Nükleik Asitlerin İzolasyonu, Saflaştırılması, Analizi ve Hibridizasyonu
Özet
Nükleik asitler hücresel rolleri yerine getiren ve önemli biyolojik makromolekül sınıfıdır. Bu makromoleküller yani nükleik asitler, yaşayan tüm organizmalarda mevcuttur. Nükleik asitlerin bulunduğu her organizmayla yapılacak olan çalışmalar için izolasyonu gereklidir. İzolasyon aşamasından sonra nükleik asitlerin diğer hücre bileşenlerinden ayrılması saf hale getirilmesi yapılacak olan çalışmalar için elzemdir. Saflaştırılan bu nükleik asitlerin ileriki çalışmalar için analizinin yapılması da çalışmanın güvenirliliğini artırmak için gerekli bir adımdır. Bu bölümde bir nükleik asitin hücreden izolasyonu, saflaştırılması, analizine yer verilmiştir. Ayrıca nükleik asitlerin tespiti için hibridizasyon yöntemlerine değinilmiştir.
Referanslar
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Molecular biology of the cell. USA: New York: Garland Science;2002.p. 627.
Saenger W, Principles of Nucleic Acid Structure. New York, Springer-Verlag Inc.; 1984.doi:10.1016/0307-4412(85)90046-9
Nelson DL, Cox MM. Lehninger Principles Of Biochemistry.4th Edition, WH Freeman;2004.
Passarge E. Renkli Genetik Atlası. Nobel Tıp Kitabevleri, İstanbul; 2000. 34–39, 44–47, 72–73.
Herbert A, Karapetyan S, Poptsova M, Vasquez K M, Vicens Q, Vögeli B. A, b and z: The structure, function and genetics of z-dna and z-rna. International journal of molecular sciences;2021; 22(14):7686. doi:10.3390/ijms22147686
Higgs PG. RNA secondary structure: physical and computational aspects. Quarterly reviews of biophysics;2000;33(3):199-253. doi:10.1017/S0033583500003620
Valentin K, John U, Medlin L. Nucleic acid isolation from environmental aqueous samples. In: Methods in enzymology. Academic Press; 2005. p. 15-37.
Jeddi F, Piarroux R, Mary C. Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases. Parasite; (2013); 20, 52. doi:10.1051/parasite/2013051
Hwang KY, Kwon SH, Jung SO. Miniaturized bead-beating device to automate full DNA sample preparation processes for gram-positive bacteria. Lab Chip ;2011;11:3649e55. doi:10.1039/C1LC20692C
Neugebauer JM. Detergents: an overview. Methods Enzym;1990; 182:239e53.
Moore D, Dowhan D. Purification and concentration of DNA from aqueous solutions. Current protocols in molecular biology;2002;59(1):2-1.doi:10.1002/0471142727.mb0201as59
Bogner PN, Killeen AA. Extraction of nucleic acids. Molecular diagnostics: For the clinical laboratorian;(2005); 25-30. doi.10.1385/1-59259-928-1:025
Broemeling DJ, Pel J, Gunn DC. An instrument for automated purification of nucleic acids from contaminated forensic samples. J Lab Autom 2008;13:40e8. doi:10.1016/j.jala.2007.10.008
Hourfar MK, Michelsen U, Schmidt M. High-throughput purification of viral RNA based on novel aqueous chemistry for nucleic acid isolation. Clin Chem; 2005;51:1217e22. doi:/10.1373/clinchem.2005.048603
Martinez AW, Phillips ST, Whitesides GM, et al. Diagnostics for the developing world: microfluidic paper-based analytical devices. Anal Chem;2010;82:3e10.doi:10.1021/ac9013989
Chiu ML, Lawi W, Snyder ST, Wong PK, Liao JC, Gau V. Matrix effects—a challenge toward automation of molecular analysis. JALA: Journal of the Association for Laboratory Automation;2010;15(3):33-242.doi:10.1016/j.jala.2010.02.001
Mark AM, Butler GC. The isolation of sodium desoxyribonucleate with sodium dodecyl sulfate. J Biol Chem; 1951;190: 165e76. doi:10.1016/S0021-9258(18)56056-7
Cler L, Bu D, Lewis C, Euhus D. A comparison of five methods for extracting DNA from paucicellular clinical samples. . Molecular and Cellular Probes;2006;20:191–196.doi: 10.1016/j.mcp.2005.12.003
Jenkins AJ, Oyler JM, Cone EJ. Comparison of heroin and cocaine concentrations in saliva with concentrations in blood and plasma. Journal of analytical toxicology;1995;19(6):359-374. doi:10.1093/jat/19.6.359
Aljanabi SM, Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res;1997;25:4692–4693.doi:10.1093/nar/25.22.4692
Thangjam R, Maibam D, Sharma JG, A simple and rapid method for isolation of DNA from imbibed embryos of Parkia timoriana (DC.) Merr. for PCR analysis. Food, Agric. Environ.;2003;1:36–38.
