The complete family of ApA phosphonate analogues with the internucleotide linkage elongated by insertion of a -CH2- group was prepared and the hybridisation and structural properties of its members in interaction with polyuridylic acid were investigated using an original 2D Raman approach. Except for the conformationally restricted A(CH)pA(2'3'endo-5') modification, all of the isopolar, non-isosteric analogues form triplex-like complexes with poly(rU) at room temperature, in which two polymer strands are bound by Watson-Crick and Hoogsteen bonds to a central pseudostrand consisting of a 'chain' of A-dimers. For all of these dimers, the overall conformation of the triplexes was found to be similar according to their extracted Raman spectra. A simple semi-empirical model was introduced to explain the observed dependency of the efficiency of triplex formation on the adenine concentration. Apparently, for most of the modifications studied, the creation of a stable complex at room temperature requires the formation of a central pseudostrand, consisting of several adenine dimers. Molecular dynamics calculations were finally performed to interpret the differences in 'cooperative' behaviour between the different dimers studied. The results indicate that the exceptional properties of the Ap(CH2)A(3'-5') dimer could be caused by the 3D conformational compatibility of this modified linkage with the second (Hoogsteen) poly(rU) strand.

Charles University Institute of Physics Ke Karlovu 5 CZ 121 16 Praha 2 Czech Republic

Zobrazit více v PubMed

Blake R.D., Massoulie,J. and Fresco,J.R. (1967) Polynucleotides. 8. A spectral approach to the equilibria between polyriboadenylate and polyribouridylate and their complexes. J. Mol. Biol., 30, 291–308. PubMed

Huang W.M. and Ts’o,P.O. (1966) Physicochemical basis of the recognition process in nucleic acid interactions. I. Interactions of polyuridylic acid and nucleosides. J. Mol. Biol., 16, 523–543. PubMed

Cantor C.R. and Chin,W.W. (1968) Oligonucleotide interactions. I. Structure of 2:1 complexes between polyuridylic acid and oligoadenylic acid. Biopolymers, 6, 1745–1752 PubMed

Davies R.J. and Davidson,N. (1971) Base pairing equilibria between polynucleotides and complementary monomers. Biopolymers, 10, 1455–1479. PubMed

Damle V.N. (1970) On the helix-coil equilibrium in two- and three-stranded complexes involving complementary poly- and oligonucleotides. Biopolymers, 9, 353–372. PubMed

Damle V.N. (1970) Theory of interaction of polymer and small molecules which can aggregate in solution. Biopolymers, 9, 1437–1443. PubMed

Damle V.N. (1972) Three-stranded helix-coil equilibrium in polyuridylic acid-adenosine complex. Biopolymers, 11, 1789–1816. PubMed

Pitha P.M. and Ts’o,P.O. (1969) The interactions of adenosine and adenine heptanucleoside hexaphosphate with polyuridylic acid. Biochemistry, 8, 5206–5217. PubMed

Michelson A.M. and Monny,C. (1967) Polynucleotides. X. Oligonucleotides and their association with polynucleotides. Biochim. Biophys. Acta, 149, 107–126. PubMed

Zamecnik P.C. and Stephenson,M.L. (1978) Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. Proc. Natl Acad. Sci. USA, 75, 280–284. PubMed PMC

Milligan J.F., Matteucci,M.D. and Martin,J.C. (1993) Current concepts in antisense drug design. J. Med. Chem., 36, 1923–1937. PubMed

Monia B.P., Sasmor,H., Johnston,J.F., Freier,S.M., Lesnik,E.A., Muller,M., Geiger,T., Altman,K.-H., Moser,H. and Fabbro,D. (1996) Sequence-specific antitumor activity of a phosphorothioate oligodeoxyribonucleotide targeted to human C-raf kinase supports an antisense mechanism of action in vivo. Proc. Natl Acad. Sci. USA, 93, 15481–15484. PubMed PMC

Crooke S.T. (1998) An overview of progress in antisense therapeutics. Antisense Nucleic Acid Drug Dev., 8, 115–122. PubMed

Crooke S.T. (1998) Molecular mechanisms of antisense drugs: RNase H. Antisense Nucleic Acid Drug Dev., 8, 133–134. PubMed

Rawls R.L. (1997) Optimistic about antisense. Chem. Eng. News, 35–39.

Freier S.M. and Altmann,K.H. (1997) The ups and downs of nucleic acid duplex stability: structure–stability studies on chemically-modified DNA:RNA duplexes. Nucleic Acids Res., 25, 4429–4443. PubMed PMC

DeClercq E., Hol,A., Rosenberg,I., Sakuma,T., Balzarini,J. and Maudgal,P.C. (1986) A novel selective broad-spectrum anti-DNA virus agent. Nature, 323, 464–467. PubMed

Cihláé T., Rosenberg,I., Votruba,I. and Hol,A. (1995) Transport of 9-(2-phosphonomethoxyethyl)adenine across plasma membrane of HeLa S3 cells is protein mediated. Antimicrob. Agents Chemother., 39, 117–124. PubMed PMC

Rejman D., Snáel,J., Liboka,R., Toík,Z., Paes,O., Králíková,., Rinnová,M., Koi,P. and Rosenberg,I. (2001) Oligonucleotides with isopolar phosphonate internucleotide linkage: a new perspective for antisense compounds? Nucleosides Nucleotides Nucleic Acids, 20, 819–823. PubMed

