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. 1994 Jan 4;91(1):88–92. doi: 10.1073/pnas.91.1.88

Construction of libraries enriched for sequence repeats and jumping clones, and hybridization selection for region-specific markers.

R P Kandpal 1, G Kandpal 1, S M Weissman 1
PMCID: PMC42891  PMID: 8278412

Abstract

We describe a simple and rapid method for constructing small-insert genomic libraries highly enriched for dimeric, trimeric, and tetrameric nucleotide repeat motifs. The approach involves use of DNA inserts recovered by PCR amplification of a small-insert sonicated genomic phage library or by a single-primer PCR amplification of Mbo I-digested and adaptor-ligated genomic DNA. The genomic DNA inserts are heat denatured and hybridized to a biotinylated oligonucleotide. The biotinylated hybrids are retained on a Vectrex-avidin matrix and eluted specifically. The eluate is PCR amplified and cloned. More than 90% of the clones in a library enriched for (CA)n microsatellites with this approach contained clones with inserts containing CA repeats. We have also used this protocol for enrichment of (CAG)n and (AGAT)n sequence repeats and for Not I jumping clones. We have used the enriched libraries with an adaptation of the cDNA selection method to enrich for repeat motifs encoded in yeast artificial chromosomes.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abe K. Rapid isolation of desired sequences from lone linker PCR amplified cDNA mixtures: application to identification and recovery of expressed sequences in cloned genomic DNA. Mamm Genome. 1992;2(4):252–259. doi: 10.1007/BF00355435. [DOI] [PubMed] [Google Scholar]
  2. Bellanné-Chantelot C., Lacroix B., Ougen P., Billault A., Beaufils S., Bertrand S., Georges I., Glibert F., Gros I., Lucotte G. Mapping the whole human genome by fingerprinting yeast artificial chromosomes. Cell. 1992 Sep 18;70(6):1059–1068. doi: 10.1016/0092-8674(92)90254-a. [DOI] [PubMed] [Google Scholar]
  3. Chumakov I., Rigault P., Guillou S., Ougen P., Billaut A., Guasconi G., Gervy P., LeGall I., Soularue P., Grinas L. Continuum of overlapping clones spanning the entire human chromosome 21q. Nature. 1992 Oct 1;359(6394):380–387. doi: 10.1038/359380a0. [DOI] [PubMed] [Google Scholar]
  4. Church G. M., Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. doi: 10.1073/pnas.81.7.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dietrich W., Katz H., Lincoln S. E., Shin H. S., Friedman J., Dracopoli N. C., Lander E. S. A genetic map of the mouse suitable for typing intraspecific crosses. Genetics. 1992 Jun;131(2):423–447. doi: 10.1093/genetics/131.2.423. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Edwards A., Civitello A., Hammond H. A., Caskey C. T. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet. 1991 Oct;49(4):746–756. [PMC free article] [PubMed] [Google Scholar]
  7. Edwards A., Gibbs R. A., Nguyen P. N., Ansorge W., Caskey C. T. Automated DNA sequencing methods for detection and analysis of mutations: applications to the Lesch-Nyhan syndrome. Trans Assoc Am Physicians. 1989;102:185–194. [PubMed] [Google Scholar]
  8. Feinberg A. P., Vogelstein B. "A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity". Addendum. Anal Biochem. 1984 Feb;137(1):266–267. doi: 10.1016/0003-2697(84)90381-6. [DOI] [PubMed] [Google Scholar]
  9. Foote S., Vollrath D., Hilton A., Page D. C. The human Y chromosome: overlapping DNA clones spanning the euchromatic region. Science. 1992 Oct 2;258(5079):60–66. doi: 10.1126/science.1359640. [DOI] [PubMed] [Google Scholar]
  10. Harper P. S., Harley H. G., Reardon W., Shaw D. J. Anticipation in myotonic dystrophy: new light on an old problem. Am J Hum Genet. 1992 Jul;51(1):10–16. [PMC free article] [PubMed] [Google Scholar]
