Synthesis of a branched locked nucleic acid (LNA) analogue

Article abstract of DOI:10.1080/15257770701542975

A 3′-C-branched LNA-type bicyclic nucleoside, containing a furanose ring locked in an N-type conformation, was synthesized from a known 3-C-vinyl allofuranose derivative using a strategy relying on the condensation with the nucleobase after the introducti

Full text of DOI:10.1080/15257770701542975

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Synthesis of A Branched Locked Nucleic
Acid (LNA) Analogue
Pawan K. Sharma a , Surender Kumar a b & Poul Nielsen b
a Department of Chemistry , Kurukshetra University , Kurukshetra,
India
b Nucleic Acid Center, Department of Physics and Chemistry ,
University of Southern Denmark , Odense M, Denmark
Published online: 05 Dec 2007.
To cite this article: Pawan K. Sharma , Surender Kumar & Poul Nielsen (2007) Synthesis of A
Branched Locked Nucleic Acid (LNA) Analogue, Nucleosides, Nucleotides and Nucleic Acids, 26:10-12,
1505-1508, DOI: 10.1080/15257770701542975
To link to this article: http://dx.doi.org/10.1080/15257770701542975
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Nucleosides, Nucleotides, and Nucleic Acids, 26:1505–1508, 2007
Copyright ꢀ Taylor & Francis Group, LLC
C
ISSN: 1525-7770 print / 1532-2335 online
DOI: 10.1080/15257770701542975
SYNTHESIS OF A BRANCHED LOCKED NUCLEIC ACID (LNA)
ANALOGUE
Pawan K. Sharma
Department of Chemistry, Kurukshetra University,
2
Kurukshetra, India
Surender Kumar
Department of Chemistry, Kurukshetra University, Kurukshetra,
2
India and Nucleic Acid Center, Department of Physics and Chemistry, University of Southern
Denmark, Odense M, Denmark
Poul Nielsen
Nucleic Acid Center, Department of Physics and Chemistry,
2
University of Southern Denmark, Odense M, Denmark
A 3ꢁ-C-branched LNA-type bicyclic nucleoside, containing a furanose ring locked in an N-type
2
conformation, was synthesized from a known 3-C-vinyl allofuranose derivative using a strategy re-
lying on the condensation with the nucleobase after the introduction of the branching hydroxymethyl
chain by our recently developed RuO4 based protocol. This branched LNA nucleoside has a potential
as a monomer for the functionalization of LNA.
Keywords Locked nucleic acid; N-type conformation; RuO4 oxidation
In nucleic acid chemistry, conformationally restricted nucleoside build-
ing blocks are powerful tools for the design of oligodeoxynucleotides
(ODNs) with selective and high-affinity recognition of complementary nu-
cleic acids. Furthermore, the structural control embedded by these build-
ing blocks opens for the design of functional nucleic acid architectures.[1]
Locked nucleic acid (LNA) represents the most absorbing example in
which the conformation of the furanose moiety is locked in an N-type (C3ꢁ-
endo) conformation (Figure 1).[2] The incorporation of one or more LNA
monomers into an ODN strongly increases the thermal stability of the du-
plex formed with single-stranded DNA or RNA complements.[2] LNA has
The work was supported by the Sixth Framework Program Marie Curie Host Fellowships for Early
Stage Research Training under contract MEST-CT-2004-504018, by the Danish Natural Research Council
and by the Nucleic Acid Center, which is funded by the Danish Natural Research Foundation for studies
on nucleic acid chemical biology.
Address correspondence to Poul Nielsen, Nucleic Acid Center, Department of Physics and Chem-
istry, University of Southern Denmark, 5230 Odense M, Denmark. E-mail: pon@ifk.sdu.dk
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P. K. Sharma et al.
FIGURE 1 An LNA nucleotide, a 3ꢁ-C-branched nucleotide and the target 3ꢁ-C-branched LNA
nucleotide.
been shown to be very useful for antisense applications,[3] and amino-LNA
has been used for the preparation of functionalized nucleic acids.[4]
3ꢁ-C-Branched nucleoside building blocks have been made to im-
prove either enzymatic stability of the ODN or the binding affinity to-
ward complementary targets (Figure 1).[5] In general, ODNs with 3ꢁ-C-
branched nucleotides exhibit slightly decreased hybridization properties
and improved stability against 3ꢁ-exonucleases. Furthermore, they contain
branching points which can be used as conjugation sites for a variety of func-
tional moieties such as peptides or other nucleotides.[5] A 3ꢁ-substituent is
expected to be oriented in a pseudoequatorial position, driving the sugar
pucker towards a C-2ꢁ-endo conformation, thus explaining why the binding
affinity toward RNA is somewhat impaired.[5] On the other hand, the 3ꢁ-C-
alkyl substituents (including the 3ꢁ-C-hydroxymethyl substituent)point into
the major groove of DNA:DNA and DNA:RNA duplexes and are reason-
ably well tolerated in the duplex structure.[5] Therefore, it was appealing to
study this structural feature in the context of an LNA monomer, in which
the locked N-type conformation forces the 3ꢁ-hydroxymethyl group into an
axial position. Longer alkyl groups in the same position have been studied
before leading to some decrease in thermal stability.[6] However, we envi-
sioned the smaller 3ꢁ-hydroxymethyl group to be better accommodated into
duplexes.
For the introduction of the hydroxymethyl branch at the β-face of C3ꢁ
of a nucleoside, a convergent synthesis strategy starting from 1,2:5,6-di-O-
isopropylidene-α-D-glucofuranose 1 was chosen, and the known 3-C-vinyl
derivative 2[7] was prepared in three steps. In our first strategy, this com-
pound was efficiently converted into a 3ꢁ-hydroxymethyl derivative by our
recently developed ruthenium protocol for oxidative cleavage.[8] However,
all attempt of making a successful preparation of the target nucleoside from
this strategy failed due to problems with the 3ꢁ-hydroxymethyl moiety in the

Synthesis of a Branched LNA Analogue
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SCHEME 1 Key: a) i) H5IO6, EtOAc; ii) HCHO, NaOH, NaBH4, 94%; b) NaH, BnBr, DMF, 60%;
c) i) BzCl, Pyridine; ii) RuCl3 × H2O, NaIO4, H2O, EtOAc, CH3CN; iii) NaBH4, H2O, THF; iv) NaIO4;
v) NaBH4, 71%; d) NaH, BnBr, DMF, 75%; e) i) 80% Aq. AcOH; ii) Ac2O, Pyridine, 91%; f) Thymine,
BSA, CH3CN, TMS-triflate, 93%; g) NaOCH3, MeOH, 86%; h) i) MsCl, CH2Cl2, Pyridine; ii) NaH,
Dioxane, 72%; i) H2, Pd(OH)2/C, EtOH, quantitative.
subsequent steps. Therefore, we decided to apply a second strategy in which
the vinyl group is cleaved later, and 2 was eventually converted to 3 through
oxidative cleavage of the C5–C6 bond and an aldol condensation. Selective
protection followed by the ruthenium based oxidative cleavage[8] and a new
benzylation afforded 4. Adapted standard conversions gave the nucleoside
5. A deprotection, a selective mesylation, ring-closure and a debenzylation
afforded the target nucleoside 6. Efforts towards the incorporation of 6 into
functionalised ODNs are in progress.
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