NMR Study on the Photoresponsive DNA Tethering an Azobenzene. Assignment of the Absolute Configuration of Two Diastereomers and Structure Determination of Their Duplexes in the trans-Form

Journal of the American Chemical Society

Volumn 125, Issue 52, 2003, Pages 16408-16415

  Liang, Xingguo ^a   Asanuma, Hiroyuki ^a,b   Kashida, Hiromu ^a   Takasu, Akitsugu ^c,d,e   Sakamoto, Taiichi ^c   Kawai, Gota ^c   Komiyama, Makoto ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c CHIBA INSTITUTE OF TECHNOLOGY   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

^e RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BONDS; CONFORMATIONS; DNA; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; INTERCALATION COMPOUNDS; MELTING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHOTOCHEMICAL REACTIONS; PROTONS; STEREOCHEMISTRY;

DIASTEREOMERS;

AROMATIC COMPOUNDS;

2,2 BIS(HYDROXYMETHYL)PROPIONIC ACID; AZO COMPOUND; AZOBENZENE; AZOBENZENE DERIVATIVE; CROSS LINKING REAGENT; DNA; OLIGORIBONUCLEOTIDE; PROPIONIC ACID DERIVATIVE; PROTON; THYMINE; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; CHIRALITY; CONFORMATION; DIASTEREOISOMER; INTERCALATION COMPLEX; MELTING POINT; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PHOTOREACTIVITY; RADIATION EXPOSURE; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; STRUCTURE ANALYSIS; TRANS ISOMER;

AZO COMPOUNDS; CROSS-LINKING REAGENTS; DNA; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION;

EID: 0347064289     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja037248j     Document Type: Article

References (24)

1. Willner, I.; Rubin, S. Angew. Chem., Int. Ed. Engl. 1996, 35, 367.
2. Hohsaka, T.; Kawashima, K.; Sisido, M. J. Am. Chem. Soc. 1994, 116, 413.
3. (a) Asanuma, H.; Ito, T.; Yoshida, T.; Liang X. G.; Komiyama, M. Angew. Chem., Int. Ed. 1999, 38, 2393-2395.
4. (b) Asanuma, H.; Liang X. G.; Yoshida, T.; Komiyama, M. ChemBioChem. 2000, 2, 39-44.
5. (c) Yamazawa, A.; Liang, X. G.; Asanuma, H.; Komiyama, M. Angew. Chem., Int. Ed. 2000, 39, 2356-2358.
6. (d) Asanuma, H.; Tamaru, D.; Yamazawa, A.; Liu, M. Z.; Komiyama, M. ChemBioChem. 2002, 3, 786-89.
7. Asanuma, H.; Ito, T.; Komiyama, M. Tetrahedron Lett. 1998, 39, 9015-9018.
8. By this combination, X residue is additionally incorporated into the natural full-matched 6-mer duplex.
9. Although 1D and 2D NMR spectra of the duplex containing cis-azobenzene were also measured, the spectra were too complicated to be solved because of the thermal instability of the duplex of the cis-form and the influence of the much more stable trans-form duplex (only 70% is isomerized to the cis-form under the conditions employed).
10. Proton signals of the pairs of 2 and 6, 3 and 5, 8 and 12, and 9 and 11 on the azobenzene were equivalent to each other even in the duplex.
11. All of the NOEs concerning the azobenzene are displayed with lines on the structure in Supporting Information Figure 1.
12. Stereoviews of the duplexes from other angles are shown in Supporting Information Figure 2.
13. The melting curves of both Azo-α/C and Azo-β/C duplexes either in the trans- or in the cis-form are presented in Supporting Information Figure 3.
14. Azobenzene was tethered on the chiral threoninol that has a structure similar to that of the present prochiral 2,2-bis(hydroxymethyl)propionic acid (Asanuma, H.; Takarada, T.; Yoshida, T.; Tamaru, D.; Liang, X.; Komiyama, M. Angew. Chem., Int. Ed. 2001, 40, 2671-2673). A similar dependence in melting temperature (R-form > S-form) for the chirality of the linker was observed. See Supporting Information Scheme. 1 and Supporting Information Table 1.
15. In the present paper, the X residue is additionally incorporated into one strand of the full-matched natural double strands (7-mer/6-mer nonsymmetrical combination). However, placement of a nucleobase as the counterpart of the X residue, such as a 5′-CGAXGTC-3′/3′ -GCTTCAG-5′ (7-mer/7-mer symmetrical combination) duplex, destabilizes the duplex because intercalated trans-azobenzene directly faces the extra nucleobase and a mismatch-like structure is formed.
16. Jeener, J.; Meier, B. H.; Bachmann, P.; Ernst, R. R. J. Chem. Phys. 1979, 71, 4546-4553.
17. Marion, D.; Ikura, M.; Tschudin, R.; Bax, A. J. Magn. Reson. 1989, 85, 393-399.
18. Plateau, P.; Gueron, M. J. Am. Chem. Soc. 1982, 104, 7310-7311.
19. 2O by use of a 3-9-19 WATER-GATE pulse sequence and confirmed that the sets of restraints for the calculation obtained from Jump and Return and WATERGATE were almost the same.
20. Griesinger, C.; Otting, G.; Wüthrich, K.; Freeman, R. J. Am. Chem. Soc, 1988, 110, 7870-7872.
21. Shaka, A. J.; Freeman, R. J. Magn. Reson. 1983, 51, 169-173.
22. This result indicates that spin diffusion at 100 ms is still small and does not affect the distance interpretation. Note that the loose restraints were used for structural calculations.
23. Allain, F. H.-T.; Varani, G. J. Mol. Biol. 1995, 250, 333-353.
24. Dauber-Osguthorpe, P.; Roberts, V. A.; Osguthorpe, D. J.; Wolff, J.; Genest. M.; Hagler, A. T. Proteins 1988, 4, 31-47.