6-Azapyrimidine and 7-deazapurine 2′-deoxy-2′- fluoroarabinonucleosides: Synthesis, conformation and properties of oligonucleotides

Article abstract of DOI:10.1081/NCN-200059181

The synthesis of 2′-deoxy-2′-fluoro-β-D-arabinofuranosyl nucleosides (1b, 2b, and 3b) were described and their conformation in solution as well as in the solid state was determined. In addition to this, building blocks 10a,b and 13a,b were prepared and em

Full text of DOI:10.1081/NCN-200059181

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6-AZAPYRIMIDINE AND 7-DEAZAPURINE 2′-
DEOXY-2′-FLUOROARABINONUCLEOSIDES:
SYNTHESIS, CONFORMATION AND PROPERTIES OF
OLIGONUCLEOTIDES
Frank Seela a b , Padmaja Chittepu a b , Yang He a b , Junlin He a b & Kuiying Xu a b
a Laboratorium für Organische und Bioorganische Chemie , Institut für Chemie, Universität
Osnabrück , Osnabrück, Germany
b Center for Nanotechnology (CeNTech) , Münster, Germany
Published online: 15 Nov 2011.
To cite this article: Frank Seela , Padmaja Chittepu , Yang He , Junlin He & Kuiying Xu (2005) 6-AZAPYRIMIDINE
AND 7-DEAZAPURINE 2′-DEOXY-2′-FLUOROARABINONUCLEOSIDES: SYNTHESIS, CONFORMATION AND PROPERTIES OF
OLIGONUCLEOTIDES, Nucleosides, Nucleotides and Nucleic Acids, 24:5-7, 847-850, DOI: 10.1081/NCN-200059181
To link to this article: http://dx.doi.org/10.1081/NCN-200059181
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Nucleosides, Nucleotides, and Nucleic Acids, 24 (5–7):847–850, (2005)
Copyright D Taylor & Francis, Inc.
ISSN: 1525-7770 print/ 1532-2335 online
DOI: 10.1081/NCN-200059181
6-AZAPYRIMIDINE AND 7-DEAZAPURINE
2’-DEOXY-2’-FLUOROARABINONUCLEOSIDES:
SYNTHESIS, CONFORMATION AND PROPERTIES
OF OLIGONUCLEOTIDES
Frank Seela, Padmaja Chittepu, Yang He, Junlin He, and Kuiying Xu
5
Laboratorium fu¨r Organische und Bioorganische Chemie, Institut fu¨r Chemie, Universita¨t
Osnabru¨ck, Osnabru¨ck, Germany and Center for Nanotechnology (CeNTech), Mu¨nster, Germany
5
The synthesis of 2’-deoxy-2’-fluoro-b-D-arabinofuranosyl nucleosides (1b, 2b, and 3b) were
described and their conformation in solution as well as in the solid state was determined. In addition to
this, building blocks 10a,b and 13a,b were prepared and employed in solid-phase oligonucleotide
synthesis. For compounds 1a and 1b the lactime proton is protected to avoid unresolved degradation of its
phosphoramidites 10a,b. UV-melting studies have been carried out to assess the thermal stability of
oligonucleotides containing compounds 1a,b, and 3a,b.
Keywords Conformation, Imide Protection, Solid-Phase Synthesis
INTRODUCTION
The introduction of a fluorine substituent into a naturally occuring nucleoside
strongly effects the chemical, physical, and biological properties of the molecule.[1]
Among the various positions used for the fluorination, the 5-position of a
pyrimidine moiety and/or the 2’-position of the sugar moiety are the most important
modification sites. Recently, it was shown that the 2’-deoxy-2’-fluoro-b-D-
arabinofuranosyl pyrazolo[3,4-d]pyrimidines display significant activity against
HBV.[2] The 2’-fluorine atom strongly influences the S/N conformational
equilibrium of the pentofuranose ring. To explore this, we synthesized the 2’-
deoxy-2’-fluoro-b-D-arabinofuranosyl nucleosides 1b,2b,3b as well as their 2’-
deoxyribo nucleoside analogues 1a,2a,3a and investigated their conformation in
the solid state and in solution (Scheme 1).
We gratefully acknowledge the financial support by the European Community (Grant No.: QLRT-2001-
00506, ‘‘Flavitherapeutics’’).
Address correspondence to Frank Seela, Laboratorium fu¨r Organische und Bioorganische Chemie, Institut
fu¨r Chemie, Universit¨at Osnabru¨ck, Barbarastr. 7, Osnabru¨ck 49069, Germany.
847
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848
F. Seela et al.
SCHEME 1
RESULTS AND DISCUSSION
The nucleosides 3a,b were synthesized using the 5-fluoropyrrolo[2,3-
d]pyrimidine base 4[3] and the sugar components 5 or 6 by nucleobase anion
glycosylation. The intermediates 7a,b were deblocked to give pyrrolo[2,3-
d]pyrimidine nucleosides 3a,b (Scheme 2).
Single crystal X-ray analysis of compounds 1b[4] and 3b established an N-
conformation. A conformational analysis of the furanose ring was performed also in
3
3
1
solution from the J(H,H) and J(H,F) coupling constants of H-NMR spectra
measured in (D2O) applying PSEUROT program (Version 6.3).[5] According to
Table 1 the 2’-up fluorine atom shifts the sugar conformation from S to N
(2a:29%N; 2b:37%N[6] and 3a:30%N; 3b:33%N). When a nitrogen atom is located
next to the glycosylation site, both the gauche effect of the 2’-fluoro substituent and
the anomeric effect of the nucleobase drive the sugar conformation almost
exclusively to N.[7] (100% N-conformation for 1b).
In order to investigate properties of oligonucleotides containing the nucleoside
residues 1a,b and 3a,b, the phosphoramidites 10a,b and 13a,b were prepared
and employed in solid-phase synthesis. However, difficulties appeared upon the
isolation of the phosphoramidites of 1a,b without base protection. The presence of
nitrogen at position-6 makes the lactim moiety acidic and degrades the
phosphoramidite residue. To avoid this, protecting groups were introduced.
Among them, the o-anisoyl chloride was found to be the best protecting group.
Thus, compounds 8a,b were prepared and converted via 9a,b to 10a,b. In a
SCHEME 2

