Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 Nov 11;21(22):5085–5091. doi: 10.1093/nar/21.22.5085

Structure and drug interactions of parallel-stranded DNA studied by infrared spectroscopy and fluorescence.

H Fritzsche 1, A Akhebat 1, E Taillandier 1, K Rippe 1, T M Jovin 1
PMCID: PMC310621  PMID: 7504812

Abstract

The infrared spectra of three different 25-mer parallel-stranded DNAs (ps-DNA) have been studied. We have used ps-DNAs containing either exclusively dA x dT base pairs or substitution with four dG x dC base pairs and have them compared with their antiparallel-stranded (aps) reference duplexes in a conventional B-DNA conformation. Significant differences have been found in the region of the thymine C = O stretching vibrations. The parallel-stranded duplexes showed characteristic marker bands for the C2 = O2 and C4 = O4 carbonyl stretching vibrations of thymine at 1685 cm-1 and 1668 cm-1, respectively, as compared to values of 1696 cm-1 and 1663 cm-1 for the antiparallel-stranded reference duplexes. The results confirm previous studies indicating that the secondary structure in parallel-stranded DNA is established by reversed Watson--Crick base pairing of dA x dT with hydrogen bonds between N6H...O2 and N1...HN3. The duplex structure of the ps-DNA is much more sensitive to dehydration than that of the aps-DNA. Interaction with three drugs known to bind in the minor groove of aps-DNA--netropsin, distamycin A and Hoechst 33258--induces shifts of the C = O stretching vibrations of ps-DNA even at low ratio of drug per DNA base pair. These results suggest a conformational change of the ps-DNA to optimize the DNA-drug interaction. As demonstrated by excimer fluorescence of strands labeled with pyrene at the 5'-end, the drugs induce dissociation of the ps-DNA duplex with subsequent formation of imperfectly matched aps-DNA to allow the more favorable drug binding to aps-DNA. Similarly, attempts to form a triple helix of the type d(T)n.d(A)n.d(T)n with ps-DNA failed and resulted in the dissociation of the ps-DNA duplex and reformation of a triple helix based upon an aps-DNA duplex core d(T)10.d(A)10.