  11. Ichikawa H., Shimizu K., Saito A., Wang D. N., Oliva R., Kobayashi H., Kaneko Y., Miyoshi H., Smith C. L., Cantor C. R. Long-distance restriction mapping of the proximal long arm of human chromosome 21 with Not I linking clones. Proc Natl Acad Sci U S A. 1992 Jan 1;89(1):23–27. doi: 10.1073/pnas.89.1.23. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ito T., Smith C. L., Cantor C. R. Sequence-specific DNA purification by triplex affinity capture. Proc Natl Acad Sci U S A. 1992 Jan 15;89(2):495–498. doi: 10.1073/pnas.89.2.495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kandpal R. P., Shukla H., Ward D. C., Weissman S. M. A polymerase chain reaction approach for constructing jumping and linking libraries. Nucleic Acids Res. 1990 May 25;18(10):3081–3081. doi: 10.1093/nar/18.10.3081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lee J., Weissman S. M. Construction of lambda gt103, a derivative of phage lambda gt10 that has unique EcoRI, NotI, SacI and SpeI sites and retains positive selection for recombinants. Gene. 1992 Oct 12;120(1):85–88. doi: 10.1016/0378-1119(92)90012-e. [DOI] [PubMed] [Google Scholar]
  15. Litt M., Luty J. A. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet. 1989 Mar;44(3):397–401. [PMC free article] [PubMed] [Google Scholar]
  16. Lovett M., Kere J., Hinton L. M. Direct selection: a method for the isolation of cDNAs encoded by large genomic regions. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9628–9632. doi: 10.1073/pnas.88.21.9628. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Ostrander E. A., Jong P. M., Rine J., Duyk G. Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3419–3423. doi: 10.1073/pnas.89.8.3419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Parimoo S., Patanjali S. R., Shukla H., Chaplin D. D., Weissman S. M. cDNA selection: efficient PCR approach for the selection of cDNAs encoded in large chromosomal DNA fragments. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9623–9627. doi: 10.1073/pnas.88.21.9623. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Poustka A., Pohl T. M., Barlow D. P., Frischauf A. M., Lehrach H. Construction and use of human chromosome jumping libraries from NotI-digested DNA. Nature. 1987 Jan 22;325(6102):353–355. doi: 10.1038/325353a0. [DOI] [PubMed] [Google Scholar]
  20. Schlessinger D., Little R. D., Freije D., Abidi F., Zucchi I., Porta G., Pilia G., Nagaraja R., Johnson S. K., Yoon J. Y. Yeast artificial chromosome-based genome mapping: some lessons from Xq24-q28. Genomics. 1991 Dec;11(4):783–793. doi: 10.1016/0888-7543(91)90001-u. [DOI] [PubMed] [Google Scholar]
  21. Smith C. L., Lawrance S. K., Gillespie G. A., Cantor C. R., Weissman S. M., Collins F. S. Strategies for mapping and cloning macroregions of mammalian genomes. Methods Enzymol. 1987;151:461–489. doi: 10.1016/s0076-6879(87)51038-2. [DOI] [PubMed] [Google Scholar]
  22. Weber J. L. Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics. 1990 Aug;7(4):524–530. doi: 10.1016/0888-7543(90)90195-z. [DOI] [PubMed] [Google Scholar]
  23. Weber J. L., May P. E. Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet. 1989 Mar;44(3):388–396. [PMC free article] [PubMed] [Google Scholar]
  24. Weissenbach J., Gyapay G., Dib C., Vignal A., Morissette J., Millasseau P., Vaysseix G., Lathrop M. A second-generation linkage map of the human genome. Nature. 1992 Oct 29;359(6398):794–801. doi: 10.1038/359794a0. [DOI] [PubMed] [Google Scholar]
  25. Zabarovsky E. R., Boldog F., Erlandsson R., Kashuba V. I., Allikmets R. L., Marcsek Z., Kisselev L. L., Stanbridge E., Klein G., Sumegi J. New strategy for mapping the human genome based on a novel procedure for construction of jumping libraries. Genomics. 1991 Dec;11(4):1030–1039. doi: 10.1016/0888-7543(91)90029-e. [DOI] [PubMed] [Google Scholar]

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