Synthesis of modified nucleosides for incorporation of formyletheno and carboxyetheno adducts of adenine nucleosides into oligonucleotides

Article abstract of DOI:10.1080/15257770701527836

Three protected derivatives of 1,N6-ethenoadenine nucleosides, viz. 3-[5-O-(4,4′-dimethoxytrityl) of 7-formyl-(1) and 7-(1,2- diacetyloxypropyl)-2′-deoxyadenosine (2), and 3-[5-O-(4,4′- dimethoxytrityl)-2-O-(tert-butyldimethylsilyl)-7-(ethoxycarbonyl)adenosine (3), expected to allow introduction of formyletheno and carboxyethenoadenine adducts into oligonucleotides by the conventional phosphoramidite chemistry, have been synthesized. Copyright Taylor & Francis Group, LLC.

Full text of DOI:10.1080/15257770701527836

This article was downloaded by: [University of Tennessee At Martin]
On: 07 October 2014, At: 01:38
Publisher: Taylor & Francis
Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered
office: Mortimer House, 37-41 Mortimer Street, London W1T 3JH, UK
Nucleosides, Nucleotides and Nucleic
Acids
Publication details, including instructions for authors and
subscription information:
http://www.tandfonline.com/loi/lncn20
Synthesis of Modified Nucleosides for
Incorporation of Formyletheno and
Carboxyetheno Adducts of Adenine
Nucleosides into Oligonucleotides
Niangoran Koissi a & Harri Lönnberg a
a Department of Chemistry , University of Turku , Turku, Finland
Published online: 10 Dec 2007.
To cite this article: Niangoran Koissi & Harri Lönnberg (2007) Synthesis of Modified Nucleosides
for Incorporation of Formyletheno and Carboxyetheno Adducts of Adenine Nucleosides
into Oligonucleotides, Nucleosides, Nucleotides and Nucleic Acids, 26:8-9, 1203-1206, DOI:
10.1080/15257770701527836
To link to this article: http://dx.doi.org/10.1080/15257770701527836
PLEASE SCROLL DOWN FOR ARTICLE
Taylor & Francis makes every effort to ensure the accuracy of all the information (the
“Content”) contained in the publications on our platform. However, Taylor & Francis,
our agents, and our licensors make no representations or warranties whatsoever as to
the accuracy, completeness, or suitability for any purpose of the Content. Any opinions
and views expressed in this publication are the opinions and views of the authors,
and are not the views of or endorsed by Taylor & Francis. The accuracy of the Content
should not be relied upon and should be independently verified with primary sources
of information. Taylor and Francis shall not be liable for any losses, actions, claims,
proceedings, demands, costs, expenses, damages, and other liabilities whatsoever or
howsoever caused arising directly or indirectly in connection with, in relation to or arising
out of the use of the Content.
This article may be used for research, teaching, and private study purposes. Any
substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing,
systematic supply, or distribution in any form to anyone is expressly forbidden. Terms &
Conditions of access and use can be found at http://www.tandfonline.com/page/terms-
and-conditions

Nucleosides, Nucleotides, and Nucleic Acids, 26:1203–1206, 2007
Copyright ꢀ Taylor & Francis Group, LLC
C
ISSN: 1525-7770 print / 1532-2335 online
DOI: 10.1080/15257770701527836
SYNTHESIS OF MODIFIED NUCLEOSIDES FOR INCORPORATION
OF FORMYLETHENO AND CARBOXYETHENO ADDUCTS OF
ADENINE NUCLEOSIDES INTO OLIGONUCLEOTIDES
Niangoran Koissi and Harri Lo¨ nnberg
Department of Chemistry, University of
2
Turku, Turku, Finland.
Three protected derivatives of 1,N6-ethenoadenine nucleosides, viz. 3-[5-O-(4,4 ꢁ-dimethoxytrityl)
2
of 7-formyl- (1) and 7-(1,2-diacetyloxypropyl)-2 ꢁ-deoxyadenosine (2), and 3-[5-O-(4,4 ꢁ-dimethoxy-
trityl)-2-O-(tert-butyldimethylsilyl)-7-(ethoxycarbonyl)adenosine (3), expected to allow introduction
of formyletheno and carboxyethenoadenine adducts into oligonucleotides by the conventional phos-
phoramidite chemistry, have been synthesized.
Keywords DNA base modifications; etheno adducts
INTRODUCTION
Lipid peroxidation (LPO) generates several aldehydes α,β-unsaturated
aldehydes that generate a variety of DNA adducts, many of which are cyclic
adducts bearing an extra ring. This additional ring prevents normal hy-
drogen bonds formation upon hybridization and, hence, interferes with
the transfer of genetic information. While the cyclic adducts as such may
be classified as mutagenic DNA lesions, those bearing an additional func-
tional group that is able to interfere with the base-pairing and form cross-
links, are of particular interest. A major hurdle for evaluation of the muta-
genic potential or genotoxicity of this kind of adducted bases is their site-
specific incorporation into oligonucleotides.[1,2] We now report on synthe-
sis of three appropriately protected 1,N 6-ethenoadenine nucleosides (1–3)
that are aimed at allowing introduction of formyletheno and carboxyetheno
adducts of adenine into oligonucleotides by conventional phosphoramidite
chemistry.
Address correspondence to Niangoran Koissi, Department of Chemistry, University of Turku, FIN
20014, Turku, Finland. E-mail: koissi@gmail.com
1203

