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Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1981 Jan;78(1):616–620. doi: 10.1073/pnas.78.1.616

Isolation and partial nucleotide sequence of a cDNA clone for human histocompatibility antigen HLA-B by use of an oligodeoxynucleotide primer.

A K Sood, D Pereira, S M Weissman
PMCID: PMC319105  PMID: 6165999

Abstract

We have isolated a cDNA clone for one of the HLA-B locus alloantigens by hybridization with a 30-nucleotide-long DNA probe. The probe was isolated from a reverse transcriptase (RNA-dependent DNA nucleotidyltransferase)-catalyzed cDNA synthesis reaction on poly(A)-mRNA in which an oligonucleotide (5'-32P)dC-T-T-C-T-C-C-A-C-A-TOH served as a primer and in which dideoxynucleoside triphosphates were used to reduce the size and heterogeneity of the cDNA products. The desired cDNA clone was isolated from a library of recombinant cDNA clones in the plasmid pBR322. The partial nucleotide sequence of the cDNA clone corresponds to the amino acid sequence of HLA-B7 antigen. The approach described in this paper is extremely sensitive and may be useful in cloning other genes for which the corresponding mRNA is present at low levels. This cDNA clone is nearly full length and can be used to isolate and to study the genes within the HLA region and to obtain expression of HLA-B peptides in cells.

