Synthesis of nucleosides with additional nucleobases

Article abstract of DOI:10.1080/15257770701542199

The syntheses of two nucleosides with additional nucleobases in the 2′-position are presented. The nucleosides have two- and one-carbon linkers to the additional nucleobase, respectively. The two nucleosides are synthesized from different strategies. The

Full text of DOI:10.1080/15257770701542199

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Nucleosides, Nucleotides and Nucleic
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Synthesis of Nucleosides with Additional
Nucleobases
Charlotte Andersen a , S⊘ren L. Pedersen a & Poul Nielsen a
a Nucleic Acid Center, Department of Chemistry and Physics ,
University of Southern Denmark , Odense, Denmark
Published online: 05 Dec 2007.
To cite this article: Charlotte Andersen , S⊘ren L. Pedersen & Poul Nielsen (2007) Synthesis of
Nucleosides with Additional Nucleobases, Nucleosides, Nucleotides and Nucleic Acids, 26:10-12,
1435-1438, DOI: 10.1080/15257770701542199
To link to this article: http://dx.doi.org/10.1080/15257770701542199
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Nucleosides, Nucleotides, and Nucleic Acids, 26:1435–1438, 2007
Copyright ꢀ Taylor & Francis Group, LLC
C
ISSN: 1525-7770 print / 1532-2335 online
DOI: 10.1080/15257770701542199
SYNTHESIS OF NUCLEOSIDES WITH ADDITIONAL NUCLEOBASES
Charlotte Andersen, Søren L. Pedersen, and Poul Nielsen
Nucleic Acid
2
Center, Department of Chemistry and Physics, University of Southern Denmark,
Odense, Denmark
The syntheses of two nucleosides with additional nucleobases in the 2ꢁ-position are presented.
2
The nucleosides have two- and one-carbon linkers to the additional nucleobase, respectively. The two
nucleosides are synthesized from different strategies. The nucleoside with two carbons in the linker
has been incorporated into oligonucleotides and showed stabilization of a tree-way junction.
Keywords Double-headed nucleobase; RNA secondary structure; 2ꢁ-modification
The secondary structures of RNA are targets for modified oligonucleotides.
In order to bind to RNA, forming other secondary structures than du-
plexes, oligonucleotides with additional nucleobases are suggested.[1,2] For
this purpose, we have developed different strategies in synthesizing dou-
ble headed nucleosides. These also can be useful in the design of double
coding DNA.[3] A linear strategy with uridine as starting material resulted
in the synthesis of 2ꢁ-deoxy-2ꢁ-C-(2-(thymine-1-yl)ethyl)uridine.[1] A conver-
gent strategy starting from D-ribose resulted in 2ꢁ-deoxy-2ꢁ-C-(thymine-1-
ylmethyl)uridine.
For the linear approach (Scheme 1), uridine was selectively protected at
the 3ꢁ-O- and 5ꢁ-O−positions and the 2ꢁ-hydroxygroup was replaced by the
allyl group in a radical deoxygenation reaction.[4] The olefin was converted
to the alcohol by an oxidative cleavage followed by a reduction. To avoid
intramolecular ring formation, the N3-position of uracil was protected by a
benzoyl group with a selective and very efficient phase-tranfer procedure.[5]
The additional nucleobase was introduced by a Mitsunobu reaction, and
deprotection gave the desired compound 1. The coupling constant JH1 ,H2
ꢁ
ꢁ
of 1 was 8.5 Hz indicating that the molecule primarily adopts an S-type
conformation. Compound 1 was converted to the phosphoramidite and
The Danish National Research Foundation, The Danish Natural Research Council and The Danish
Centre for Scientific Computing are thanked for financial support.
Address correspondence to Poul Nielsen, Nucleic Acid Center, Department of Chemistry and
Physics, University of Southern Denmark, DK-5230 M. Odense, Denmark. E-mail: pon@ifk.sdu.dk
1435

