16 June 2017; publ. 07.05.2018, bull. no. 13 (in Russian).
  39. 39. Survilo V. L. Study of the physicochemical parameters of commercial magnetic sorbents for nucleic acid isolatoion. Molekulyarnaya diagnostika – 2017: sb. tr. IX Vseros. nauch.-prakt. konf. s mezhdunar. uchastiem (18–20 apr. 2017, Moskva) [Molecular diagnostics: coll. of works of IX All-Russ. sci.-pract. conf. with intern. part (April 18–20, 2017, Moscow)]. Moscow, Yulius Publ., 2017, vol. 2, pp. 473–474 (in Russian).
  40. 40. Kapustin D. V., Yagudayeva E. Yu., Zavada L. L., Zhigis L. S., Zubov V. P., Yaroshevskaya E. M., Plobner L., Laizer R.-M., Brem G. A Composite PolyanilineContaining Silica Sorbent for DNA Isolation. Russian Journal of Bioorganic Chemistry, 2003, vol. 29, no. 3, pp. 310–315 (in Russian).
  41. 41. Kapustin D. V., Prostyakova A. I., Alekseyev Ya. I., Varlamov D. A., Zubov V. P., Zavriev S. K. Highly effective method of single-stage DNA isolation for PCR diagnostics Mycobacterium tuberculosis. Acta Naturae, 2014, vol. 6, no. 2 (21) , pp. 52–57 (in Russian).
  42. 42. Yagudaeva E., Zybin D., Vikhrov A., Prostyakova A., Ischenko A., Zubov V., Kapustin D. Sorption of nucleic acids and proteins on polyaniline and polyaramide nano-coatings as studied by spectral-correlation interferometry in a real time mode. Colloids and Surfaces B: Biointerfaces, 2018, vol. 163, pp. 83–90. https://doi. org/10.1016/j.colsurfb.2017.12.025
  43. 43. Liaw D.-J., Zybin D. I., Prostyakova A. I., Yagudaeva E. Yu., Vikhrov A. A., Ischenko A. A., Zubov V. P., Kapustin D. V. Static and dynamic sorption of nucleic acids and proteins on the surface of sorbents modifi ed with nanosized polymer layers. Izvestiya Vysshikh Uchebnykh Zavedenii. Khimiya i Khimicheskaya Tekhnologiya, 2018, vol. 61, iss. 1, pp. 4–21 (in Russian).
  44. 44. Yagudaeva E. Yu., Bukina Ya. A., Prostyakova A. I., Zubov V. P., Tverskoy V. A., Kapustin D. V. Oxidative polymerization of aniline on the surface of silica in the presence of poly(sulfonic acids) as a method of preparing efficient biosorbents. Polym. Sci. Ser. A, 2009, vol. 51, no. 6, pp. 675–682. https://doi.org/10.1134/ S0965545X09060121
  45. 45. Kapustin D. V., Prostyakova A. I., Ryazantcev D. Yu., Zubov V. P. Novel composite matrices modifi ed with nanolayers of polymers as perspective materials for bioseparation and bioanalysis. Nanomedicine, 2011, vol. 6, no. 2, pp. 241–255. https://doi.org/10.2217/ NNM.11.6
  46. 46. Liaw D.-J., Yagudaeva E., Prostyakova A., Lazov M., Zybin D., Ischenko A., Zubov V., Chang C.-H., Huang Y.-C., Kapustin D. Sorption behavior of polyaramides in relation to isolation of nucleic acids and proteins. Colloids and Surfaces B: Biointerfaces, 2016, vol. 145, pp. 912–921. https://doi.org/10.1016/j.colsurfb.2016.05.068
  47. 47. Zybin D. I., Prostyakova A. I., Kapustin D. V. Single-step isolation of DNA from the soil samples for PCR-analysis using two-component system containing polyanilinemodifi ed silica and alginate microspheres. Microchemical Journal, 2021, vol. 166, pp. 106225. https://doi. org/10.1016/j.microc.2021.106225
  48. 48. Yagudaeva E. Yu., Liaw D.-J., Ischenko A. A., Bagratashvili V. N., Zubov V. P., Prostyakova A. I., Ryazantsev D. Yu., Sviridov A. P., Kapustin D. V. New polyamide-containing sorbents for one-step isolation of DNA. J. Mater Sci., 2014, vol. 49, pp. 3491–3496. https://doi.org/10.1007/s10853-014-8062-1
  49. 49. Yang Y., Xu C., Cao X., Lin H., Wang J. Antibiotic resistance genes in surface water of eutrophic urban lakes are related to heavy metals, antibiotics, lake morphology and anthropic impact. Ecotoxicology, 2017, vol. 26, no. 6, pp. 831–840. https://doi.org/10.1007/s10646-017-1814-3
  50. 50. Sorbent material having a covalently attached perfluorinated surface with functional groups: Pat. US 2006/0243658 A1. Appl. 10/534,031; fi led: 10.11.2003; publication date: 2.11.2006.
  51. 51. Yoza B., Arakaki A., Matsunaga T. DNA extraction using bacterial magnetic particles modified with hyperbranched polyamidoamine dendrimer. Journal of Biotechnology, 2003, vol. 101, pp. 219–228. https://doi.org/10.1016/ S0168-1656(02)00342-5
  52. 52. Vanzetti L., Pasquardini L., Potrich C., Vaghi V., Battista E., Causa F., Pederzolli C. XPS analysis of genomic DNA adsorbed on PEI-modifi ed surfaces. Surface and Interface Analysis, 2016, vol. 48, no. 7, pp. 611–615. https://doi.org/10.1002/sia.5932
  53. 53. Hu L.-L., Hu B., Shen L.-M., Zhang D.-D., Chenn X.-W., Wang J.-H. Polyethyleneimine–iron phosphate nanocomposite as a promising adsorbent for the isolation of DNA. Talanta, 2015, vol. 132, pp. 857–863. https://doi. org/10.1016/j.talanta.2014.10.047
  54. 54. Emaus M. N., Varona M., Eitzmann D. R., Hsieh S.-A., Zeger V. R., Anderson J. L. Nucleic acid extraction: Fundamentals of sample preparation methodologies, current advancements, and future endeavors. Trends in Analytical Chemistry, 2020, vol. 130, pp. 115985. https:// doi.org/10.1016/j.trac.2020.115985
  55. 55. Biologic sample collection devices and methods of production and use thereof: Pat. US 9,359,600 B2.
  56. 56. Shishkina I. G., Levina A. S. Affi nnye sorbenty, soderzhashchie nukleinovye kisloty i ikh fragment [Affi ne sorbents containing nucleic acids and their fragments]. Russian Chemical Revieews, 2001, vol. 70, iss. 6, pp. 581–607 (in Russian).
Received: 
10.01.2022
Accepted: 
19.01.2022
Published: 
30.06.2022
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