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Selected References

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  1. Agarwal K. L., Riftina F. Chemical synthesis of a self-complementary octanucleotide, dG-G-T-T-A-A-C-C by a modified triester method. Nucleic Acids Res. 1978 Aug;5(8):2809–2823. doi: 10.1093/nar/5.8.2809. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arentzen R., Reese C. B. The phosphotriester approach to oligonucleotide synthesis: Preparation of oligo- and poly-thymidylic acids. J Chem Soc Perkin 1. 1977;4:445–460. doi: 10.1039/p19770000445. [DOI] [PubMed] [Google Scholar]
  3. Bodmer W. F., Bodmer J. G. Evolution and function of the HLA system. Br Med Bull. 1978 Sep;34(3):309–316. doi: 10.1093/oxfordjournals.bmb.a071518. [DOI] [PubMed] [Google Scholar]
  4. Britten R. J., Davidson E. H. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Q Rev Biol. 1971 Jun;46(2):111–138. doi: 10.1086/406830. [DOI] [PubMed] [Google Scholar]
  5. Duncan C., Biro P. A., Choudary P. V., Elder J. T., Wang R. R., Forget B. G., de Riel J. K., Weissman S. M. RNA polymerase III transcriptional units are interspersed among human non-alpha-globin genes. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5095–5099. doi: 10.1073/pnas.76.10.5095. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Galau G. A., Klein W. H., Davis M. M., Wold B. J., Britten R. J., Davidson E. H. Structural gene sets active in embryos and adult tissues of the sea urchin. Cell. 1976 Apr;7(4):487–505. doi: 10.1016/0092-8674(76)90200-2. [DOI] [PubMed] [Google Scholar]
  7. Ghosh P. K., Reddy V. B., Swinscoe J., Choudary P. V., Lebowitz P., Weissman S. M. The 5'-terminal leader sequence of late 16 S mRNA from cells infected with simian virus 40. J Biol Chem. 1978 May 25;253(10):3643–3647. [PubMed] [Google Scholar]
  8. Gillam S., Jahnke P., Smith M. Enzymatic synthesis of oligodeoxyribonucleotides of defined sequence. J Biol Chem. 1978 Apr 25;253(8):2532–2539. [PubMed] [Google Scholar]
  9. Grantham R. Viral, prokaryote and eukaryote genes contrasted by mRNA sequence indexes. FEBS Lett. 1978 Nov 1;95(1):1–11. doi: 10.1016/0014-5793(78)80041-6. [DOI] [PubMed] [Google Scholar]
  10. Grunstein M., Hogness D. S. Colony hybridization: a method for the isolation of cloned DNAs that contain a specific gene. Proc Natl Acad Sci U S A. 1975 Oct;72(10):3961–3965. doi: 10.1073/pnas.72.10.3961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Itakura K., Katagiri N., Bahl C. P., Wightman R. H., Narang S. A. Improved triester approach for the synthesis of pentadecathymidylic acid. J Am Chem Soc. 1975 Dec 10;97(25):7327–7332. doi: 10.1021/ja00858a020. [DOI] [PubMed] [Google Scholar]
  12. Jay E., Bambara R., Padmanabhan R., Wu R. DNA sequence analysis: a general, simple and rapid method for sequencing large oligodeoxyribonucleotide fragments by mapping. Nucleic Acids Res. 1974 Mar;1(3):331–353. doi: 10.1093/nar/1.3.331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Khorana H. G., Agarwal K. L., Büchi H., Caruthers M. H., Gupta N. K., Kleppe K., Kumar A., Otsuka E., RajBhandary U. L., Van de Sande J. H. Studies on polynucleotides. 103. Total synthesis of the structural gene for an alanine transfer ribonucleic acid from yeast. J Mol Biol. 1972 Dec 28;72(2):209–217. doi: 10.1016/0022-2836(72)90146-5. [DOI] [PubMed] [Google Scholar]
  14. Maat J., Smith A. J. A method for sequencing restriction fragments with dideoxynucleoside triphosphates. Nucleic Acids Res. 1978 Dec;5(12):4537–4545. doi: 10.1093/nar/5.12.4537. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Maniatis T., Hardison R. C., Lacy E., Lauer J., O'Connell C., Quon D., Sim G. K., Efstratiadis A. The isolation of structural genes from libraries of eucaryotic DNA. Cell. 1978 Oct;15(2):687–701. doi: 10.1016/0092-8674(78)90036-3. [DOI] [PubMed] [Google Scholar]
  16. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Mears J. G., Ramirez F., Leibowitz D., Bank A. Organization of human delta--and beta-globin genes in cellular DNA and the presence of intragenic inserts. Cell. 1978 Sep;15(1):15–23. doi: 10.1016/0092-8674(78)90079-x. [DOI] [PubMed] [Google Scholar]
  18. Montgomery D. L., Hall B. D., Gillam S., Smith M. Identification and isolation of the yeast cytochrome c gene. Cell. 1978 Jul;14(3):673–680. doi: 10.1016/0092-8674(78)90250-7. [DOI] [PubMed] [Google Scholar]
  19. Noyes B. E., Mevarech M., Stein R., Agarwal K. L. Detection and partial sequence analysis of gastrin mRNA by using an oligodeoxynucleotide probe. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1770–1774. doi: 10.1073/pnas.76.4.1770. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Nunberg J. H., Kaufman R. J., Chang A. C., Cohen S. N., Schimke R. T. Structure and genomic organization of the mouse dihydrofolate reductase gene. Cell. 1980 Feb;19(2):355–364. doi: 10.1016/0092-8674(80)90510-3. [DOI] [PubMed] [Google Scholar]
  21. Orr H. T., Lopez de Castro J. A., Parham P., Ploegh H. L., Strominger J. L. Comparison of amino acid sequences of two human histocompatibility antigens, HLA-A2 and HLA-B7: location of putative alloantigenic sites. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4395–4399. doi: 10.1073/pnas.76.9.4395. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Ploegh H. L., Cannon L. E., Strominger J. L. Cell-free translation of the mRNAs for the heavy and light chains of HLA-A and HLA-B antigens. Proc Natl Acad Sci U S A. 1979 May;76(5):2273–2277. doi: 10.1073/pnas.76.5.2273. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Richardson C. C. Phosphorylation of nucleic acid by an enzyme from T4 bacteriophage-infected Escherichia coli. Proc Natl Acad Sci U S A. 1965 Jul;54(1):158–165. doi: 10.1073/pnas.54.1.158. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Robb R. J., Terhorst C., Strominger J. L. Sequence of the COOH-terminal hydrophilic region of histocompatibility antigens HLA-A2 and HLA-B7. J Biol Chem. 1978 Aug 10;253(15):5319–5324. [PubMed] [Google Scholar]
  25. Royal A., Garapin A., Cami B., Perrin F., Mandel J. L., LeMeur M., Brégégègre F., Gannon F., LePennec J. P., Chambon P. The ovalbumin gene region: common features in the organisation of three genes expressed in chicken oviduct under hormonal control. Nature. 1979 May 10;279(5709):125–132. doi: 10.1038/279125a0. [DOI] [PubMed] [Google Scholar]
  26. Seidman J. G., Leder A., Nau M., Norman B., Leder P. Antibody diversity. Science. 1978 Oct 6;202(4363):11–17. doi: 10.1126/science.99815. [DOI] [PubMed] [Google Scholar]
  27. Smith M., Leung D. W., Gillam S., Astell C. R., Montgomery D. L., Hall B. D. Sequence of the gene for iso-1-cytochrome c in Saccharomyces cerevisiae. Cell. 1979 Apr;16(4):753–761. doi: 10.1016/0092-8674(79)90091-6. [DOI] [PubMed] [Google Scholar]
  28. Sood A. K., Narang S. A. A rapid and convenient synthesis of poly-thymidylic acid by the modified triester approach. Nucleic Acids Res. 1977 Aug;4(8):2757–2765. doi: 10.1093/nar/4.8.2757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  30. Szostak J. W., Stiles J. I., Bahl C. P., Wu R. Specific binding of a synthetic oligodeoxyribonucleotide to yeast cytochrome c mRNA. Nature. 1977 Jan 6;265(5589):61–63. doi: 10.1038/265061a0. [DOI] [PubMed] [Google Scholar]
  31. Tonegawa S., Brack C., Hozumi N., Pirrotta V. Organization of immunoglobulin genes. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 2):921–931. doi: 10.1101/sqb.1978.042.01.094. [DOI] [PubMed] [Google Scholar]
  32. Tuan D., Biro P. A., deRiel J. K., Lazarus H., Forget B. G. Restriction endonuclease mapping of the human gamma globin gene loci. Nucleic Acids Res. 1979 Jun 11;6(7):2519–2544. doi: 10.1093/nar/6.7.2519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Wickens M. P., Buell G. N., Schimke R. T. Synthesis of double-stranded DNA complementary to lysozyme, ovomucoid, and ovalbumin mRNAs. Optimization for full length second strand synthesis by Escherichia coli DNA polymerase I. J Biol Chem. 1978 Apr 10;253(7):2483–2495. [PubMed] [Google Scholar]
  34. Williams K. A., Hart D. N., Fabre J. W., Morris P. J. Distribution and quantitation of HLA-ABC and DR (Ia) antigens on human kidney and other tissues. Transplantation. 1980 Apr;29(4):274–279. doi: 10.1097/00007890-198004000-00002. [DOI] [PubMed] [Google Scholar]
  35. Zimmern D., Kaesberg P. 3'-terminal nucleotide sequence of encephalomyocarditis virus RNA determined by reverse transcriptase and chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1978 Sep;75(9):4257–4261. doi: 10.1073/pnas.75.9.4257. [DOI] [PMC free article] [PubMed] [Google Scholar]

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