Pressová M., Endová,M., Toík,Z., Liboka,R. and Rosenberg,I. (1998) UV spectroscopy study on complexes of phosphonate ApA analogs with poly(U): promising step in prediction of oligonucleotide analog properties? Bioorg. Med. Chem. Lett., 8, 1225–1230. PubMed

trajbl M. and Florián,J. (1996) Ab initio investigation of the molecular structure of methyl methoxymethyl phosphonate, a promising nuclease-resistant alternative of the phosphodiester linkage. J. Biomol. Struct. Dyn., 13, 687–694. PubMed

trajbl M., Baumruk,V., Florián,J. Bednárová,L. Rosenberg,I. and tÆpánek,J. (1997) Molecular structure, vibrational spectra and quantum mechanical force fields of modified oligonucleotide linkages. 1. Methyl methoxymethanphosphonate. J. Mol. Struct., 415, 161–177.

Zajíek J. Rosenberg,I. Liboska,R. Toík,Z. Fazakerley,G.V., Guschlbauer,W. and Hol,A. (1997) Conformational studies on diribonucleoside monophosphate analogs containing a nonisosteric, isopolar, phosphonate-based internucleotide linkage. Collect. Czech Chem. Commun., 62, 83–98.

Zachová J., Císaéová,I., BudÆínsk,M., Liboka,R., Rosenberg,I. and Toík,Z. (1999) Crystal and solution structure of 5′-O-(guanosine-2′-O-phosphonomethyl) cytidine, an isopolar nonisosteric phosphonate analog of GpC. Nucl. Nucl., 18, 2581–2599.

Mojze P., tÆpánek,J., Rosenberg,I., Toík,Z., Burian,M., Pavelíková,M., Refregiers,M. and Videlot,H. (1995) Structural and conformational properties of phosphonylmethyl analogs of diribonucleoside monophosphates studied by Raman spectroscopy. J. Mol. Struct., 348, 45–48.

tÆpánek J., Hanu,J., Endová,M., Dole,J., Toík,Z. and Rosenberg,I. (1997) Impact of the internucleotide linkage modification on the conformation and structural properties of antisense oligonucleotides: a Raman spectroscopy study. In Carmona,P. et al. (eds) Spectroscopy of Biological Molecules: Modern Trends. Kluwer Academic, Dordrecht, The Netherlands, pp. 239–340.

Hanu J., Chmelová,K., tÆpánek,J. Turpin,P.-Y., Bok,J., Rosenberg,I. and Toík,Z. (1999) Raman spectroscopic study of triplex-like complexes of polyuridylic acid with the isopolar, non-isosteric phosphonate analogues of diadenosine monophosphate. J. Raman Spectrosc., 30, 667–676.

Malinowski E.R. (1991) Factor Analysis in Chemistry. Wiley, New York, NY.

Cornell W.D., Cieplak,P., Bayly,Ch.I., Gould,I.R., Merz,K.M.Jr, Ferguson,D.M., Spellmeyer,D.C., Fox,T., Caldwell,J.W. and Kollman,P.A. (1995) A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc., 117, 5179–5197.

Barvík I.Jr, tÆpánek,J. and Bok,J. (1998) Molecular dynamics simulations of the oligonucleotide with the modified phosphate/phosphonate internucleotide linkage. Czech. J. Phys., 48, 409–415. PubMed

Barvík I.Jr, tÆpánek,J. and Bok,J. (2001) Fully solvated Molecular dynamics simulation of a duplex formed by a modified oligonucleotide with alternating phosphate/phosphonate internucleoside linkages and its natural counterpart. J. Biomol. Struct. Dyn., in press. PubMed

Darden T., York,D. and Pedersen,L. (1993) Particle Mesh Ewald: an N.log(N) method for Ewald sums in large systems. J. Chem. Phys., 98, 10089–10092.

Peticolas W.L, Kubasek,W.L., Thomas,G.A. and Tsuboi,M. (1987) Nucleic acids. In Spiro,T.G. (ed.) Biological Applications of Raman Spectroscopy. Vol. 1. Raman Spectra and the Conformation of Biological Macromolecules. John Wiley & Sons, New York, NY, pp. 81–133.

Thomas G.J. and Tsuboi,M. (1993) Raman spectroscopy of nucleic acids and their complexes. Adv. Biophys. Chem., 3, 1–70.

Grygon C.A. and Spiro,T.G. (1990) UV resonance Raman spectroscopy of nucleic acid duplexes containing A-U and A-T base pairs. Biopolymers, 29, 707–715.

Leulliot N. (1999) Analyse expérimentale et théorique du repliement de l‘ARN: diffusion Raman, absorption infrarouge et ultraviolette, diffusion inélastique de neutrons et modèlisation moléculaire quantique. PhD thesis, Université Pierre et Marie Curie ParisVI, Paris, France.

Nishimura Y., Tsuboi,M., Kubasek,W.L., Bajdor,K. and Peticolas,W.L. (1987) Ultraviolet resonance Raman bands of guanosine and adenosine residues useful for the determination of nucleic acid conformation. J. Raman Spectrosc., 18, 221–227.

Borer P.N., Dengler,B., Tinoco,I.Jr and Uhlenbeck,O.C. (1974) Stability of ribonucleic acid double-stranded helices. J. Mol. Biol., 86, 843–853. PubMed

Saenger W. (1984) Principles of Nucleic Acid Structure. Springer Verlag, New York, NY.