Opposite orientation of backbone inclination in pyranosyl-RNA and homo-DNA correlates with opposite directionality of duplex properties

Angewandte Chemie - International Edition

Volumn 38, Issue 5, 1999, Pages 680-683

  Micura, Ronald ^a   Kudick, Rene ^a   Pitsch, Stefan ^a   Eschenmoser, Albert ^a  

^a NONE

Author keywords

DNA structures; Duplex stability; Homo DNA; Oligonucleotides; Pyranosyl RNA

Indexed keywords

DOUBLE STRANDED DNA; NUCLEIC ACID; OLIGONUCLEOTIDE; RNA;

ARTICLE; BASE PAIRING; CHIRALITY; DNA CONFORMATION; DNA SEQUENCE; DNA STRUCTURE; MOLECULAR STABILITY; NUCLEIC ACID ANALYSIS; RNA CONFORMATION; RNA SEQUENCE; RNA STRUCTURE; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; THERMODYNAMICS; THERMOSTABILITY;

EID: 0033106373     PISSN: 14337851     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1521-3773(19990301)38:5<680::AID-ANIE680>3.0.CO;2-C     Document Type: Article

References (23)

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2. b) S. Pitsch, R. Krishnamurthy, M. Bolli, S. Wendeborn, A. Holzner, M. Minton, C. Lesueur, I. Schlönvogt, B. Jaun, A. Eschenmoser, Helv. Chim. Acta 1995, 78, 1621-1635;
3. c) I. Schlönvogt, S. Pitsch, C. Lesueur, A. Eschenmoser, B. Jaun, R. M. Wolf, Helv. Chim. Acta 1996, 79, 2316-2345;
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5. Angew. Chem. Int. Ed. Engl. 1997, 36, 870-873;
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7. f) M. Bolli, R. Micura, S. Pitsch, A. Eschenmoser, Helv. Chim. Acta 1997, 80, 1901-1951.
8. a) A. Eschenmoser, M. Dobler, Helv. Chim. Acta 1992, 75, 218-259;
9. b) M. Böhringer, H.-J. Roth, J. Hunziker, M. Göbel, R. Krishnan, A. Giger, B. Schweizer, J. Schreiber, C. Leumann, A. Eschenmoser, Helv. Chim. Acta 1992, 75, 1416-1477;
10. c) J. Hunziker, H.-J. Roth, M. Böhringer, A. Giger, U. Diederichsen, M. Göbel, R. Krishnan, B. Jaun, C. Leumann, A. Eschenmoser, Helv. Chim. Acta 1993, 76, 259-352;
11. d) G. Otting, M. Billeter, K. Wüthrich, H.-J. Roth, C. Leumann, A. Eschenmoser, Helv. Chim. Acta 1993, 76, 2701-2756;
12. e) K. Groebke, J. Hunziker, W. Fraser, L. Peng, U. Diederichsen, K. Zimmermann, A. Holzner, C. Leumann, A. Eschenmoser, Helv. Chim. Acta 1998, 81, 375-474.
13. [11] Such an interpretation seems supported by the relative duplex stabilities of No. 9 and 10. In these sequences the (compulsory) frameshifts can occur upstream (in p-RNA) and downstream (in homo-DNA) so that duplex No. 9 with four, as opposed to three, adenine - adenine stackings is the more stable one in both systems (see Figure 2).
14. For the assessment of sequence dependence of duplex stabilities in the DNA and RNA series, empirical nearest neighbor parameters are used which do not explicitly differentiate between intra- and interstrand base stacking; see N. Sugimoto, S. Nakano, M. Yoneyama, K. Honda, Nucleic Acids Res. 1996, 24, 4501-4505;
15. J. SantaLucia, Jr., H. T. Allawi, P. A. Seneviratne, Biochemistry 1996, 35, 3555-3562, and references therein.
16. On the influence of dangling bases in the DNA and RNA series see N. Sugimoto, R. Kierzek, D. H. Turner, Biochemistry 1987, 26, 4554-4558;
17. M. Senior, R. A. Jones, K. J. Breslauer, Biochemistry 1988, 27, 3879-3885.
18. In oligonucleotide systems without (or with small) backbone inclination, base stacking is predominately intrastrand; this is the case, for instance, for DNA duplexes of the B-type (but less so for the A-type). The backbone inclination in a strongly helical duplex is not an easily discernible parameter and it is therefore understandable that it has not been used for the classification of DNA and RNA structures (see R. E. Dickerson et. al., Nucleic Acids Res. 1989, 17, 1797-1803). Backbone inclination may nevertheless become a useful parameter for natural nucleic acids when it comes to a detailed structural description of stacking-dependent biological processes such as replication, transcription and codon/anticodon recognition. Local alterations of backbone inclination can arise through corresponding local alterations of nucleosidic torsion angles. Since local strand dissociation processes may proceed with retention of intrastrand, but must occur with breakage of interstrand stacking, such local structural fluctuations can result in local fluctuations of pairing strength within a duplex. To what extent such effects are significant in biological processes of the type mentioned above is an open, yet interesting, question. The definition of backbone inclination for helical duplexes and the application of this parameter for differentiating DNA and RNA duplex structures will be described in a forthcoming paper together with M. Egli (Northwestern University, Illinois, USA).
19. For CD spectroscopy of oligonucleotides of the natural series see W. C. Johnson, Jr. in Circular Dichroism and the Conformational Analysis of Biomolecules (Ed.: G. D. Fasman), Plenum Press, New York, 1996, p. 433-468.
20. See for example: I. Jodal, A. Kovacs, J. Ott, G. Snatzke, Chem. Ber. 1989, 122, 1207-1210.
21. The NMR structure analysis of the p-RNA and homo-DNA duplexes described in references [1c, 2d] did not allow the determination of these data.
22. L. Marky, K. J. Breslauer, Biopolymers 1987, 26, 1601-1620.
23. Data of the homo-DNA duplexes No. 7, 9, and 10 were determined by S. Guntha (ETH, Zürich).