Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1997 Mar 15;25(6):1100–1107. doi: 10.1093/nar/25.6.1100

Parallel-stranded linear homoduplexes of d(A+-G)n > 10 and d(A-G)n > 10 manifesting the contrasting ionic strength sensitivities of poly(A+.A+) and DNA.

N G Dolinnaya 1, A Ulku 1, J R Fresco 1
PMCID: PMC146566  PMID: 9092616

Abstract

In contrast to shorter homologs which only form a single-stranded nucleic acid alpha-helix in acid solution at [Na+]</=0.02 M Na+, d(A-G)20,30 form in addition a parallel-stranded duplex with (A+.A+) and (G.G) base pairs and interstrand dA+...PO2-ionic and dA+NH2... O=P H-bonds. Under conditions where duplex prevails over alpha-helix, the contribution of the base-backbone interactions to stability varies directly with [H+] and inversely with [Na+], just as in poly(A+.A+). These duplexes are characterized by intense circular dichroism and a large cooperative thermally-induced hyperchromic transition that is dependent on oligomer concentration. Dimethylsulfate reactivity of the dG residues indicates G.G and therefore dA+.dA+rather than dA+.G base pairs. At much higher ionic strength (Na+>/=0.2 M) the protonated base-backbone interactions are so weakened that duplex stability becomes increasingly dependent upon H-bonded base pairing and stacking and almost independent of pH. Between pH 6 and 8 this duplex structure is devoid of protonated dA residues and shows positive dependence of T m on ionic strength similar to that of DNA.

Full Text

The Full Text of this article is available as a PDF (182.2 KB).

