Synthesis of conformationally restricted nucleic acid fragments using ring-closing alkene and enyne metathesis reactions

Article abstract of DOI:10.1081/NCN-200060347

In the aim of constructing conformationally restricted nucleic acid fragments for the recognition of secondary RNA structures, we have synthesized different mono- and dinucleotides containing extra rings. These rings were prepared by ring-closing alkene o

Full text of DOI:10.1081/NCN-200060347

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SYNTHESIS OF CONFORMATIONALLY RESTRICTED
NUCLEIC ACID FRAGMENTS USING RING-CLOSING
ALKENE AND ENYNE METATHESIS REACTIONS
a
a
a
a
Signe I. Steffansen , Mikkel S. Christensen , Philip B⊘rsting & Poul Nielsen
a
Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Odense,
Denmark
Published online: 15 Nov 2011.
To cite this article: Signe I. Steffansen , Mikkel S. Christensen , Philip B⊘rsting & Poul Nielsen (2005): SYNTHESIS OF
CONFORMATIONALLY RESTRICTED NUCLEIC ACID FRAGMENTS USING RING-CLOSING ALKENE AND ENYNE METATHESIS REACTIONS,
Nucleosides, Nucleotides and Nucleic Acids, 24:5-7, 1015-1018
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Nucleosides, Nucleotides, and Nucleic Acids, 24 (5–7):1015–1018, (2005)
Copyright D Taylor & Francis, Inc.
ISSN: 1525-7770 print/ 1532-2335 online
DOI: 10.1081/NCN-200060347
SYNTHESIS OF CONFORMATIONALLY RESTRICTED NUCLEIC ACID
FRAGMENTS USING RING-CLOSING ALKENE AND ENYNE
METATHESIS REACTIONS
Signe I. Steffansen, Mikkel S. Christensen, Philip Børsting, and Poul Nielsen
5
Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Odense,
Denmark
5
In the aim of constructing conformationally restricted nucleic acid fragments for the recognition of
secondary RNA structures, we have synthesized different mono- and dinucleotides containing extra
rings. These rings were prepared by ring-closing alkene or enyne metathesis reactions from nucleotide
substrates in which double or triple bonds have been introduced.
INTRODUCTION
Long single stranded RNAs tend to fold into secondary structures. This makes
[1]
the primary structure of RNA less accessible. Secondary structures in RNA such
as hairpins and loops are therefore targets for modified oligonucleotides. If an
oligonucleotide has to bind, e.g., across a hairpin loop, a preorganization of the
[2]
oligonuclotide to form the right bend would be preferable. Recently, we have
introduced the idea of using the ring-closing metathesis (RCM) reaction for the
synthesis of conformationally restricted nucleic acid fragments targeting secondary
[
3–8]
nucleic acid structures.
In this study, we present our efforts toward cyclic
dinucleotides with linkages between the 2’-position and the phosphate. Further-
more, we expand the scope of this strategy towards the first enyne metathesis
reactions with nucleoside or nucleotide substrates. In general, we have applied
[9]
Grubbs 2nd generation precatalyst A (Scheme 1) in this study.
First, four different nucleoside building blocks were synthesized using uridine 1
as the starting material. Thus, a selective protection of the 3’-O- and 5’-O-positions by
the TIPDS-group to give 2 was followed by oxidation of the 2’-position giving 3.
After a Grignard reaction leading to 4, the appropriate deprotection and
The Nucleic Acid Center is funded by the Danish National Research Foundation for the studies on nucleic
acid chemical biology.
Address correspondence to Poul Nielsen, Nucleic Acid Center, Department of Chemistry, University of
Southern Denmark, Odense DK-5230, Denmark.
1015
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1016
S. I. Steffansen et al.
SCHEME 1 a) TIPDSCl
THF, 69%; d) TBAF, THF, 86%; e) TBDMSCl, imidazole, DMF, 70%; f) H
g) TBDMSCl, DABCO, AgNO , THF; 79%; h) 1-bromo-2-butyne, NaH, THF, 75%; i) TBAF, THF, 84%;
j) TBDMSCl, imidazole, DMF, 55%.
2
, pyridine, 85%; b) CrO
3
, Ac
2
2 2 3
O, pyridine, CH Cl , 93%; c) propynyl-MgBr, CeCl ,
2
, Lindlar Cat., quinoline, MeOH, 95%;
3
reprotection reactions gave the first monomer 6, which, after controlled reduction
of the triple bond, gave the second monomer 7 (Scheme 1). The TIPDS-protection
proved to be problematic when used in an alkylation reaction leading to partial
hydrolysis of the TIPDS-group. Therefore, the TBDMS-group was introduced
[10]
for selective 3’-O- and 5’-O-protection,
and a subsequent 2’-O-alkylation gave
the intermediate 9. After deprotection and reprotection, the third monomer 11
was obtained.
[11]
A well-known radical-reaction was used for synthesizing the last monomer
(
Scheme 2). Again, 2 was used as the starting material and converted in two steps to
the 2’-C-allyl-2’-deoxy derivative 12. Deprotection and reprotecton afforded the
monomer 14. The phosphoramidite 16 was prepared from 3’-O-TBDMS-
thymidine 15 as a building block for incorporating the allyl group via the
internucleotide phosphate.
SCHEME 2 a) PhOCSCl, pyridine, CH
Amberlite IR-120, pyridine/MeOH/H O, 90%; d) TBDMSCl, AgNO
dicyanoimidazole, CH Cl , 63%.
2
Cl
2
, 74%; b) allylSnBu
3
, AIBN, toluene, 72%; c) TBAF, THF then
= CHCH OP(N(iPr))
2
3
, pyridine, 85%; e) CH
2
2
2
,
2
2