F. Seela et al.
849
TABLE 1 Sugar Conformation of the Modified
Nucleosides in Solution
Conformation
Compound
% N
% S
1a
1b
2a
2b
3a
3b
58
100
29
37
30
42
0
71
63
70
67
33
similar way the nucleosides 3a,b were transformed to 13a,b (Scheme 3). Both
phosphoramidites gave high coupling yields (>99%) in oligonucleotide synthesis.
Oligonucleotides containing 1a,b or 3a,b were synthesized and hybridized to
form the duplexes shown in Table 2. As only hybridization experiments have been
performed in the DNA series it was expected that a modification with 1a,b
decreases the Tm values due to the presence of a nitrogen at the 6-position.[8]
A
fluorine substituent present in the 5-position as in compound 3a stabilizes the
duplex slightly, while two fluorine residues as in compound 3b lead to the same Tm
as found for the standard duplex. Studies with respect to DNA-RNA hybrids are
currently performed.
The conformational analysis of a number of 2’-deoxy-2’-fluoro-b-D-arabinonu-
cleosides in solution as well as in solid state was performed. The most striking
observation is that some of the ortho-azanucleosides (1b) with a fluoro subtituent
on the 2’-arabino position exclusively exists in an unusually rigid N-conformation in
SCHEME 3

850
F. Seela et al.
TABLE 2 Tm Values, Thermodynamic Data of Oligonucleotide Duplexes Containing Regular and Base
Modified Nucleosides 1a, 1b, 3a, 4b
DG310° (kcal/mol)c
b
Duplex
Tm (°C)
DTm
5’-d(AGTATTGACCTA)3’-d(TCATAACTGGAT)
5’-d(AG1aATTGACC1aA)3’-d(TCATAACTGGAT)
5’-d(TAGG1aCAA1aACT)3’-d(ATCCAGTTATGA)
5’d(AG1bA1b1bGACC1bA)3’-d(TCATAACTGGAT)
5’-d(AGT3aTTG3aCCTA)3’-d(TCATAACTGGAT)
5’-d(AGT3bTTG3bCCTA)3’-d(TCATAACTGGAT)
50a
42a
38a
20a
53a
50a
0
À4
À6
À7.5
1.5
0
À12.0
À8.5
À7.0
À3.7
À12.4
À10.9
aData measured in 1 M NaCl, 100 mM MgCl2, and 60 mM Na-cacodylate buffer (pH 7.0).
bPer modified base pair.
c1 cal = 4.184 J.
solution due to the presence of a nitrogen atom located next to the glycosylation
site. Both the gauche effect of the 2’-fluoro atom and the anomeric effect of the
nucleobase drives the sugar moieties to adopt almost exclusively to the N-
conformation. Additionally, the importance of the lactime protecting group (N-3)
for the successful isolation of the phosphoramidites 10a,b was described. The
o-anisoylchloride was found to be the best protecting group.
REFERENCES
1. Fox, J.J.; Watanabe, K.A.; Chou, T.C.; Shinazi, R.F.; Soike, K.F.; Fourel, I.; Hantz, G.; Trepo, C. Flourinated
Carbohydrates; Taylor, N.F., Ed.; American Chemical Society, 1988; 176–190.
2. Shortnacy-Fowler, A.T.; Tiwari, K.N.; Montgomery, J.A.; Buckheit, R.W., Jr.; Secrist, J.A., III; Seela, F. Helv.
Chim. Acta 1999, 82, 2240–2245.
3. Wang, X.; Seth, P.P.; Ranken, R.; Swayze, E.E.; Migawa, M.T. Nucleosides Nucleotides Nucleic Acids 2004,
23(1–2), 161–170.
4. Seela, F.; Chittepu, P.; He, J.; Eickmeier, H. Acta Cryst. 2004, C60, submitted.
5. Van Wijk, L.; Haasnoot, C.A.G.; De Leeuw, F.A.A.M.; Huckriede, B.D.; Westra Hoekzema, A.J.A.; Altona, C.
PSEUROT 6.3; Leiden Institute of Chemistry, Leiden University: The Netherlands, 1999.
6. Peng, X.; Seela, F. Org. Biomol. Chem. 2004, in press.
7. He, J.; Mikhailopulo, I.; Seela, F. J. Org. Chem. 2003, 68, 5519–5524.
8. Sanghvi, Y.S.; Hoke, G.D.; Freier, S.M.; Zounes, M.C.; Gonzalez, C.; Cummins, L.; Sasmor, H.; Cook, P.D.
Nucleic Acids Res. 1993, 21(14), 3197–3203.