Abstract
It is well known that the local conformation of a segment of DNA is dependent upon both the sequence of the segment and the conditions under which the DNA is prepared. In extreme cases, the DNA may contain regions of both right and left-handed conformations, mandating the existence of a conformational junction between the two. These B-Z junctions have been observed in plasmids but, to date, no model systems have been characterized to determine the molecular nature of these junctions. Preliminary CD, UV, and NMR studies on such a model are presented here. A 16 base pair oligonucleotide, containing a potential B-Z junction, has been synthesized and characterized by the above techniques. The results suggest that this molecule contains both right and left-handed conformations under condition of high salt, and thus a B-Z junction.
Full text
PDF
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Azorin F., Hahn R., Rich A. Restriction endonucleases can be used to study B-Z junctions in supercoiled DNA. Proc Natl Acad Sci U S A. 1984 Sep;81(18):5714–5718. doi: 10.1073/pnas.81.18.5714. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Chen C., Cohen J. S., Behe M. B to Z transition of double-stranded poly[deoxyguanylyl(3'-5')-5-methyldeoxycytidine] in solution by phosphorus-31 and carbon-13 nuclear magnetic resonance spectroscopy. Biochemistry. 1983 Apr 26;22(9):2136–2142. doi: 10.1021/bi00278a013. [DOI] [PubMed] [Google Scholar]
- Hartmann B., Thuong N. T., Pouyet J., Ptak M., Leng M. Spectroscopic studies of (m5dC-dG)3: thermal stability of B- and Z-forms. Nucleic Acids Res. 1983 Jul 11;11(13):4453–4466. doi: 10.1093/nar/11.13.4453. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Johnston B. H., Rich A. Chemical probes of DNA conformation: detection of Z-DNA at nucleotide resolution. Cell. 1985 Oct;42(3):713–724. doi: 10.1016/0092-8674(85)90268-5. [DOI] [PubMed] [Google Scholar]
- Kilpatrick M. W., Wei C. F., Gray H. B., Jr, Wells R. D. BAL 31 nuclease as a probe in concentrated salt for the B-Z DNA junction. Nucleic Acids Res. 1983 Jun 11;11(11):3811–3822. doi: 10.1093/nar/11.11.3811. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Patel D. J., Canuel L. L., Pohl F. M. "Alternating B-DNA" conformation for the oligo(dG-dC) duplex in high-salt solution. Proc Natl Acad Sci U S A. 1979 Jun;76(6):2508–2511. doi: 10.1073/pnas.76.6.2508. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pochet S., Huynh-Dinh T., Neumann J. M., Tran-Dinh S., Adam S., Taboury J., Taillandier E., Igolen J. NMR, CD and IR spectroscopies of a tridecanucleotide containing a no-base residue: coexistence of B and Z conformations. Nucleic Acids Res. 1986 Jan 24;14(2):1107–1126. doi: 10.1093/nar/14.2.1107. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Singleton C. K., Klysik J., Stirdivant S. M., Wells R. D. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature. 1982 Sep 23;299(5881):312–316. doi: 10.1038/299312a0. [DOI] [PubMed] [Google Scholar]
- Sinha N. D., Biernat J., McManus J., Köster H. Polymer support oligonucleotide synthesis XVIII: use of beta-cyanoethyl-N,N-dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product. Nucleic Acids Res. 1984 Jun 11;12(11):4539–4557. doi: 10.1093/nar/12.11.4539. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stirdivant S. M., Kłysik J., Wells R. D. Energetic and structural inter-relationship between DNA supercoiling and the right- to left-handed Z helix transitions in recombinant plasmids. J Biol Chem. 1982 Sep 10;257(17):10159–10165. [PubMed] [Google Scholar]