1204
N. Koissi and H. Lo¨nnberg
RESULTS AND DISCUSSION
Previous studies on 3-formylindole 2ꢁ-deoxyribonucleoside phospho-
ramidites suggest that the chain assembly without any protection at the
aldehyde group is possible.[3] Accordingly, nucleoside 1 could be used for
introduction of the formyletheno adduct. This nucleoside was obtained
by the reaction of appropriately protected 2ꢁ-deoxyadenosine with bromo-
malonaldehyde (BMA), a reaction shown to compete with formation of
1,N 6-etheno-2ꢁ-deoxyadenosine in aqueous solution.[4] When 3ꢁ,5ꢁ-di-O-tert-
butyldimethylsilyl-2ꢁ-deoxyadenosine was allowed to react in DMF with 6
equiv. of BMA in the presence of formic acid (1 equiv) and 2,6-lutidine (4.5
equiv), the formyletheno adduct was obtained in 64% yield (Scheme 1). The
5ꢁ-silyl protection was, however, partially removed under these conditions:
the 3ꢁ,5ꢁ-disilylated (4a) and 3ꢁ-monosilylated (4b) adducts were obtained in
SCHEME 1 (a) BMA, HCOOH/2,6-lutidine, 3 hours at 70◦C; (b) DMTrCl (1.1 equiv), Py, 3 hours; (c)
TBAF, THF, rt, 6 hours; (d) Et3N.3HF/THF, 3 hours.

Synthesis of Modified Nucleosides
1205
SCHEME 2 (a) HPE/H2O2/THF, 3 hours at 70◦C; (b) Ac2O/DMAP, pyr, 3 hours; (c) TBAF/THF, rt, 6
hours.
3:1 ratio. No depurination was observed. 4a was desilylated with tetrabuty-
lammonium fluoride (TBAF) in THF to obtain 5 and the 5ꢁ-hydroxy group
was protected with 4,4-dimethoxytrityl chloride in pyridine. 4b was, in turn,
first tritylated to obtain 6 and the 3ꢁ-silyl protection was then selectively re-
moved with triethylamine trihydrofluoride in THF.[5] It is worth noting that
1[6] withstood overnight ammonolysis at room temperature. The imine for-
mation of the formyl group was fully reversible.
In case protection of the formyl group turns out to be necessarry, nu-
cleoside 2 may be used for the same purpose: The 1,2-diol exposed upon
ammonolysis readily can be oxidized to formyl group by sodium perio-
date under very mild conditions.[7,8] The method described recently[9]
for preparation of (1-hydroxyhexyl)etheno adduct of 2ꢁ-deoxyadenosine
was applied to the synthesis of nucleoside 2. The key step of that ap-
proach is the reaction of adenine base with an appropriate formyl epox-
ide obtained from an α,β-unsaturated aldehyde by treatment with a mix-
ture of trifluoroacetone, Oxone and EDTA in aqueous MeCN. Accord-
ingly, 4-hydroxy-2-pentenal (HPE) was oxidized with hydrogen peroxide
to 2,3-epoxy-4-hydroxypentenal and this was allowed to react with 5ꢁ-O-
(4,4ꢁ-dimethoxytrityl)-2ꢁ-O-(tert-butyldimethylsilyl)-2ꢁ-deoxyadenosine (7) to
obtain the (1,2-dihydroxypropyl)etheno adduct 8 (Scheme 2). The hydroxy
functions were then acetylated with acetic anhydride in pyridine (9) and the
3ꢁ-silyl protection was removed with TBAF in THF to obtain 2.[10]
Nucleoside 3 allows introduction of a carboxyetheno adduct into
oligonucleotides, providing that after the chain assembly the ethyl es-
ter function is subjected to hydroxide ion catalyzed hydrolysis prior
to ammonolysis. This nucleoside was prepared by reacting 5ꢁ-O-(4,4ꢁ-
dimethoxytrityl)adenosine with methyl 2-bromo-3-oxopropanoate in diox-
ane to obtain 10 and protecting the 2ꢁ-hydroxy function of with a TB-
DMS group (Scheme 3). Silylation with 1 equiv. of TBDMSCl in THF
expectedly gave a mixture of 3 and its 3ꢁ-silylated isomer, which was re-
solved by silica gel chromatography to obtain 3.[11] Reaction of 5ꢁ-O-
(4,4ꢁ-dimethoxytrityl)adenosine with 2-bromo-3-oxopropanoate was also at-
tempted, but it turned out to be less efficient. 2-Bromo-3-oxopropanoate

