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. 1993 Mar 25;21(6):1433–1438. doi: 10.1093/nar/21.6.1433

Demonstration of Z-d(5BrCGAT5BrCG) and B-d(CGCGATCGCG) form crystal structures in DNA-cobalt hexammine complexes by Kr 647.1 nm excitation of Raman spectra.

J M Benevides 1, A H Wang 1, G J Thomas Jr 1
PMCID: PMC309329  PMID: 8464735

Abstract

Cobalt hexammine [Co(NH3)6(3+)] is an efficient DNA complexing agent which significantly perturbs nucleic acid secondary structure. We have employed red excitation (647.1 nm) from a krypton laser to obtain Raman spectra of the highly colored complexes formed between cobalt hexammine and crystals of the DNA oligomers, d(5BrCGAT5BrCG) and d(CGCGATCGCG), both of which incorporate out-of-alternation pyrimidine/purine sequences. The Co(NH3)6(3+) complex of d(5BrCGAT5BrCG) exhibits a typical Z-form Raman signature, similar to that reported previously for the alternating d(CGCGCG) sequence. Comparison of the Raman bands of d(5BrCGAT5BrCG) with those of other oligonucleotide and polynucleotide structures suggests that C3'-endo/syn and C3'-endo/anti thymidines may exhibit distinctive nucleoside conformation markers, and tentative assignments are proposed. The Raman markers for C2'-endo/anti adenosine in this Z-DNA are consistent with those reported previously for B-DNA crystals containing C2'-endo/anti dA. Raman bands of the cobalt hexammine complex of d(CGCGATCGCG) are those of B-DNA, but with significant differences from the previously characterized B-DNA dodecamer, d(CGCAAATTTGCG). The observed differences suggest an unusual deoxyguanosine conformer, possibly related to a previously characterized structural intermediate in the B-->Z transition. The present results show that crystallization of d(CGCGATCGCG) in the presence of cobalt hexammine is not alone sufficient to induce the left-handed Z-DNA conformation. This investigation represents the first application of off-resonance Raman spectroscopy for characterization of highly chromophoric DNA and illustrates the feasibility of the Raman method for investigating other structurally perturbed states of DNA-cobalt hexammine complexes.

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Selected References

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  1. 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]
  2. Benevides J. M., Wang A. H., van der Marel G. A., van Boom J. H., Rich A., Thomas G. J., Jr The Raman spectra of left-handed DNA oligomers incorporating adenine-thymine base pairs+. Nucleic Acids Res. 1984 Jul 25;12(14):5913–5925. doi: 10.1093/nar/12.14.5913. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Benevides J. M., Wang A. H., van der Marel G. A., van Boom J. H., Thomas G. J., Jr Crystal and solution structures of the B-DNA dodecamer d(CGCAAATTTGCG) probed by Raman spectroscopy: heterogeneity in the crystal structure does not persist in the solution structure. Biochemistry. 1988 Feb 9;27(3):931–938. doi: 10.1021/bi00403a014. [DOI] [PubMed] [Google Scholar]
  4. Erfurth S. C., Kiser E. J., Peticolas W. L. Determination of the backbone structure of nucleic acids and nucleic acid oligomers by laser Raman scattering. Proc Natl Acad Sci U S A. 1972 Apr;69(4):938–941. doi: 10.1073/pnas.69.4.938. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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]
  6. Grzeskowiak K., Yanagi K., Privé G. G., Dickerson R. E. The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair reversals. J Biol Chem. 1991 May 15;266(14):8861–8883. doi: 10.2210/pdb1d23/pdb. [DOI] [PubMed] [Google Scholar]
  7. Ho P. S., Frederick C. A., Saal D., Wang A. H., Rich A. The interactions of ruthenium hexaammine with Z-DNA: crystal structure of a Ru(NH3)6+3 salt of d(CGCGCG) at 1.2 A resolution. J Biomol Struct Dyn. 1987 Feb;4(4):521–534. doi: 10.1080/07391102.1987.10507657. [DOI] [PubMed] [Google Scholar]
  8. Prescott B., Steinmetz W., Thomas G. J., Jr Characterization of DNA structures by laser Raman spectroscopy. Biopolymers. 1984 Feb;23(2):235–256. doi: 10.1002/bip.360230206. [DOI] [PubMed] [Google Scholar]
  9. Quintana J. R., Grzeskowiak K., Yanagi K., Dickerson R. E. Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G. J Mol Biol. 1992 May 20;225(2):379–395. doi: 10.1016/0022-2836(92)90928-d. [DOI] [PubMed] [Google Scholar]
  10. Rich A., Nordheim A., Wang A. H. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem. 1984;53:791–846. doi: 10.1146/annurev.bi.53.070184.004043. [DOI] [PubMed] [Google Scholar]
  11. Ridoux J. P., Liquier J., Taillandier E. Raman spectroscopy of Z-form poly[d(A-T)].poly[d(A-T)]. Biochemistry. 1988 May 17;27(10):3874–3878. doi: 10.1021/bi00410a052. [DOI] [PubMed] [Google Scholar]
  12. Thamann T. J., Lord R. C., Wang A. H., Rich A. The high salt form of poly(dG-dC).poly(dG-dC) is left-handed Z-DNA: Raman spectra of crystals and solutions. Nucleic Acids Res. 1981 Oct 24;9(20):5443–5457. doi: 10.1093/nar/9.20.5443. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Urpi L., Ridoux J. P., Liquier J., Verdaguer N., Fita I., Subirana J. A., Iglesias F., Huynh-Dinh T., Igolen J., Taillandier E. Conformations in crystals and solutions of d(CACGTG), d(CCGCGG) and d(GGCGCC) studied by vibrational spectroscopy. Nucleic Acids Res. 1989 Aug 25;17(16):6669–6680. doi: 10.1093/nar/17.16.6669. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Wang A. H., Gessner R. V., van der Marel G. A., van Boom J. H., Rich A. Crystal structure of Z-DNA without an alternating purine-pyrimidine sequence. Proc Natl Acad Sci U S A. 1985 Jun;82(11):3611–3615. doi: 10.1073/pnas.82.11.3611. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Wang A. J., Quigley G. J., Kolpak F. J., van der Marel G., van Boom J. H., Rich A. Left-handed double helical DNA: variations in the backbone conformation. Science. 1981 Jan 9;211(4478):171–176. doi: 10.1126/science.7444458. [DOI] [PubMed] [Google Scholar]
  16. Wang Y., Thomas G. A., Peticolas W. L. Sequence dependent conformations of oligomeric DNA's in aqueous solutions and in crystals. J Biomol Struct Dyn. 1987 Oct;5(2):249–274. doi: 10.1080/07391102.1987.10506392. [DOI] [PubMed] [Google Scholar]
  17. Yuan H., Quintana J., Dickerson R. E. Alternative structures for alternating poly(dA-dT) tracts: the structure of the B-DNA decamer C-G-A-T-A-T-A-T-C-G. Biochemistry. 1992 Sep 1;31(34):8009–8021. [PubMed] [Google Scholar]

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