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. 1988 Nov 25;16(22):10643–10655. doi: 10.1093/nar/16.22.10643

Immunochemical detection of multiple conformations within a 36 base pair oligonucleotide.

D G Sanford 1, K J Kotkow 1, B D Stollar 1
PMCID: PMC338930  PMID: 2462714

Abstract

A 36 base pair chimeric oligonucleotide containing a central core of DNA duplex flanked by RNA/DNA hybrid at each end was synthesized. These distinct regions of the oligonucleotide adopt different conformations which were detected with antibody probes. Enzyme linked immunosorbent assays (ELISA) and a gel electrophoresis retardation assay were used to demonstrate the binding of antibodies which recognize B-DNA, Z-DNA and RNA/DNA hybrid. The DNA duplex core of this oligonucleotide adopts the B-conformation in 0.14 M NaCl. In high salt solution (4 M NaCl) the DNA core adopts the Z-conformation. The RNA/DNA hybrid at the ends of the oligomer adopt a conformation which is distinct from both B-DNA and A-RNA.

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Selected References

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

  1. Ali R., Dersimonian H., Stollar B. D. Binding of monoclonal anti-native DNA autoantibodies to DNA of varying size and conformation. Mol Immunol. 1985 Dec;22(12):1415–1422. doi: 10.1016/0161-5890(85)90065-3. [DOI] [PubMed] [Google Scholar]
  2. Benevides J. M., Thomas G. J., Jr A solution structure for poly(rA).poly(dT) with different furanose pucker and backbone geometry in rA and dT strands and intrastrand hydrogen bonding of adenine 8CH. Biochemistry. 1988 May 17;27(10):3868–3873. doi: 10.1021/bi00410a051. [DOI] [PubMed] [Google Scholar]
  3. Benevides J. M., Wang A. H., Rich A., Kyogoku Y., van der Marel G. A., van Boom J. H., Thomas G. J., Jr Raman spectra of single crystals of r(GCG)d(CGC) and d(CCCCGGGG) as models for A DNA, their structure transitions in aqueous solution, and comparison with double-helical poly(dG).poly(dC). Biochemistry. 1986 Jan 14;25(1):41–50. doi: 10.1021/bi00349a007. [DOI] [PubMed] [Google Scholar]
  4. Haasnoot C. A., Hilbers C. W., van der Marel G. A., van Boom J. H., Singh U. C., Pattabiraman N., Kollman P. A. On loop folding in nucleic acid hairpin-type structures. J Biomol Struct Dyn. 1986 Apr;3(5):843–857. doi: 10.1080/07391102.1986.10508468. [DOI] [PubMed] [Google Scholar]
  5. Kitagawa Y., Stollar B. D. Comparison of poly(A).poly(dT) and poly(I).poly(dC) as immunogens for the induction of antibodies to RNA-DNA hybrids. Mol Immunol. 1982 Mar;19(3):413–420. doi: 10.1016/0161-5890(82)90207-3. [DOI] [PubMed] [Google Scholar]
  6. Kmiec E. B., Holloman W. K. Homologous pairing of DNA molecules by Ustilago rec1 protein is promoted by sequences of Z-DNA. Cell. 1986 Feb 28;44(4):545–554. doi: 10.1016/0092-8674(86)90264-3. [DOI] [PubMed] [Google Scholar]
  7. Lilley D. M. The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6468–6472. doi: 10.1073/pnas.77.11.6468. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Marini J. C., Levene S. D., Crothers D. M., Englund P. T. Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664–7668. doi: 10.1073/pnas.79.24.7664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Milman G., Langridge R., Chamberlin M. J. The structure of a DNA-RNA hybrid. Proc Natl Acad Sci U S A. 1967 Jun;57(6):1804–1810. doi: 10.1073/pnas.57.6.1804. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Möller A., Gabriels J. E., Lafer E. M., Nordheim A., Rich A., Stollar B. D. Monoclonal antibodies recognize different parts of Z-DNA. J Biol Chem. 1982 Oct 25;257(20):12081–12085. [PubMed] [Google Scholar]