1206
N. Koissi and H. Lo¨nnberg
SCHEME 3 (a) DMTrCl, Py; (b) OHC-CHBr-COOEt,[12] dioxane, 2 hours reflux, yield; (c) TBDM-
SCl/Im, 24 hours, chromatographic separation.
was synthesized from ethyl bromoacetate and ethyl formate as described
previously.[12]
REFERENCES
1. Iwai, S. Nucleosides, Nucleotides, and Nucleic Acids 2006, 25, 561.
2. Barbin, A. Mutat. Res. 2000, 462, 55.
3. Okamoto, A.; Tainaka, K.; Saito, I. Tetrahedron Lett. 2002, 43, 4581.
4. a) Nair, V.; Offerman, R.J.; Turner, G.A. J. Org. Chem. 1984, 49, 4021; b) Kronberg, L.; Sjo¨holm,
R.; Karlsson, S. Chem. Res. Toxicol. 1992, 5, 852; c) Mikkola, S.; Koissi, N.; Ketoma¨ki, K.; Rauvala, S.;
Neuvonen, K.; Lo¨nnberg, H. Eur. J. Org. Chem. 2000, 12, 2315.
5. Pirrung, M.C.; Shuey, S.W.; Lever, D.C.; Fallon, L. Bioorg. Med. Chem. Lett. 1994, 4, 1345.
6. Compd. 1: 1H NMR (CDCl3): δ 10.04 (CHO, s, 1H), 10.01 (H-5, s, 1H), 8.39 (H-2, s, 1H), 8.27 (H-8,
s, 1H), 7.43–7.21 (DMTr, m, 9H), 6.81 (DMTr, dd, J = 4.0 and 9.5 Hz, 4H), 6.58 (H-1ꢁ, d, J = 6.4,
1H), 4.77 (H-3ꢁ, m, 1H), 4.23 (H-4ꢁ, m, 1H), 3.78 (2 × OMe, s, 6H), 3.50 (H-5ꢁ, dd, J = 4.7 and 10.2
Hz, 1H), 3.43 (H-5ꢁꢁ, dd, J = 5.3 and 10.2 Hz, 1H), 2.88 (H-2ꢁ, m, 1H), 2.65 (H-2ꢁꢁ, m, 1H); HRMS
(FAB) MH+: found 606.2352, calcd for C34H31N5O6 606.2351.
7. Trevisiol, E.; Renard, A.; Defrancq, E.; Lhomme, J. Tetrahedron Lett. 1997, 38, 8687.
8. Karino, N.; Ueno, Y.; Matsuda, A. Nucleic Acids Res. 2001, 29, 2456.
9. Carvalho, V.M.; Gasparutto, D.; Di Mascio, P.; Medeiros, M.H.G.; Cadet, J. Bioorg. Med. Chem. 2003,
11, 2445.
10. Compd. 2: 1H NMR (CDCl3) 7.98 (H-5, s, 1H), 7.83 (H-2, s, 1H), 7.20–7.35 (DMTr, m, 9H), 6.85
(H-8, s, 1H), 6.69-6.77 (DMTr, m, 4H), 6.30 (H-1, dd, J = 8.0 and 5.6 Hz, 1H), 5.35 [-CH(OAc)-
CH(OAc)Me, m, 1H], 4.27 [H-3 & -CH(OAc)-CH(OAc)Me, m, 2H), 3.99 (H-4, m, 1H), 3.71 (2 ×
OMe, s, 6H,), 2.88 (H-5ꢁ & H-5ꢁꢁ, m, 2H), 2.51 (H-2ꢁ & H-2ꢁꢁ, m, 2H), 2.04 & 2.00 (2 × Ac, s, 2 ×
3H), 1.18 (s, 3H, Me).
11. Compd. 3: δ 7.98 (H-5, s, 1H), 7.97 (H-2, s, 1H), 7.20-7.32 (DMTr, m, 9H), 6.95 (H-8, s, 1H), 6.77-
6.79 (DMTr, m, 4H), 5.88 (H-1, d, J = 6.0 Hz, 1H), 4.38 (H-2, m, 1H), 3.77 (3 × OMe, s, 9H),
3.72-2.83 (H-3ꢁ& H-4ꢁ,m, 2H), 3.42-3.46 (H5, dd, J = 13.0 and < 2 Hz, 1H), 3.16-3.20 (H-5, dd, J =
13.0 and < 2 Hz, 1H), 0.72 (C-Me3, s, 6H), 0.51 (C-Me3, s, 3H), −0.08 (Si-Me, s, 6H).
12. Gangjee, A.; Vidwands, A.; Elzein, E.; McGuire, J.J.; Queener, S.F.; Kisliuk, R.L. J. Med. Chem. 2001,
44, 1993.