Yuan S, Cohen DB, Ravel J. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS ONE;2012;7:e33865.doi:10.1371/journal.pone.0033865
Vogelstein B, Gillespie D. Preparative and analytical purification of DNA from agarose. Proc Natl Acad Sci;1979; 76:615e9. doi:10.1073/pnas.76.2.615
Rivero E, Neves AC, Silva-Valenzuela MG, Sousa SO, Nunes, FD. Simple salting-out method for DNA extraction from formalin-fixed, paraffin-embedded tissues. Pathology-Research and Practice;2006;202(7):523529.doi:10.1016/j.prp.2006.02.007
Senguven B, Baris E, Oygur T, Berktas, M. Comparison of methods for the extraction of DNA from formalin-fixed, paraffin-embedded archival tissues. International journal of medical sciences;2014;11(5):494.doi:10.7150%2Fijms.8842
Nilsen TW. The fundamentals of RNA purification. Cold Spring Harbor Protocols;2013(7);pdb-top075838.
Pawlowski K, Kunze R, De Vries S, Bisseling T. Isolation of total, poly (A) and polysomal RNA from plant tissues. Plant molecular biology manual;(1994);231-243.doi:10.1007/978-94-011-0511-8_16
Shen C. Diagnostic Molecular Biology.January 2019 In book;pp.143-166.
Varma A, Padh H, Shrivastava N. Plant genomic DNA isolation: an art or a science. Biotechnology Journal: Healthcare Nutrition Technology; (2007);2(3):386-392.doi:10.1002/biot.200600195
Puchooa D, Khoyratty SUSS. Genomic DNA extraction from Victoria amazonica. Plant Molecular Biology Reporter;2004;22(2):195a.
Huang Q, Fu WL. Comparative analysis of the DNA staining efficiencies of different fluorescent dyes inpreparative agarose gel electrophoresis. Clin Chem Lab Med;2005;43(8): 841-2.
Murray PR, Rosenthal KS, Kobayashi GS, Pfaller MA. Medical Microbiology. Mosby Inc., St. Louis;1998;140-144.
Brown T.Southern blotting. Current protocols in molecular biology;1993;21(1):29.doi:10.1002/0471142727.mb0209as21
He SL, Green R. Northern blotting. In Methods in enzymology;2013;530:pp.75-87.
Ozdemir K, Muranlı FG, Kanev M. In situ Hibridizasyon Yöntemleri. Düzce Üniversitesi Bilim ve Teknoloji Dergisi; 2015;3(2): 613-621.
Borekci GFlüoresan in situ hibridizasyon (FISH) yönteminin klinik mikrobiyolojide kullanımı. Türk Mikrobiyol Cem. Dergisi; 2010; 40(3):131-142.
Referanslar
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Molecular biology of the cell. USA: New York: Garland Science;2002.p. 627.
Saenger W, Principles of Nucleic Acid Structure. New York, Springer-Verlag Inc.; 1984.doi:10.1016/0307-4412(85)90046-9
Nelson DL, Cox MM. Lehninger Principles Of Biochemistry.4th Edition, WH Freeman;2004.
Passarge E. Renkli Genetik Atlası. Nobel Tıp Kitabevleri, İstanbul; 2000. 34–39, 44–47, 72–73.
Herbert A, Karapetyan S, Poptsova M, Vasquez K M, Vicens Q, Vögeli B. A, b and z: The structure, function and genetics of z-dna and z-rna. International journal of molecular sciences;2021; 22(14):7686. doi:10.3390/ijms22147686
Higgs PG. RNA secondary structure: physical and computational aspects. Quarterly reviews of biophysics;2000;33(3):199-253. doi:10.1017/S0033583500003620
Valentin K, John U, Medlin L. Nucleic acid isolation from environmental aqueous samples. In: Methods in enzymology. Academic Press; 2005. p. 15-37.
Jeddi F, Piarroux R, Mary C. Application of the NucliSENS easyMAG system for nucleic acid extraction: optimization of DNA extraction for molecular diagnosis of parasitic and fungal diseases. Parasite; (2013); 20, 52. doi:10.1051/parasite/2013051
Hwang KY, Kwon SH, Jung SO. Miniaturized bead-beating device to automate full DNA sample preparation processes for gram-positive bacteria. Lab Chip ;2011;11:3649e55. doi:10.1039/C1LC20692C
Neugebauer JM. Detergents: an overview. Methods Enzym;1990; 182:239e53.
