Chromosomal detection of simple sequence repeats (SSRs) using nondenaturing FISH (ND-FISH).
Simple Sequence Repeats (SSRs) are known to be scattered and present in high number in eukaryotic genomes. We demonstrate that dye-labeled oligodeoxyribonucleotides with repeated mono-, di-, tri, or tetranucleotide motifs (15-20 nucleotides in length) have an unexpected ability to recognize SSR target sequences in non-denatured chromosomes. The results show that all these probes are able to invade chromosomes, independent of the size of the repeat motif, their nucleotide sequence, or their ability to form alternative B-DNA structures such as triplex DNA. This novel and remarkable property of binding SSR oligonucleotides to duplex DNA targets permitted the development of a non-denaturing fluorescence in situ hybridization method that quickly and efficiently detects SSR-enriched chromosome regions in mitotic, meiotic, and polytene chromosome spreads of different model organisms. These results have implications for genome analysis and for investigating the roles of SSRs in chromosome structure and function.
Cuadrado
Ángeles
Á
Department of Cell Biology and Genetics, University of Alcalá de Henares, 28871, Alcalá de Henares, Madrid, Spain. angeles.cuadrado@uah.es
Jouve
Nicolás
N
D000818:Animals; D032461:Chromosomes, Plant / Q000737:chemistry*; D004247:DNA; D004331:Drosophila melanogaster / Q000235:genetics; D001467:Hordeum / Q000235:genetics; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D018895:Microsatellite Repeats; D015345:Oligonucleotide Probes
D015345:Oligonucleotide Probes; C051802:triplex DNA; D004247:DNA
Nucleic Acids Res. 1984 May 25;12(10):4127-38
6328411
Nucleic Acids Res. 1979 Dec 11;7(7):1869-85
537913
Genomics. 1992 Apr;12(4):627-31
1572635
Mol Cell Probes. 2003 Aug;17(4):165-9
12944118
Curr Med Chem. 2000 Jan;7(1):17-37
10637355
Chromosome Res. 1994 Jan;2(1):65-71
8162323
Electrophoresis. 1991 Feb-Mar;12(2-3):193-203
2040266
Proc Natl Acad Sci U S A. 1996 Aug 6;93(16):8761-5
8710945
Mol Cell Biol. 1989 Mar;9(3):1173-82
2725493
Am J Hum Genet. 1999 Feb;64(2):346-53
9973271
Mol Biol Evol. 2001 Jul;18(7):1161-7
11420357
Genes Dev. 2005 Jul 15;19(14):1635-55
16024654
BMC Genomics. 2005 Feb 18;6:23
15720707
Chromosome Res. 2009;17(6):755-62
19669910
Chromosoma. 2002 Sep;111(3):201-13
12355210
EMBO J. 1987 Jun;6(6):1781-9
3111846
Genome Res. 2000 Jul;10(7):967-81
10899146
Methods Mol Biol. 2009;558:433-44
19685339
J Hered. 1988 Nov-Dec;79(6):409-17
3062083
Nucleic Acids Res. 2000 Sep 1;28(17):3332-8
10954602
Chromosoma. 1999 Jul;108(3):181-9
10398847
Chromosoma. 1998 Dec;107(8):587-94
9933412
Bioinformatics. 2003 Apr 12;19(6):681-5
12691979
Expert Rev Mol Diagn. 2003 Jul;3(4):481-96
12877387
Chromosome Res. 2007;15(6):711-20
17874212
Cell Res. 2008 Jan;18(1):198-213
18166978
Chromosoma. 1988;96(3):213-9
3282831
Genetics. 1993 Aug;134(4):1149-74
8375654
Nature. 2007 May 24;447(7143):399-406
17522672
Genetica. 2002 May;115(1):93-103
12188051
Curr Opin Cell Biol. 1997 Jun;9(3):364-72
9159084
Cytogenet Genome Res. 2008;120(3-4):210-9
18504349
Nature. 1985 Mar 7-13;314(6006):67-73
3856104
EMBO J. 1994 Dec 15;13(24):5977-83
7813435
Biosci Biotechnol Biochem. 2007 Feb;71(2):627-32
17284819
Cytogenet Genome Res. 2007;119(1-2):91-9
18160787