1436
C. Andersen et al.
SCHEME 1 Ref. 1, a) i) TIPDSCl2, pyridine; ii) PhOCSCl, DMAP, CH3CN; iii) Bu3SnAllyl, AIBN,
toluene (36%) ref. 4; b) i) OsO4, NMO, acetone, H2O; ii) NaIO4, dioxane, H2O; iii) NaBH4, methanol
(64%); c) BzCl, Na2CO3(aq), Bu4NBr, CH2Cl2 (93%); d) TBz, Ph3P, DEAD, THF; e) i) TBAF, THF;
ii) NH3 aq. MeOH (67%); f) i) DMTCl, pyridine; ii) 4,5-dicyanoimidazol, NC(CH2)2OP(N(i-Pr)2)2,
CH3CN (33%).
incorporated successfully into oligonucleotides. The hybridization data
shows slightly destabilization of dsDNA and DNA:RNA duplexes when 1 is
incorporated in the middle of the sequences.[1] This shows, on the other
hand, that the additional base is reasonably well accommodated in the du-
plexes. When the target is a tree-way junction, stabilization is observed when
the additional nucleobase is positioned in the branching point.[1]
Compound 2, 2ꢁ-deoxy-2ꢁ-C-(thymine-1-ylmethyl)uridine, was synthe-
sized to investigate whether this stabilizing effect is dependent on the length
and flexibility of the carbon linker. In the first attempt, the same starting ma-
terial was used in a similar linear strategy. The double bond in the allyl group
was rearranged in an ene-reaction, and the new double bond was cleaved to
SCHEME 2 a) Methyltriazoline, DCM (70%); b) i) O3, DCM; ii) NaBH4, MeOH, ref. 6 (74%); c) BzCl,
Na2CO3 (aq), Bu4NBr, DCM (63%); d) TBz, Ph3P, DEAD, THF; e) i) MsCl, NEt3, DCM; ii) Cs2CO3, TBz
DMF.
,

Nucleosides with Additional Nucleobases
1437
SCHEME 3 a) i) MeOH, H2SO4; ii) pClBnCl, NaH, DMSO (43%); b) SnCl4 DCM, ref. 7 (74%); c) i)
Dess-matrin periodinane, DCM; ii) Ph3PCH3Br, BuLi, THF (42%); d) i) 9-BBN, THF; ii) H2O2, NaOH
(87%); e) TBOM, Ph3P, DEAD, THF (87%); f) Uracil, BSA, TMSOTf, CH3CN (48%); g) H2, Pd(OH)2/C,
MeOH.
give the alcohol by ozonolysis followed by a reduction.[6] The strategy was
again to introduce the additional nucleobase by an SN2 reaction, and to
prevent an anhydro formation, N3 was protected by a benzoyl group. Never-
theless, Mitsunobu conditions as well as other attempts were not successful
in introducing the additional nucleobase (Scheme 2).
An alternative strategy for the synthesis of 2 started from D-ribose fol-
lowing a convergent strategy. A published procedure for the preparation of
a 5,3-diprotected methyl furanoside was used (Scheme 3).[7] The free hy-
droxyl group was oxidized, followed by a Wittig reaction and hydroboration
to give the primary hydroxyl group at the 2-position. The nucleobase was
successfully introduced by a Mitsunobu reaction, and a Vorbru¨ggen method
resulted in the coupling of the uracil. Finally, a hydrogenation gave the de-
sired nucleoside 2. The JH1 ,H2
ꢁ of 2 was 9.3 Hz indicating an S-type con-
ꢁ
formation. Incorporation of this nucleoside 2 into oligonucleotides is in
progress.
In conclusion, nucleoside 1 was incorporated into oligonucleotides
and hybridization studies showed increased stability of a tree-way junction
when arranged with the additional nucleobase in the branching point. The
shorter linkage in nucleoside 2 will lead to a less flexible organisation of the
additional base. The consequences of this in nucleic acid recognition are
currently studied.
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of nucleic acid secondary structures by oligonucleotides with an additional nucleobase; synthe-
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3575.
2. For a recent study on nucleosides with additional bases in the 4ꢁ-position, see; Wu, T.; Nauwelaerts,
K.; Van Aerschot, A.; Froeyen, M.; Lescrinier, E.; Herdewijn, P. Base-Base Interactions in the Minor
Groove of Double-stranded DNA. J. Org. Chem. 2006, 71, 5423–5431.

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