Moore D, Dowhan D. Purification and concentration of DNA from aqueous solutions. Current protocols in molecular biology;2002;59(1):2-1.doi:10.1002/0471142727.mb0201as59
Bogner PN, Killeen AA. Extraction of nucleic acids. Molecular diagnostics: For the clinical laboratorian;(2005); 25-30. doi.10.1385/1-59259-928-1:025
Broemeling DJ, Pel J, Gunn DC. An instrument for automated purification of nucleic acids from contaminated forensic samples. J Lab Autom 2008;13:40e8. doi:10.1016/j.jala.2007.10.008
Hourfar MK, Michelsen U, Schmidt M. High-throughput purification of viral RNA based on novel aqueous chemistry for nucleic acid isolation. Clin Chem; 2005;51:1217e22. doi:/10.1373/clinchem.2005.048603
Martinez AW, Phillips ST, Whitesides GM, et al. Diagnostics for the developing world: microfluidic paper-based analytical devices. Anal Chem;2010;82:3e10.doi:10.1021/ac9013989
Chiu ML, Lawi W, Snyder ST, Wong PK, Liao JC, Gau V. Matrix effects—a challenge toward automation of molecular analysis. JALA: Journal of the Association for Laboratory Automation;2010;15(3):33-242.doi:10.1016/j.jala.2010.02.001
Mark AM, Butler GC. The isolation of sodium desoxyribonucleate with sodium dodecyl sulfate. J Biol Chem; 1951;190: 165e76. doi:10.1016/S0021-9258(18)56056-7
Cler L, Bu D, Lewis C, Euhus D. A comparison of five methods for extracting DNA from paucicellular clinical samples. . Molecular and Cellular Probes;2006;20:191–196.doi: 10.1016/j.mcp.2005.12.003
Jenkins AJ, Oyler JM, Cone EJ. Comparison of heroin and cocaine concentrations in saliva with concentrations in blood and plasma. Journal of analytical toxicology;1995;19(6):359-374. doi:10.1093/jat/19.6.359
Aljanabi SM, Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res;1997;25:4692–4693.doi:10.1093/nar/25.22.4692
Thangjam R, Maibam D, Sharma JG, A simple and rapid method for isolation of DNA from imbibed embryos of Parkia timoriana (DC.) Merr. for PCR analysis. Food, Agric. Environ.;2003;1:36–38.
Yuan S, Cohen DB, Ravel J. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS ONE;2012;7:e33865.doi:10.1371/journal.pone.0033865
Vogelstein B, Gillespie D. Preparative and analytical purification of DNA from agarose. Proc Natl Acad Sci;1979; 76:615e9. doi:10.1073/pnas.76.2.615
Rivero E, Neves AC, Silva-Valenzuela MG, Sousa SO, Nunes, FD. Simple salting-out method for DNA extraction from formalin-fixed, paraffin-embedded tissues. Pathology-Research and Practice;2006;202(7):523529.doi:10.1016/j.prp.2006.02.007
Senguven B, Baris E, Oygur T, Berktas, M. Comparison of methods for the extraction of DNA from formalin-fixed, paraffin-embedded archival tissues. International journal of medical sciences;2014;11(5):494.doi:10.7150%2Fijms.8842
Nilsen TW. The fundamentals of RNA purification. Cold Spring Harbor Protocols;2013(7);pdb-top075838.
Pawlowski K, Kunze R, De Vries S, Bisseling T. Isolation of total, poly (A) and polysomal RNA from plant tissues. Plant molecular biology manual;(1994);231-243.doi:10.1007/978-94-011-0511-8_16
Shen C. Diagnostic Molecular Biology.January 2019 In book;pp.143-166.
Varma A, Padh H, Shrivastava N. Plant genomic DNA isolation: an art or a science. Biotechnology Journal: Healthcare Nutrition Technology; (2007);2(3):386-392.doi:10.1002/biot.200600195
Puchooa D, Khoyratty SUSS. Genomic DNA extraction from Victoria amazonica. Plant Molecular Biology Reporter;2004;22(2):195a.
Huang Q, Fu WL. Comparative analysis of the DNA staining efficiencies of different fluorescent dyes inpreparative agarose gel electrophoresis. Clin Chem Lab Med;2005;43(8): 841-2.
Murray PR, Rosenthal KS, Kobayashi GS, Pfaller MA. Medical Microbiology. Mosby Inc., St. Louis;1998;140-144.
Brown T.Southern blotting. Current protocols in molecular biology;1993;21(1):29.doi:10.1002/0471142727.mb0209as21
He SL, Green R. Northern blotting. In Methods in enzymology;2013;530:pp.75-87.
Ozdemir K, Muranlı FG, Kanev M. In situ Hibridizasyon Yöntemleri. Düzce Üniversitesi Bilim ve Teknoloji Dergisi; 2015;3(2): 613-621.
Borekci GFlüoresan in situ hibridizasyon (FISH) yönteminin klinik mikrobiyolojide kullanımı. Türk Mikrobiyol Cem. Dergisi; 2010; 40(3):131-142.
