Suppression subtractive hybridization

Nucleic Acids Hybridization: Modern Applications

Volumn , Issue , 2007, Pages 53-84

  Lukyanov, Sergey A ^a   Rebrikov, Denis ^a   Buzdin, Anton A ^a  

^a SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

Author keywords

adapter sequence; background; cap switch; differential screening; Differentially regulated genes; disadvantage; drawback; efficiency of SSH; enrichment; equalization; false positive; heat denaturation; high complexity; highly abundant cDNA; hybridization time; level of enrichment; mathematical model; mirror orientation selection; mirror oriented selection (MOS); Northern blot; physical separation; primer annealing site; protocol; random clones; reannealing; removal of the adapter sequences; restriction endonuclease; size of cDNA fragments; suppression polymerase chain reaction (PCR) effect; tagging RNA 5 ends; target sequence; technical comments

Indexed keywords

EID: 77957769435     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4020-6040-3_3     Document Type: Chapter

References (29)

1. Akopyants NS, Fradkov A, Diatchenko L, Hill JE, Siebert PD, Lukyanov SA, Sverdlov ED, Berg DE (1998) PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori. Proc Natl Acad Sci USA 95:13108-13113.
2. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162:156-159.
3. Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert PD (1996) Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93:6025-6030.
4. Ermolaeva OD, Wagner MC (1995) SUBTRACT: A computer program for modeling the process of subtractive hydridization. Comput Appl Biosci 11:457-462.
5. Ermolaeva OD, Lukyanov SA, Sverdlov ED (1996) The mathematical model of subtractive hybridization and its practical application. Proc Int Conf Intell Syst Mol Biol 4:52-58.
6. Garcia-Fernandez J, Marfany G, Baguna J, Salo E (1993) Infiltration of mariner elements. Nature 364:109-110.
7. Gubler U, Hoffman BJ (1983) A simple and very efficient method for generating cDNA libraries. Gene 25:263-269.
8. Gurskaya NG, Diatchenko L, Chenchik A, Siebert PD, Khaspekov GL, Lukyanov KA, Vagner LL, Ermolaeva OD, Lukyanov SA, Sverdlov ED (1996) Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate. Anal Biochem 240:90-97.
9. Hames BD, Higgins SJ (eds) (1985) Nucleic acid hybridization. A practical approach. IRL Press, Oxford, Washington, DC.
10. Hara E, Kato T, Nakada S, Sekiya S, Oda K (1991) Subtractive cDNA cloning using oligo(dT)30- latex and PCR: isolation of cDNA clones specific to undifferentiated human embryonal carcinoma cells. Nucleic Acids Res 19:7097-7104.
11. Hedrick SM, Cohen DI, Nielsen EA, Davis MM (1984) Isolation of cDNA clones encoding T cellspecific membrane-associated proteins. Nature 308:149-153.
12. Hubank M, Schatz DG (1994) Identifying differences in mRNA expression by representational difference analysis of cDNA. Nucleic Acids Res 22:5640-5648.
13. Jin H, Cheng X, Diatchenko L, Siebert PD, Huang CC (1997) Differential screening of a subtracted cDNA library: A method to search for genes preferentially expressed in multiple tissues. Biotechniques 23:1084-1086.
14. Kellogg DE, Rybalkin I, Chen S, Mukhamedova N, Vlasik T, Siebert PD, Chenchik A (1994) TaqStart Antibody: "hot start" PCR facilitated by a neutralizing monoclonal antibody directed against Taq DNA polymerase. Biotechniques 16:1134-1137.
15. Ko MS (1990) An "equalized cDNA library" by the reassociation of short double-stranded cDNAs. Nucleic Acids Res 18:5705-5711.
16. Luk'ianov KA, Gurskaia NG, Bogdanova EA, Luk'ianov SA (1999) Selective suppression of polymerase chain reaction. Bioorg Khim 25:163-170.
17. Luk'ianov SA, Gurskaia NG, Luk'ianov KA, Tarabykin VS, Sverdlov ED (1994) Highly-effective subtractive hybridization of cDNA. Bioorg Khim 20:701-704.
18. Lukyanov K, Diatchenko L, Chenchik A, Nanisetti A, Siebert P, Usman N, Matz M, Lukyanov S (1997) Construction of cDNA libraries from small amounts of total RNA using the suppression PCR effect. Biochem Biophys Res Commun 230:285-288.
19. Lukyanov KA, Launer GA, Tarabykin VS, Zaraisky AG, Lukyanov SA (1995) Inverted terminal repeats permit the average length of amplified DNA fragments to be regulated during preparation of cDNA libraries by polymerase chain reaction. Anal Biochem 229:198-202.
20. Lukyanov KA, Matz MV, Bogdanova EA, Gurskaya NG, Lukyanov SA (1996) Molecule by molecule PCR amplification of complex DNA mixtures for direct sequencing: An approach to in vitro cloning. Nucleic Acids Res 24:2194-2195.
21. Maruyama K, Sugano S (1994) Oligo-capping: A simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138:171-174.
22. Rebrikov DV, Britanova OV, Gurskaya NG, Lukyanov KA, Tarabykin VS, Lukyanov SA (2000) Mirror orientation selection (MOS): A method for eliminating false positive clones from libraries generated by suppression subtractive hybridization. Nucleic Acids Res 28:e90.
23. Rebrikov DV, Desai SM, Siebert PD, Lukyanov SA (2004) Suppression subtractive hybridization. Methods Mol Biol 258:107-134.
24. Sargent TD, Dawid IB (1983) Differential gene expression in the gastrula of Xenopus laevis. Science 222:135-139.
25. Siebert PD, Chenchik A, Kellogg DE, Lukyanov KA, Lukyanov SA (1995) An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res 23:1087-1088.
26. Takarada Y (1994) Highly sensitive and specific amplification by primer digestion. Nucleic Acids Res 22:2170-2172.
27. Wang Z, Brown DD (1991) A gene expression screen. Proc Natl Acad Sci USA 88:11505-11509.
28. Zhumabayeva B, Chang C, McKinley J, Diatchenko L, Siebert PD (2001a) Generation of full-length cDNA libraries enriched for differentially expressed genes for functional genomics. Biotechniques 30:512-516, 518-520.
29. Zhumabayeva B, Diatchenko L, Chenchik A, Siebert PD (2001b) Use of SMART-generated cDNA for gene expression studies in multiple human tumors. Biotechniques 30:158-163.