Yeni Nesil Nükleotid Dizileme Metotlarının Biyokimyasal Temelleri

Yıl 2017, Cilt: 20 Sayı: 1, 1 - 15, 01.01.2017

İsmail Akyol , Mehmet Ali Yıldız Esen Tutar

Öz

Sanger ve Maxam-Gilbert dizileme metotları birinci nesil dizileme olarak ifade edilmektedir. Zincir sonlandırma yaklaşımı ile dizileme yaygın olarak kullanılmış ve ilk genom projesi olan insan genomu bu yöntem ile tamamlanmıştır. Ancak metodun hız, kolaylık ve maliyet açılarından sınırlamaları bulunmaktadır. Yeni nesil dizileme yaklaşımları çok sayıda paralel analiz, yüksek verimlilik ve düşük maliyetler açısından önem taşımaktadır. Bu derlemede, yeni nesil dizileme işlemleri için gerekli olan yeterli miktarda ışımayı sağlayacak kalıp DNA amplifikasyonunun yapıldığı Emülsiyon PCR yaklaşımı açıklanmıştır. Ayrıca yeni nesil dizileme yaklaşımları; piro dizileme, dönüştürülebilir terminatör dizileme, ligasyon yaklaşımlı dizileme, nanopor dizileme ve yarı iletken dizileme yaklaşımlarının biyokimyasal temelleri açıklanmıştır.   

Anahtar kelimeler: emülsiyon PCR, piro dizileme, dönüştürülebilir terminatör dizileme, ligasyon dizileme, nanopor dizileme, yarı iletken dizileme      

 

Biochemical Basis of New Generation Nucleotide Sequencing Methods

 

ABSTRACT : Sanger and Maxam-Gilbert sequencing methods are pronounced as the first generation sequencing. Chain termination sequencing approach is widely used and the first human genome project was completed by this method. However, this method has certain limitations especially in terms of speed, ease of use and cost. New generation sequencing approaches are important thanks to their capacity to work with many parallels, high efficiency and low cost. In this review, emulsion PCR approach, which is required for the amplification of template DNA so that it can produce sufficient amount of emission on the next generation sequencing, is described. Moreover, biochemical basis of the new generation sequencing approaches; pyro sequencing, reversible terminator sequencing, ligation sequencing, nanopore sequencing and semiconductor sequencing, are also described. 

Key words: emulsion PCR, pyrosequencing, reversible terminator sequencing, ligation sequencing, nanopore sequencing, semiconductor sequencing

