Abstract
The DNA mismatch repair (MMR) pathway plays a prominent role in the correction of errors made during DNA replication and genetic recombination and in the repair of small deletions and loops in DNA. Mismatched nucleotides can occur by replication errors, damage to nucleotide precursors, damage to DNA, or during heteroduplex formation between two homologous DNA molecules in the process of genetic recombination. Defects in MMR can precipitate instability in simple sequence repeats (SSRs), also referred to as microsatellite instability (MSI), which appears to be important in certain types of cancers, both spontaneous and hereditary. Variations in the highly polymorphic alleles of specific microsatellite repeats can be identified using PCR with primers derived from the unique flanking sequences. These PCR products are analyzed on denaturing polyacrylamide gels to resolve differences in allele sizes of >2 bp. Although (CA)n repeats are the most abundant class among dinucleotide SSRs, trinucleotide and tetranucleotide repeats are also frequent. These polymorphic repeats have the advantage of producing band patterns that are easy to analyze and can be used as an indication of a possible MMR defect in a cell. The presumed association between such allelic variation and an MMR defect should be confirmed by molecular analysis of the structure and/or expression of MMR genes.
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References
Fishel R, Acharya S, Berardini M et al (2000) Signalling mismatch repair: the mechanics of an adenosine-nucleotide molecular switch. Cold Spring Harbor Symp Quant Biol 65:217–224
Yang W, Junop MS, Ban C, Obmolova G, Hsieh P (2000) DNA mismatch repair: from structure to mechanism. Cold Spring Harbor Symp Quant Biol 65:225–232
Modrich P, Lahue R (1996) Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Annu Rev Biochem 65:101–133
Schär P, Jiricny J (1998) Eukaryotic mismatch repair. In: Eckstein F, Lilley DMJ (eds) Nucleic acids and molecular biology, vol 12. Springer, New York, pp 199–247
Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445
Minnick DT, Kunkel TA (1996) DNA synthesis errors, mutators and cancer. Cancer Surv 28:3–20
Buermeyer AB, Deshenes SM, Baker SM, Liskey RM (1999) Mammalian DNA mismatch repair. Annu Rev Genet 33:533–564
Bebenek K, Kunkel TA (2000) Streisinger revisited: DNA synthesis errors mediated by substrate misalignments. Cold Spring Harbor Symp Quant Biol 65:81–91
Peltomäki P, Lothe RA, Aaltonen LA et al (1993) Microsatellite instability is associated with tumors that characterize the hereditary non-polyposis colorectal carcinoma syndrome. Cancer Res 53:5853–5855
Saha A, Dhir A, Ranjan A, Gupta V, Bairwa N, Bamezai R (2005) Functional IFNG polymorphism in intron 1 in association with an increased risk to promote sporadic breast cancer. Immunogenetics 57:165–171
Saha A, Bairwa NK, Ranjan A, Gupta V, Bamezai R (2003) Two novel somatic mutations in the human interleukin 6 promoter region in a patient with sporadic breast cancer. Eur J Immunogenet 30:397–400
Mueller J, Gazzoli I, Bandipalliam P, Garber JE, Syngal S, Kolodner RD (2009) Comprehensive molecular analysis of mismatch repair gene defects in suspected Lynch syndrome (hereditary nonpolyposis colorectal cancer) cases. Cancer Res 69:7053–7061
Wenger SL, Senft JR, Sargent LM, Bamezai R, Bairwa N, Grant SG (2004) Comparison of established cell lines at different passages by karyotype and comparative genomic hybridization. Biosci Rep 24:631–639
Miller JH, Yeung A, Funchain P et al (2000) Temporary and permanent mutators lacking the mismatch repair system: the enhancement of mutators in cell populations. Cold Spring Harbor Symp Quant Biol 65:241–252
Jiricny J (1998) Replication errors: cha(lle)nging the genome. EMBO J 17:6427–6436
Kolodner RD (1995) Mismatch repair: mechanisms and relationship to cancer susceptibility. Trends Biochem Sci 20:397–401
Jiricny J (1996) Mismatch repair and cancer. Cancer Surv 28:47–68
Papadopoulos N, Nicolaides NC, Liu B et al (1995) Mutations of GTBP in genetically unstable cells. Science 268:1915–1917
Kunkel TA (1993) Nucleotide repeats. Slippery DNA and diseases. Nature 365:207–208
Palombo F, Iaccarino L, Nakajima E, Ikcjima M, Shimada T, Jiricny J (1996) hMutSβ, a heterodimer of hMSH2 and hMSH3, binds to insertion/deletion loops in DNA. Curr Biol 6:1181–1184
Iaccarino L, Marra G, Dufner P, Jiricny J (2000) Mutation in the magnesium binding site of hMSH6 disables the hMutSα sliding clamp from translocating along DNA. J Biol Chem 275:2080–2086
Mir MM, Dar NA, Gochhait S, Zargar SA, Ahangar AG, Bamezai RN (2005) p53 mutation profile of squamous cell carcinomas of the esophagus in Kashmir (India): a high-incidence area. Int J Cancer 116:62–68
Don RH, Cox PT, Wainwright BJ, Baker K, Mattick JS (1991) ‘Touchdown’ PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19:4008
Harada S, Komatsu H, Seto M et al (1998) Microsatellite instability is rare in the clinical course of myelodysplastic syndrome studied with DNA from fresh and paraffin-embedded tissues. J Cancer Res Clin Oncol 124:231–235
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Bairwa, N.K., Saha, A., Gochhait, S., Pal, R., Gupta, V., Bamezai, R.N.K. (2014). Microsatellite Instability: An Indirect Assay to Detect Defects in the Cellular Mismatch Repair Machinery. In: Keohavong, P., Grant, S. (eds) Molecular Toxicology Protocols. Methods in Molecular Biology, vol 1105. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-739-6_35
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DOI: https://doi.org/10.1007/978-1-62703-739-6_35
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