S. I. Steffansen et al.
1017
t
SCHEME 3 a) 1H-tetrazole, CH
0 65%.
3
CN then BuOOH, 17 65%, 19 85%; b) A, CH
2
Cl
2
2
then 70 atm H , 18 11%,
2
Monomer 7 and 14 were both coupled to the phosphoramidite 16 and the
resulting dimers 17 and 19 were subjected to a tandem RCM/hydrogenation
procedure leading to the saturated products 18 and 20 in a low and good yield,
respectively (Scheme 3). The latter was subsequently separated to give the two pure
phosphorus epimers, which were deprotected and incorporated into oligonucleo-
[
12]
tides.
Finally, the monomer 6 was coupled to phosphoramidite 16 giving a
dimer 21 as a substrate for enyne metathesis. However, under varying metathesis
conditions the dimer did not react at all. Instead, an enyne-nucleoside model was
synthesis by alkylating 11 with allylbromide giving the enyne 22, which
successfully was ring-closed to give the diene 23. This nucleoside model possesses
some of the qualities that have been experienced to positively contribute to ring
[13]
formation, i.e., heteroatoms in the 1- and 4-positions of the formed ring.
In summary, nucleosides with allyl or propenyl moieties in the 2’-positions have
been successfully incorporated into dinucleotides being substrates in a tandem
RCM/hydrogenation procedure. On the other hand a dinucleotide containing a
2
’-C-propynyl moiety was not a substrate for an enyne metathesis reaction. In
contrast, a 3’-O-allyl-2’-O-(2-butynyl)-nucleoside was successfully ring-closed, leaving
hope for the use of enyne metathesis for the synthesis of conformationally restricted
dinucleotides with a potential for further functionalization. We expect the present
metathesis-based strategy for the preparation of conformationally restricted nucleic
2 2 2 2 2 2
SCHEME 4 a) Dicyanoimidazole, CH Cl , 52%; b) A, CH Cl ; c) CH = CHCH Br, NaH, THF, 38%; d) A,
CH Cl , 71%.
2
2

1018
S. I. Steffansen et al.
acid fragments to be a general future tool for modeling and targeting secondary
nucleic acid structures (Scheme 4).
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