Beilstein J. Org. Chem. 2019, 15, 79–88.
dicate that the 6’-diF-bc4,3-DNA and the 6’F-bc4,3-DNA may the natural DNA/RNA duplex. This is a promising finding
find application in therapeutic gapmer oligonucleotides.
which points to a possible application for both modifications in
therapeutic gapmer oligonucleotides.
Supporting Information
Supporting Information File 1
Additional information, experimental procedures, NMR
Acknowledgements
We gratefully acknowledge the financial support by the Swiss
National Science Foundation (grant-no: 200020_165778). We
thank the group of Chemical Crystallography of the University
of Bern (Prof. Dr. P. Macci) for the X-ray structure and the
Swiss National Science Foundation (R’equip project
Figure 5: Hydrolysis products of the RNase H activation assay. The
DNA served as positive control, whereas C1 (no antisense strand) and
C2 (no enzyme) were negative controls.
2
06021_128724) for co-funding of the single crystal X-ray
diffractometer at the Department of Chemistry and Biochem-
istry of the University of Bern.
Conclusion
In this report, we presented the successful synthesis of the
6
’-diF-bc4,3-T building block where the gem-difluorinated ORCID® iDs
bicyclic unit was formed starting from a previously described
tricyclic siloxydifluorocyclopropane. The reaction of this
tricyclic sugar under NIS-mediated nucleosidation produced References
two diiodo-substituted intermediates which were reduced by
Bu3SnH yielding the β-nucleoside 6 as the only diastereoiso-
mer. The crystal structure of nucleoside 6 exhibited the C2’-
endo conformation of the furanose ring and the gauche orienta-
tion of the torsions angle γ. Conversion of this nucleoside into
the corresponding phosphoramidite building block and its incor-
poration into oligonucleotides was then successfully achieved.
Thermal melting experiment of the modified oligonucleotides
paired to complementary DNA or RNA revealed a prominent
duplex destabilization for both duplex types (ΔTm/mod = −1.6
to −5.5 °C). A lesser degree of destabilization was observed for
oligonucleotides containing several consecutive modifications
hybridized to complementary RNA. The reason for the destabi-
lization might be accounted to repulsive electrostatic interac-
tions between the equatorial fluorine atom and the 5’-oxygen.
CD spectroscopy of the duplexes disclosed that the helical
structure of the modified oligonucleotides paired to comple-
mentary DNA was still of a B-type, whereas an intermediate
A/B-type helix was observed for RNA as complement. Further-
more, the RNase H assay of the oligonucleotide containing
either five consecutive 6’-diF-bc4,3-Ts or 6’F-bc4,3-Ts paired to
complementary RNA revealed that both modifications were
able to recruit this enzyme. In both cases the RNase H cleaved
the complementary RNA strand less efficiently as compared to
2.
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3
.
.
4
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5.
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9
1
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Kawasaki, A. M.; Casper, M. D.; Freier, S. M.; Lesnik, E. A.;
Damha, M. J.; Wilds, C. J.; Noronha, A.; Brukner, I.; Borkow, G.;
0.Ikeda, H.; Fernandez, R.; Barchi, J. J., Jr.; Huang, X.; Marquez, V. E.;
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