REVIEW

Molecular biology applications of the red king crab duplex-specific nuclease

About authors

1 Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia

2 Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia

Correspondence should be addressed: Denis V. Rebrikov
Oparina, 4, Moscow, 117997, Russia; moc.liamg@4pigacn

About paper

Funding: the study was supported by the grant no. 075-15-2019-1789, Center for High Precision Genomic Editing and Genetic Technologies for Biomedicine.

Author contribution: DA Shagin — preparation of the manuscript; DV Rebrikov — editing of the manuscript.

Received: 2022-02-22 Accepted: 2022-02-27 Published online: 2022-02-28
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  1. Shagin DA, Rebrikov DV, Kozhemyako VB, Altshuler IM, Shcheglov AS, Zhulidov PA, Bogdanova EA, Staroverov DB, Rasskazov VA, Lukyanov S. A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. Genome Res. 2002; 12 (12): 1935–42. DOI: 10.1101/gr.547002.
  2. Anisimova VE, Rebrikov DV, Shagin DA, Kozhemyako VB, Menzorova NI, Staroverov DB, Ziganshin R, Vagner LL, Rasskazov VA, Lukyanov SA, Shcheglov AS. Isolation, characterization and molecular cloning of duplex-specific nuclease from the hepatopancreas of the Kamchatka crab. BMC Biochem. 2008; 9: 14. DOI: 10.1186/1471-2091-9-14.
  3. Anisimova VE, Rebrikov DV, Zhulidov PA, Staroverov DB, Lukyanov SA, Shcheglov AS. Renaturation, activation, and practical use of recombinant duplex-specific nuclease from Kamchatka crab. Biochemistry (Mosc). 2006; 71: 513–9. DOI: 10.1134/s0006297906050075.
  4. Anisimova VE, Shcheglov AS, Bogdanova EA, Rebrikov DV, Nekrasov AN, Barsova EV, Shagin DA, Lukyanov SA. Is crab duplex-specific nuclease a member of the Serratia family of nonspecific nucleases? Gene. 2008; 418: 41–8. DOI: 10.1016/j. gene.2008.04.005.
  5. Vodolazhsky DI, Mayakovskaya AV, Kubyshkin AV, Aliev KA, Fomochkina II. Clinical significance of gene polymorphisms for hereditary predisposition to breast and ovarian cancer (review of literature). Klin Lab Diagn. 2021; 66 (12): 760–67. English. DOI: 10.51620/0869-2084-2021-66-12-760-767.
  6. Yan M, Fan X, Si H, Wang X, Wang Z, Wang Z, Lv X, Yin H, Jia Y, Jiang L, Xia Y, Liu Y. Association between gene polymorphism and adverse effects in cancer patients receiving docetaxel treatment: a meta-analysis. Cancer Chemother Pharmacol. 2022; 89 (2): 173–181. DOI: 10.1007/s00280-021-04374-3.
  7. Haddrill PR. Developments in forensic DNA analysis. Emerg Top Life Sci. 2021; 5 (3): 381–393. DOI: 10.1042/ETLS20200304.
  8. Kling D, Phillips C, Kennett D, Tillmar A. Investigative genetic genealogy: Current methods, knowledge and practice. Forensic Sci Int Genet. 2021; 52: 102474. DOI: 10.1016/j. fsigen.2021.102474.
  9. Borinskaya SA, Gureev AS, Orlova AA, Sanina ED, Kim AA, Gasemianrodsari F, Shirmanov VI, Balanovsky OP, Rebrikov DV, Koshechkin AV, Yankovsky NK. [Allele frequency distributions of -174G/C polymorphism in regulatory region of interleukin 6 gene (IL6) in Russian and worldwide populations]. Genetika. 2013; 49 (1): 113–24. Russian. DOI: 10.7868/s0016675813010037.
  10. Al'tshuler IM, Zhulidov PA, Bogdanova EA, Mudrik NN, Shagin DA. [Application of the duplex-specific nuclease preference method to the analysis of point mutations in human genes]. Bioorg Khim. 2005; 31 (6): 627–36. Russian.
  11. Syvänen AC. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet. 2001; 2 (12): 930–42. DOI: 10.1038/35103535.
  12. Syvänen AC, Taylor GR. Approaches for analyzing human mutations and nucleotide sequence variation: a report from the Seventh International Mutation Detection meeting, 2003. Hum Mutat. 2004; 23 (5): 401–5. DOI: 10.1002/humu.20031.
  13. Stewart CA, Horton R, Allcock RJ, Ashurst JL, Atrazhev AM, Coggill P, Dunham I, Forbes S, Halls K, Howson JM, Humphray SJ, Hunt S, Mungall AJ, Osoegawa K, Palmer S, Roberts AN, Rogers J, Sims S, Wang Y, Wilming LG, Elliott JF, de Jong PJ, Sawcer S, Todd JA, Trowsdale J, Beck S. Complete MHC haplotype sequencing for common disease gene mapping. Genome Res. 2004; 14 (6): 1176–87. DOI: 10.1101/gr.2188104.