Kaynakça

• Akeson M, Branton D, Kasianowicz JJ, Brandin E, Deamer DW 1999. Microsecond Time-Scale Discrimination Among Polycytidylic Acid, Polyadenylic Acid, and Polyuridylic Acid As Homopolymers or As Segments Within Single RNA Molecules. Biophys J, 77(6):3227-3233.
• Ansorge WJ, 2009. Next-Generation DNA Sequencing Techniques. New Biotechnol, 25(4):195-203.
• Ansorge W, Sproat B, Stegemann J, Schwager C, Zenke M 1987. Automated DNA Sequencing - Ultrasensitive Detection of Fluorescent Bands during Electrophoresis. Nucleic Acids Res, 15(11):4593-4602.
• Bayley H, 2006. Sequencing Single Molecules Of DNA. Curr Opin Chem Biol, 10(6):628-637.
• Bentley DR 2006. Whole-Genome Re-Sequencing. Curr Opin Genet Dev, 16(6):545-552.
• Bentley DR, Balasubramanian S, Swerdlow HP, Smith … , A.J. Smith. 2008. Accurate Whole Human Genome Sequencing Using Reversible Terminator Chemistry. Nature, 456(7218):53-59.
• Bhakdi S, Tranumjensen J 1991. Alpha-Toxin of Staphylococcus-Aureus. Microbiol Rev, 55(4):733-751.
• Bowers J, Mitchell J, Beer E, Buzby, PR, Causey …, Thompson, JF.2009. Virtual Terminator Nucleotides For Next-Generation DNA Sequencing. Nat Methods, 6(8):593-U560.
• Branton D, Deamer DW, Marziali, A. …, Schloss JA 2008. The Potential and Challenges Of Nanopore Sequencing. Nat Biotechnol, 26(10):1146-1153.
• Chen F, Gaucher EA, Leal NA, Hutter D, Havemann SA, Govindarajan S, Ortlund EA, Benner SA 2010. Reconstructed Evolutionary Adaptive Paths Give Polymerases Accepting Reversible Terminators For Sequencing and SNP Detection. P Natl Acad Sci, 107(5):1948-1953.
• Cherf GM, Lieberman KR, Rashid H, Lam CE, Karplus K, Akeson M 2012. Automated Forward And Reverse Ratcheting Of DNA In A Nanopore At 5-Angstrom Precision. Nat Biotechnol, 30(4):344-348.
• Deamer DW, Branton D 2002. Characterization of Nucleic Acids by Nanopore Analysis. Accounts Chem Ref, 35(10):817-825.
• Dekker C 2007. Solid-State Nanopores. Nat Nanotechnol, 2(4):209-215.
• Edwards A, Voss HP, Rice A, Civitello J, Stegemann C, Schwager J, Zimmermann H, Erfle C, Caskey T, Ansorge W 1990. Automated DNA Sequencing of the Human Hprt Locus. Genomics, 6(4):593-608.
• Eriksson J, Gharizadeh B, Nordstrom T, Nyren P 2004a. Pyrosequencing (TM) Technology at Elevated Temperature. Electrophoresis, 25(1):20-27.
• Eriksson J, Gharizadeh B, Nourizad N, Nyren P 2004b. 7-Deaza-2 '-Deoxyadenosine-5 '-Triphosphate as An Alternative Nucleotide for The Pyrosequencing Technology. Nucleos Nucleot Nucl, 23(10):1583-1594.
• Eriksson J, Nordstrom T, Nyren P 2003. Method Enabling Firefly Luciferase-Based Bioluminometric Assays at Elevated Temperatures. Anal Biochem, 314(1):158-161.
• Fields S 2007. Site-seeing by Sequencing. Science, 316(5830):1441-1442.
• Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang XH, Jovanovich SB, Nelson JR Schloss JA, Schwartz DC, Vezenov DV 2009. The Challenges of Sequencing by Synthesis. Nat Biotechnol, 27(11):1013-1023.
• Gardner AF, Wang JC, Wu, WD, Karouby J, Li H, Stupi BP, Jack WE, Hersh MN, Metzker ML 2012. Rapid Incorporation Kinetics and Improved Fidelity Of A Novel Class Of 3 '-OH Unblocked Reversible Terminators. Nucleic Acids Res, 40(15):7404-7415.
• Gharizadeh B, Ghaderi M, Donnelly D, Amini B, Wallin KL, Nyren P 2003a. Multiple-Primer DNA Sequencing Method. Electrophoresis, 24(7-8):1145-1151.
• Gharizadeh B, Ohlin A, Molling P, Backman A, Amini B, Olcen P, Nyren P 2003b. Multiple Group-Specific Sequencing Primers For Reliable and Rapid DNA Sequencing. Molecular and Cellular Probes, 17(4):203-210.
• Gharizadeh B, Eriksson J, Nourizad N, Nordstrom T, Nyren P 2004. Improvements in Pyrosequencing Technology by Employing Sequenase Polymerase. Anal Biochem, 330(2):272-280.
• Gharizadeh B, Oggionni M, Zheng B, Akom E, Pourmand N, Ahmadian A, Wallin KL, Nyren P 2005. Type-Specific Multiple Sequencing Primers: A Novel Strategy For Reliable And Rapid Genotyping Of Human Papillomaviruses By Pyrosequencing Technology. J Mol Diagn, 7(2):198-205.
• Gharizadeh B, Nordstrom T, Ahmadian A, Ronaghi M, Nyren P 2002. Long-Read Pyrosequencing Using Pure 2 '-Deoxyadenosine-5 '-O '-(1-Thiotriphosphate) Sp-Isomer. Anal Biochem, 301(1):82-90.
• Guo J, Yu L, Turro NJ, Ju JY 2010. An Integrated System for DNA Sequencing by Synthesis Using Novel Nucleotide Analogues. Accounts Chem Res, 43(4):551-563.
• Guo J, Xu N, Li ZM, Zhang SL, Wu J, Kim DH, Marma MS, Meng QL, Cao HY, Li XX, Shi SD, Yu L, Kalachikov S, Russo JJ, Turro NJ, Ju, JY 2008. Four-Color DNA Sequencing With 3'-O-Modified Nucleotide Reversible Terminators and Chemically Cleavable Fluorescent Dideoxynucleotides. P Natl Acad Sci, USA 105(27):9145-9150.