Selected References

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

  1. Aharoni A., Baran N., Manor H. Characterization of a multisubunit human protein which selectively binds single stranded d(GA)n and d(GT)n sequence repeats in DNA. Nucleic Acids Res. 1993 Nov 11;21(22):5221–5228. doi: 10.1093/nar/21.22.5221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brown T., Leonard G. A., Booth E. D., Chambers J. Crystal structure and stability of a DNA duplex containing A(anti).G(syn) base-pairs. J Mol Biol. 1989 May 20;207(2):455–457. doi: 10.1016/0022-2836(89)90268-4. [DOI] [PubMed] [Google Scholar]
  3. Casasnovas J. M., Huertas D., Ortiz-Lombardía M., Kypr J., Azorín F. Structural polymorphism of d(GA.TC)n DNA sequences. Intramolecular and intermolecular associations of the individual strands. J Mol Biol. 1993 Oct 20;233(4):671–681. doi: 10.1006/jmbi.1993.1544. [DOI] [PubMed] [Google Scholar]
  4. Dolinnaya N. G., Braswell E. H., Fossella J. A., Klump H., Fresco J. R. Molecular and thermodynamic properties of d(A(+)-G)10, a single-stranded nucleic acid helix without paired or stacked bases. Biochemistry. 1993 Sep 28;32(38):10263–10270. doi: 10.1021/bi00089a049. [DOI] [PubMed] [Google Scholar]
  5. Dolinnaya N. G., Fresco J. R. Single-stranded nucleic acid helical secondary structure stabilized by ionic bonds: d(A(+)-G)10. Proc Natl Acad Sci U S A. 1992 Oct 1;89(19):9242–9246. doi: 10.1073/pnas.89.19.9242. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. FRESCO J. R., KLEMPERER E. Polyriboadenylic acid, a molecular analogue of ribonucleic acid and desoxyribonucleic acid. Ann N Y Acad Sci. 1959 Sep 4;81:730–741. doi: 10.1111/j.1749-6632.1959.tb49354.x. [DOI] [PubMed] [Google Scholar]
  7. Guschlbauer W. Protonated polynucleotide structures. I. The thermal denaturation of polycytidylic acid in acid solution. Proc Natl Acad Sci U S A. 1967 May;57(5):1441–1448. doi: 10.1073/pnas.57.5.1441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hoffman E. K., Trusko S. P., Murphy M., George D. L. An S1 nuclease-sensitive homopurine/homopyrimidine domain in the c-Ki-ras promoter interacts with a nuclear factor. Proc Natl Acad Sci U S A. 1990 Apr;87(7):2705–2709. doi: 10.1073/pnas.87.7.2705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Huertas D., Bellsolell L., Casasnovas J. M., Coll M., Azorín F. Alternating d(GA)n DNA sequences form antiparallel stranded homoduplexes stabilized by the formation of G.A base pairs. EMBO J. 1993 Oct;12(10):4029–4038. doi: 10.1002/j.1460-2075.1993.tb06081.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hunter W. N., Brown T., Kennard O. Structural features and hydration of d(C-G-C-G-A-A-T-T-A-G-C-G); a double helix containing two G.A mispairs. J Biomol Struct Dyn. 1986 Oct;4(2):173–191. doi: 10.1080/07391102.1986.10506338. [DOI] [PubMed] [Google Scholar]
  11. Kolluri R., Torrey T. A., Kinniburgh A. J. A CT promoter element binding protein: definition of a double-strand and a novel single-strand DNA binding motif. Nucleic Acids Res. 1992 Jan 11;20(1):111–116. doi: 10.1093/nar/20.1.111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lee J. S., Evans D. H., Morgan A. R. Polypurine DNAs and RNAs form secondary structures which may be tetra-stranded. Nucleic Acids Res. 1980 Sep 25;8(18):4305–4320. doi: 10.1093/nar/8.18.4305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Mukerji I., Shiber M. C., Fresco J. R., Spiro T. G. A UV resonance Raman study of hairpin dimer helices of d(A-G)10 at neutral pH containing intercalated dA residues and alternating dG tetrads. Nucleic Acids Res. 1996 Dec 15;24(24):5013–5020. doi: 10.1093/nar/24.24.5013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Mukerji I., Shiber M. C., Spiro T. G., Fresco J. R. A UV resonance Raman study of d(A(+)-G)10, a single-stranded helix without stacked or paired bases. Biochemistry. 1995 Nov 7;34(44):14300–14303. doi: 10.1021/bi00044a006. [DOI] [PubMed] [Google Scholar]
  15. Privé G. G., Heinemann U., Chandrasegaran S., Kan L. S., Kopka M. L., Dickerson R. E. Helix geometry, hydration, and G.A mismatch in a B-DNA decamer. Science. 1987 Oct 23;238(4826):498–504. doi: 10.1126/science.3310237. [DOI] [PubMed] [Google Scholar]
  16. RICH A., DAVIES D. R., CRICK F. H., WATSON J. D. The molecular structure of polyadenylic acid. J Mol Biol. 1961 Feb;3:71–86. doi: 10.1016/s0022-2836(61)80009-0. [DOI] [PubMed] [Google Scholar]
  17. Reaban M. E., Griffin J. A. Induction of RNA-stabilized DNA conformers by transcription of an immunoglobulin switch region. Nature. 1990 Nov 22;348(6299):342–344. doi: 10.1038/348342a0. [DOI] [PubMed] [Google Scholar]
  18. Rippe K., Fritsch V., Westhof E., Jovin T. M. Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex. EMBO J. 1992 Oct;11(10):3777–3786. doi: 10.1002/j.1460-2075.1992.tb05463.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Shiber M. C., Lavelle L., Fossella J. A., Fresco J. R. Alpha-DNA, a single-stranded secondary structure stabilized by ionic and hydrogen bonds: d(A(+)-G)n. Biochemistry. 1995 Nov 7;34(44):14293–14299. doi: 10.1021/bi00044a005. [DOI] [PubMed] [Google Scholar]
  20. Topal M. D., Fresco J. R. Complementary base pairing and the origin of substitution mutations. Nature. 1976 Sep 23;263(5575):285–289. doi: 10.1038/263285a0. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES