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. 1996 Feb 15;24(4):676–682. doi: 10.1093/nar/24.4.676

Neomycin, spermine and hexaamminecobalt (III) share common structural motifs in converting B- to A-DNA.

H Robinson 1, A H Wang 1
PMCID: PMC145680  PMID: 8604309

Abstract

The (dG)n.(dC)n-containing 34mer DNA duplex [d(A2G15C15T2)]2 can be effectively converted from the B-DNA to the A-DNA conformation by neomycin, spermine and Co(NH3)6(3+). Conversion is demonstrated by a characteristic red shift in the circular dichroism spectra and dramatic NMR spectral changes in chemical shifts. Additional support comes from the substantially stronger CH6/GH8-H3'NOE intensities of the ligand-DNA complexes than those from the native DNA duplex. Such changes are consistent with a deoxyribose pucker transition from the predominate C2'-endo (S-type) to the C3'-endo (N-type). The changes for all three ligand-DNA complexes are identical, suggesting that those three complex cations share common structural motifs for the B- to A-DNA conversion. The A-DNA structure of the 4:1 complex of Co(NH3)6(3+)/d(ACCCGCGGGT) has been analyzed by NOE-restrained refinement. The structural basis of the transition may be related to the closeness of the two negatively charged sugar-phosphate backbones along the major groove in A-DNA, which can be effectively neutralized by the multivalent positively charged amine functions of these ligands. In addition, ligands like spermine or Co(NH3)6(3+) can adhere to guanine bases in the deep major groove of the double helix, as is evident from the significant direct NOE cross-peaks from the protons of Co(NH3)6(3+) to GH8, GH1 (imino) and CH4 (amino) protons. Our results point to future directions in preparing more potent derivatives of Co(NH3)6(3+) for RNA binding or the induction of A-DNA.