  11. Nakazato H. Fractionation and characterization of antibodies elicited phi X174 deoxyribonucleic acid-ribonucleic acid hybrid. Biochemistry. 1980 Jun 24;19(13):2835–2840. doi: 10.1021/bi00554a003. [DOI] [PubMed] [Google Scholar]
  12. O'Brien E. J., MacEwan A. W. Molecular and crystal structure of the polynucleotide complex: polyinosinic acid plus polydeoxycytidylic acid. J Mol Biol. 1970 Mar 14;48(2):243–261. doi: 10.1016/0022-2836(70)90159-2. [DOI] [PubMed] [Google Scholar]
  13. Panayotatos N., Wells R. D. Cruciform structures in supercoiled DNA. Nature. 1981 Feb 5;289(5797):466–470. doi: 10.1038/289466a0. [DOI] [PubMed] [Google Scholar]
  14. Runkel L., Nordheim A. Chemical footprinting of the interaction between left-handed Z-DNA and anti-Z-DNA antibodies by diethylpyrocarbonate carbethoxylation. J Mol Biol. 1986 Jun 5;189(3):487–501. doi: 10.1016/0022-2836(86)90319-0. [DOI] [PubMed] [Google Scholar]
  15. Selsing E., Wells R. D. Polynucleotide block polymers consisting of a DNA.RNA hybrid joined to a DNA.DNA duplex. Synthesis and characterization of dGn.rCidCk duplexes. J Biol Chem. 1979 Jun 25;254(12):5410–5416. [PubMed] [Google Scholar]
  16. Stollar B. D. Antibodies to DNA. CRC Crit Rev Biochem. 1986;20(1):1–36. doi: 10.3109/10409238609115899. [DOI] [PubMed] [Google Scholar]
  17. Stollar B. D. Doubls-helical polynucleotides: immunochemical recognition of differing conformations. Science. 1970 Aug 7;169(3945):609–611. doi: 10.1126/science.169.3945.609. [DOI] [PubMed] [Google Scholar]
  18. Stollar B. D. The specificity and applications of antibodies to helical nucleic acids. CRC Crit Rev Biochem. 1975 May;3(1):45–69. doi: 10.3109/10409237509102552. [DOI] [PubMed] [Google Scholar]
  19. Stollar B. D., Zon G., Pastor R. W. A recognition site on synthetic helical oligonucleotides for monoclonal anti-native DNA autoantibody. Proc Natl Acad Sci U S A. 1986 Jun;83(12):4469–4473. doi: 10.1073/pnas.83.12.4469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Wang A. H., Fujii S., van Boom J. H., van der Marel G. A., van Boeckel S. A., Rich A. Molecular structure of r(GCG)d(TATACGC): a DNA--RNA hybrid helix joined to double helical DNA. Nature. 1982 Oct 14;299(5884):601–604. doi: 10.1038/299601a0. [DOI] [PubMed] [Google Scholar]
  21. Zahn K., Blattner F. R. Direct evidence for DNA bending at the lambda replication origin. Science. 1987 Apr 24;236(4800):416–422. doi: 10.1126/science.2951850. [DOI] [PubMed] [Google Scholar]
  22. Zimmerman S. B., Pheiffer B. H. A RNA.DNA hybrid that can adopt two conformations: an x-ray diffraction study of poly(rA).poly(dT) in concentrated solution or in fibers. Proc Natl Acad Sci U S A. 1981 Jan;78(1):78–82. doi: 10.1073/pnas.78.1.78. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Zouali M., Stollar B. D. A rapid ELISA for measurement of antibodies to nucleic acid antigens using UV-treated polystyrene microplates. J Immunol Methods. 1986 Jun 10;90(1):105–110. doi: 10.1016/0022-1759(86)90390-x. [DOI] [PubMed] [Google Scholar]

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