  14. Mu DQ, Peng YS, Xu QJ. Values of mutations of K-ras oncogene at codon 12 in detection of pancreatic cancer: 15-year experience. World J Gastroenterol. 2004;10 (4): 471–5. DOI: 10.3748/wjg.v10.i4.471.
  15. Itabashi T, Maesawa C, Uchiyama M, Higuchi T, Masuda T. Quantitative detection of mutant alleles of the K-ras gene with minor groove binder-conjugated fluorogenic DNA probes. Int J Oncol. 2004; 24 (3): 687–96.
  16. Young BD, Anderson MLM. Quantitative analysis of solution hybridisation. In: Hames BD, Higgins SJ, eds. Nucleic acid hybridisation: a practical approach. Pp. 47–71. Oxford: IRL Press Limited, 1985.
  17. Ko MS. An 'equalized cDNA library' by the reassociation of short double-stranded cDNAs. Nucleic Acids Res. 1990; 18 (19): 5705–11. DOI: 10.1093/nar/18.19.5705.
  18. Coche T, Dewez M. Reducing bias in cDNA sequence representation by molecular selection. Nucleic Acids Res. 1994 Oct 25; 22 (21): 4545–6. DOI: 10.1093/nar/22.21.4545.
  19. Carninci P, Shibata Y, Hayatsu N, Sugahara Y, Shibata K, Itoh M, Konno H, Okazaki Y, Muramatsu M, Hayashizaki Y. Normalization and subtraction of cap-trapper-selected cDNAs to prepare fulllength cDNA libraries for rapid discovery of new genes. Genome Res. 2000; 10 (10): 1617–30. DOI: 10.1101/gr.145100.
  20. Soares MB, Bonaldo MF, Jelene P, Su L, Lawton L, Efstratiadis A. Construction and characterization of a normalized cDNA library. Proc Natl Acad Sci U S A. 1994; 91 (20): 9228–32. DOI: 10.1073/ pnas.91.20.9228.
  21. Sasaki YF, Ayusawa D, Oishi M. Construction of a normalized cDNA library by introduction of a semi-solid mRNA-cDNA hybridization system. Nucleic Acids Res. 1994; 22 (6): 987–92. DOI: 10.1093/nar/22.6.987.
  22. Luk'ianov KA, Gurskaia NG, Matts MV, Khaspekov GL, D'iachenko LB, Chenchik AA, Il'evich-Stuchkov SG, Luk'ianov SA. Metod polucheniia normalizovannykh bibliotek kDNK, osnovannyĭ na éffekte supressii polimeraznoĭ tsepnoĭ reaktsii [A method for obtaining the normalized cDNA libraries based on the effect of suppression of polymerase chain reaction]. Bioorg Khim. 1996; 22 (9): 686–90. Russian.
  23. Zhulidov PA, Bogdanova EA, Shcheglov AS, Vagner LL, Khaspekov GL, Kozhemyako VB, Matz MV, Meleshkevitch E, Moroz LL, Lukyanov SA, Shagin DA. Simple cDNA normalization using kamchatka crab duplex-specific nuclease. Nucleic Acids Res. 2004; 32 (3): e37. DOI: 10.1093/nar/gnh031.
  24. Shagin DA, Lukyanov KA, Vagner LL, Matz MV. Regulation of average length of complex PCR product. Nucleic Acids Res. 1999; 27 (18): e23. DOI: 10.1093/nar/27.18.e23.
  25. Song C, Liu Y, Fontana R, Makrigiorgos A, Mamon H, Kulke MH, Makrigiorgos GM. Elimination of unaltered DNA in mixed clinical samples via nuclease-assisted minor-allele enrichment. Nucleic Acids Res. 2016; 44 (19): e146. DOI: 10.1093/nar/ gkw650.
  26. Yuan Y, SanMiguel PJ, Bennetzen JL. Methylation-spanning linker libraries link gene-rich regions and identify epigenetic boundaries in Zea mays. Genome Res. 2002; 12 (9): 1345–9. DOI: 10.1101/ gr.185902.
  27. Emberton J, Ma J, Yuan Y, SanMiguel P, Bennetzen JL. Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Res. 2005; 15 (10): 1441–6. DOI: 10.1101/gr.3362105.
  28. Palmer LE, Rabinowicz PD, O'Shaughnessy AL, Balija VS, Nascimento LU, Dike S, de la Bastide M, Martienssen RA, McCombie WR. Maize genome sequencing by methylation filtration. Science. 2003; 302 (5653): 2115–7. DOI: 10.1126/science.1091265.
  29. Peterson DG, Schulze SR, Sciara EB, Lee SA, Bowers JE, Nagel A, Jiang N, Tibbitts DC, Wessler SR, Paterson AH. Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res. 2002; 12 (5): 795–807. DOI: 10.1101/gr.226102.
  30. Yuan Y, SanMiguel PJ, Bennetzen JL. High-Cot sequence analysis of the maize genome. Plant J. 2003; 34 (2): 249–55. DOI: 10.1046/j.1365-313x.2003.01716.x.
  31. Shagina I, Bogdanova E, Mamedov IZ, Lebedev Y, Lukyanov S, Shagin D. Normalization of genomic DNA using duplexspecific nuclease. Biotechniques. 2010; 48 (6): 455–9. DOI: 10.2144/000113422.
  32. Deng H, Ren Y, Shen W, Gao Z. An ultrasensitive homogeneous chemiluminescent assay for microRNAs. Chem Commun (Camb). 2013; 49 (82): 9401–3. DOI: 10.1039/c3cc44824j.
  33. Shen W, Yeo KH, Gao Z. A simple and highly sensitive fluorescence assay for microRNAs. Analyst. 2015; 140 (6): 1932–8. DOI: 10.1039/c4an02146k.