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Selected References

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  1. Ban C., Ramakrishnan B., Sundaralingam M. Crystal structure of the highly distorted chimeric decamer r(C)d(CGGCGCCG)r(G).spermine complex--spermine binding to phosphate only and minor groove tertiary base-pairing. Nucleic Acids Res. 1994 Dec 11;22(24):5466–5476. doi: 10.1093/nar/22.24.5466. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bancroft D., Williams L. D., Rich A., Egli M. The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove. Biochemistry. 1994 Feb 8;33(5):1073–1086. doi: 10.1021/bi00171a005. [DOI] [PubMed] [Google Scholar]
  3. Behe M., Felsenfeld G. Effects of methylation on a synthetic polynucleotide: the B--Z transition in poly(dG-m5dC).poly(dG-m5dC). Proc Natl Acad Sci U S A. 1981 Mar;78(3):1619–1623. doi: 10.1073/pnas.78.3.1619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Braunlin W. H., Anderson C. F., Record M. T., Jr Competitive interactions of Co(NH3)6(3+) and Na+ with helical B-DNA probed by 59Co and 23Na NMR. Biochemistry. 1987 Dec 1;26(24):7724–7731. doi: 10.1021/bi00398a028. [DOI] [PubMed] [Google Scholar]
  6. Braunlin W. H., Xu Q. Hexaamminecobalt(III) binding environments on double-helical DNA. Biopolymers. 1992 Dec;32(12):1703–1711. doi: 10.1002/bip.360321212. [DOI] [PubMed] [Google Scholar]
  7. Duckett D. R., Murchie A. I., Lilley D. M. The role of metal ions in the conformation of the four-way DNA junction. EMBO J. 1990 Feb;9(2):583–590. doi: 10.1002/j.1460-2075.1990.tb08146.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gao Y. G., Robinson H., van Boom J. H., Wang A. H. Influence of counter-ions on the crystal structures of DNA decamers: binding of [Co(NH3)6]3+ and Ba2+ to A-DNA. Biophys J. 1995 Aug;69(2):559–568. doi: 10.1016/S0006-3495(95)79929-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gessner R. V., Quigley G. J., Wang A. H., van der Marel G. A., van Boom J. H., Rich A. Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations. Biochemistry. 1985 Jan 15;24(2):237–240. doi: 10.1021/bi00323a001. [DOI] [PubMed] [Google Scholar]
  10. Johnson A., Qu Y., Van Houten B., Farrell N. B----Z DNA conformational changes induced by a family of dinuclear bis(platinum) complexes. Nucleic Acids Res. 1992 Apr 11;20(7):1697–1703. doi: 10.1093/nar/20.7.1697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kim J. L., Nikolov D. B., Burley S. K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 1993 Oct 7;365(6446):520–527. doi: 10.1038/365520a0. [DOI] [PubMed] [Google Scholar]
  12. Kim Y., Geiger J. H., Hahn S., Sigler P. B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 1993 Oct 7;365(6446):512–520. doi: 10.1038/365512a0. [DOI] [PubMed] [Google Scholar]
  13. Peck L. J., Nordheim A., Rich A., Wang J. C. Flipping of cloned d(pCpG)n.d(pCpG)n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling. Proc Natl Acad Sci U S A. 1982 Aug;79(15):4560–4564. doi: 10.1073/pnas.79.15.4560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Plum G. E., Bloomfield V. A. Equilibrium dialysis study of binding of hexammine cobalt(III) to DNA. Biopolymers. 1988 Jun;27(6):1045–1051. doi: 10.1002/bip.360270611. [DOI] [PubMed] [Google Scholar]
  15. Purohit P., Stern S. Interactions of a small RNA with antibiotic and RNA ligands of the 30S subunit. Nature. 1994 Aug 25;370(6491):659–662. doi: 10.1038/370659a0. [DOI] [PubMed] [Google Scholar]
  16. Robinson H., Wang A. H. 5'-CGA sequence is a strong motif for homo base-paired parallel-stranded DNA duplex as revealed by NMR analysis. Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5224–5228. doi: 10.1073/pnas.90.11.5224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Robinson H., Wang A. H. A simple spectral-driven procedure for the refinement of DNA structures by NMR spectroscopy. Biochemistry. 1992 Apr 7;31(13):3524–3533. doi: 10.1021/bi00128a029. [DOI] [PubMed] [Google Scholar]
  18. Robinson H., van der Marel G. A., van Boom J. H., Wang A. H. Unusual DNA conformation at low pH revealed by NMR: parallel-stranded DNA duplex with homo base pairs. Biochemistry. 1992 Nov 3;31(43):10510–10517. doi: 10.1021/bi00158a014. [DOI] [PubMed] [Google Scholar]
  19. Stage T. K., Hertel K. J., Uhlenbeck O. C. Inhibition of the hammerhead ribozyme by neomycin. RNA. 1995 Mar;1(1):95–101. [PMC free article] [PubMed] [Google Scholar]
  20. Tan R., Frankel A. D. Costabilization of peptide and RNA structure in an HIV Rev peptide-RRE complex. Biochemistry. 1994 Dec 6;33(48):14579–14585. doi: 10.1021/bi00252a025. [DOI] [PubMed] [Google Scholar]
  21. Wang A. H., Fujii S., van Boom J. H., Rich A. Molecular structure of the octamer d(G-G-C-C-G-G-C-C): modified A-DNA. Proc Natl Acad Sci U S A. 1982 Jul;79(13):3968–3972. doi: 10.1073/pnas.79.13.3968. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Widom J., Baldwin R. L. Cation-induced toroidal condensation of DNA studies with Co3+(NH3)6. J Mol Biol. 1980 Dec 25;144(4):431–453. doi: 10.1016/0022-2836(80)90330-7. [DOI] [PubMed] [Google Scholar]
  23. Xu Q., Shoemaker R. K., Braunlin W. H. Induction of B-A transitions of deoxyoligonucleotides by multivalent cations in dilute aqueous solution. Biophys J. 1993 Sep;65(3):1039–1049. doi: 10.1016/S0006-3495(93)81163-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Zapp M. L., Stern S., Green M. R. Small molecules that selectively block RNA binding of HIV-1 Rev protein inhibit Rev function and viral production. Cell. 1993 Sep 24;74(6):969–978. doi: 10.1016/0092-8674(93)90720-b. [DOI] [PubMed] [Google Scholar]
  25. von Ahsen U., Noller H. F. Footprinting the sites of interaction of antibiotics with catalytic group I intron RNA. Science. 1993 Jun 4;260(5113):1500–1503. doi: 10.1126/science.8502993. [DOI] [PubMed] [Google Scholar]

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