Full text

PDF
5089

Selected References

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

  1. Adam S., Bourtayre P., Liquier J., Taillandier E. Interaction of transition metal ions with Z form poly d(A-C).poly d(G-T) and poly d(A-T) studied by I.R. spectroscopy. Nucleic Acids Res. 1986 Apr 25;14(8):3501–3513. doi: 10.1093/nar/14.8.3501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Adnet F., Liquier J., Taillandier E., Singh M. P., Rao K. E., Lown J. W. FTIR study of specific binding interactions between DNA minor groove binding ligands and polynucleotides. J Biomol Struct Dyn. 1992 Dec;10(3):565–575. doi: 10.1080/07391102.1992.10508668. [DOI] [PubMed] [Google Scholar]
  3. Arnott S., Selsing E. Structures for the polynucleotide complexes poly(dA) with poly (dT) and poly(dT) with poly(dA) with poly (dT). J Mol Biol. 1974 Sep 15;88(2):509–521. doi: 10.1016/0022-2836(74)90498-7. [DOI] [PubMed] [Google Scholar]
  4. Cheng Y. K., Pettitt B. M. Stabilities of double- and triple-strand helical nucleic acids. Prog Biophys Mol Biol. 1992;58(3):225–257. doi: 10.1016/0079-6107(92)90007-s. [DOI] [PubMed] [Google Scholar]
  5. Edwards K. J., Jenkins T. C., Neidle S. Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties. Biochemistry. 1992 Aug 11;31(31):7104–7109. doi: 10.1021/bi00146a011. [DOI] [PubMed] [Google Scholar]
  6. Ghomi M., Letellier R., Liquier J., Taillandier E. Interpretation of DNA vibrational spectra by normal coordinate analysis. Int J Biochem. 1990;22(7):691–699. doi: 10.1016/0020-711x(90)90003-l. [DOI] [PubMed] [Google Scholar]
  7. Letellier R., Ghomi M., Taillandier E. Interpretation of DNA vibration modes. II--The adenosine and thymidine residues involved in oligonucleotides and polynucleotides. J Biomol Struct Dyn. 1987 Feb;4(4):663–683. doi: 10.1080/07391102.1987.10507667. [DOI] [PubMed] [Google Scholar]
  8. Liquier J., Mchami A., Taillandier E. FTIR study of netropsin binding to poly d(A-T) and poly dA.poly dT. J Biomol Struct Dyn. 1989 Aug;7(1):119–126. doi: 10.1080/07391102.1989.10507755. [DOI] [PubMed] [Google Scholar]
  9. Otto C., Thomas G. A., Rippe K., Jovin T. M., Peticolas W. L. The hydrogen-bonding structure in parallel-stranded duplex DNA is reverse Watson-Crick. Biochemistry. 1991 Mar 26;30(12):3062–3069. doi: 10.1021/bi00226a012. [DOI] [PubMed] [Google Scholar]
  10. Pattabiraman N. Can the double helix be parallel? Biopolymers. 1986 Sep;25(9):1603–1606. doi: 10.1002/bip.360250903. [DOI] [PubMed] [Google Scholar]
  11. Pilet J., Brahms J. Dependence of B-A conformational change in DNA on base composition. Nat New Biol. 1972 Mar 29;236(65):99–100. doi: 10.1038/newbio236099a0. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Rippe K., Jovin T. M. Parallel-stranded duplex DNA. Methods Enzymol. 1992;211:199–220. doi: 10.1016/0076-6879(92)11013-9. [DOI] [PubMed] [Google Scholar]
  14. Rippe K., Ramsing N. B., Jovin T. M. Spectroscopic properties and helical stabilities of 25-nt parallel-stranded linear DNA duplexes. Biochemistry. 1989 Nov 28;28(24):9536–9541. doi: 10.1021/bi00450a043. [DOI] [PubMed] [Google Scholar]
  15. Rippe K., Ramsing N. B., Klement R., Jovin T. M. A parallel stranded linear DNA duplex incorporating dG.dC base pairs. J Biomol Struct Dyn. 1990 Jun;7(6):1199–1209. doi: 10.1080/07391102.1990.10508559. [DOI] [PubMed] [Google Scholar]
  16. TSUBOI M., KYOGOKU Y., SHIMANOUCHI T. Infrared absorption spectra of protonated and deprotonated nucleosides. Biochim Biophys Acta. 1962 Jan 22;55:1–12. doi: 10.1016/0006-3002(62)90925-3. [DOI] [PubMed] [Google Scholar]
  17. Taillandier E., Liquier J. Infrared spectroscopy of DNA. Methods Enzymol. 1992;211:307–335. doi: 10.1016/0076-6879(92)11018-e. [DOI] [PubMed] [Google Scholar]
  18. Taillandier E., Ridoux J. P., Liquier J., Leupin W., Denny W. A., Wang Y., Thomas G. A., Peticolas W. L. Infrared and Raman studies show that poly(dA).poly(dT) and d(AAAAATTTTT)2 exhibit a heteronomous conformation in films at 75% relative humidity and a B-type conformation at high humidities and in solution. Biochemistry. 1987 Jun 16;26(12):3361–3368. doi: 10.1021/bi00386a017. [DOI] [PubMed] [Google Scholar]
  19. Tchurikov N. A., Chernov B. K., Golova Y. B., Nechipurenko Y. D. Parallel DNA: generation of a duplex between two Drosophila sequences in vitro. FEBS Lett. 1989 Nov 6;257(2):415–418. doi: 10.1016/0014-5793(89)81585-6. [DOI] [PubMed] [Google Scholar]
  20. Zhou N., Germann M. W., van de Sande J. H., Pattabiraman N., Vogel H. J. Solution structure of the parallel-stranded hairpin d(T8<text text>C4A8) as determined by two-dimensional NMR. Biochemistry. 1993 Jan 19;32(2):646–656. doi: 10.1021/bi00053a033. [DOI] [PubMed] [Google Scholar]
  21. Zimmer C., Wähnert U. Nonintercalating DNA-binding ligands: specificity of the interaction and their use as tools in biophysical, biochemical and biological investigations of the genetic material. Prog Biophys Mol Biol. 1986;47(1):31–112. doi: 10.1016/0079-6107(86)90005-2. [DOI] [PubMed] [Google Scholar]

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

RESOURCES