• Harrell CC, Choi Y, Horne LP, Baker LA, Siwy ZS, Martin CR 2006. Resistive-Pulse DNA Detection With A Conical Nanopore Sensor. Langmuir, 22(25):10837-10843.
• Healy K 2007. Nanopore-Based Single-Molecule DNA Analysis. Nanomedicine, 2(4):459-481.
• Hutter D, Kim MJ, Karalkar N, Leal NA, Chen F, Guggenheim E, Visalakshi V, Olejnik J, Gordon S, Benner SA 2010. Labeled Nucleoside Triphosphates with Reversibly Terminating Aminoalkoxyl Groups. Nucleos Nucleot Nucl, 29(11-12):879-895.
• Karamohamed S, Nyren P 1999. Real-time Detection And Quantification of Adenosine Triphosphate Sulfurylase Activity by A Bioluminometric Approach. Anal Biochem., 271(1):81-85.
• Kasianowicz JJ, Brandin E, Branton D, Deamer DW 1996. Characterization of Individual Polynucleotide Molecules Using A Membrane Channel. P Natl Acad Sci, 93(24):13770-13773.
• Li ZM, Bai XP, Ruparel H, Kim S, Turro NJ, Ju JY 2003. A Photocleavable Fluorescent Nucleotide For DNA Sequencing and Analysis. P Natl Acad Sci, USA, 100(2):414-419.
• Lieberman KR, Cherf GM, Doody MJ, Olasagasti F, Kolodji Y, Akeson M 2010. Processive Replication of Single DNA Molecules in a Nanopore Catalyzed by phi29 DNA Polymerase. J Am Chem Soc, 132(50):17961-17972.
• Litosh VA, Wu WD, Stupi BP, Wang JC, Morris SE, Hersh MN, Metzker ML 2011. Improved Nucleotide Selectivity And Termination Of 3'-OH Unblocked Reversible Terminators By Molecular Tuning Of 2-Nitrobenzyl Alkylated Homedu Triphosphates. Nucleic Acids Res, 39(6): 1-13.
• Liu L, Li Y, Li S, Hu N, He, Y, Pong R, Lin DN, Lu LH, Law M 2012. Comparison of Next-Generation Sequencing Systems. J Biomed Biotechnol, 2012 (2012): 1-11.
• Manrao EA, Derrington IM, Laszlo AH, Langford KW, Hopper MK, Gillgren N, Pavlenok M, Niederweis M, Gundlach JH 2012. Reading DNA At Single-Nucleotide Resolution With a Mutant Mspa Nanopore and Phi29 DNA Polymerase. Nat Biotechnol, 30(4):349-353.
• Mardis ER 2008. Next-Generation DNA Aequencing methods. Annu. Rev. Genom. Human Genet, 9: 387-402.
• Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, ... & Dewell, SB 2005. Genome Sequencing in Microfabricated High-Density Picolitre Reactors. Nature, 437(7057) 376-380.
• Meller A, Nivon L, Branton D 2001. Voltage-Driven DNA Translocations Through A Nanopore. Phys Rev Lett, 86(15):3435-3438.
• Meller A, Nivon L, Brandin E, Golovchenko J, Branton D 2000. Rapid Nanopore Discrimination Between Single Polynucleotide Molecules. P Natl Acad Sc, USA, 97(3):1079-1084.
• Metzker ML 2010. Applications of Next-Generation Sequencing Sequencing Technologies - The Next Generation. Nat Rev Genet, 11(1):31-46.
• Mikheyev AS, Tin MMY 2014. A First Look At The Oxford Nanopore Minion Sequencer. Mol Ecol Resour, 14(6):1097-1102.
• Nakane JJ, Akeson M, Marziali A 2003. Nanopore Sensors For Nucleic Acid Analysis. J Phys-Condens Mat, 15(32): 1365-1393.
• Nordstrom T, Alderborn A, Nyren P 2002. Method For One-Step Preparation of Double-Stranded DNA Template Applicable For Use With Pyrosequencing (TM) Technology. J Biochem Bioph Meth, 52(2):71-82.
• Nyren P 1994. Apyrase Immobilized On Paramagnetic Beads Used To Improve Detection Limits In Bioluminometric Atp Monitoring. J Biolum Chemilum, 9(1):29-34.
• Pennisi E 2010. Genomics Semiconductors Inspire New Sequencing Technologies. Science, 327(5970):1190-1190.
• Perkel J 2011. Making Contact with Sequencing's Fourth Generation. Biotechniques, 50(2):93-95.
• Purushothaman S, Toumazou C, Ou CP 2006. Protons and Single Nucleotide Polymorphism Detection: A Simple Use for The Ion Sensitive Field Effect Transistor. Sensor Actuat B-Chem, 114(2):964-968.
• Ronaghi M 2000. Improved Performance of Pyrosequencing Using Single-Stranded DNA-Binding Protein. Anal Biochem, 286(2):282-288.
• Ronaghi M, Uhlen M, Nyren P 1998. A Sequencing Method Based on Real-Time Pyrophosphate. Science, 281(5375):363-365.
• Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P 1996. Real-Time DNA Sequencing Using Detection of Pyrophosphate Release. Anal Biochem, 242(1):84-89.
• Rusk N 2011. Torrents of Sequence. Nat Methods, 8(1):44-44.
• Shendure J, Ji HL 2008. Next-Generation DNA Sequencing. Nat Biotechnol, 26(10):1135-1145.
• Smith LM, Sanders JZ, Kaiser RJ, Hughes P, Dodd C, Connell CR, Heiner C, Kent SBH, Hood LE 1986. Fluorescence Detection in Automated DNA-Sequence Analysis Nature, 321(6071):674-679.
• Wu W, Stupi BP, Litosh VA, Mansouri D, Farley D, Morris S, Metzker S, Metzker ML 2007. Termination of DNA Synthesis by N-6-Alkylated, Not 3-O-Alkylated, Photocleavable 2-Deoxyadenosine Triphosphates. Nucleic Acids Res, 35(19):6339-6349.