Synthesis of a 2′-amino-α-L-LNA-T phosphoramidite

Article abstract of DOI:10.1080/15257770500276866

A convergent route to 2′-amino-α-L-LNA-T phosphoramidite building block 16 has been developed. Key steps include 1) introduction of a C2-azido group prior to nucleobase-coupling, 2) tandem Staudinger and intramolecular nucleophilic substitution reaction,

Full text of DOI:10.1080/15257770500276866

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SYNTHESIS OF A 2′-AMINO-α-L-LNA-T
PHOSPHORAMIDITE
Patrick J. Hrdlicka a , T. Santhosh Kumar a & Jesper Wengel a
a Nucleic Acid Center, University of Southern Denmark, Department of Chemistry , Odense
M, Denmark
Published online: 15 Nov 2011.
To cite this article: Patrick J. Hrdlicka , T. Santhosh Kumar & Jesper Wengel (2005) SYNTHESIS OF A 2′-AMINO-α-L-LNA-T
PHOSPHORAMIDITE, Nucleosides, Nucleotides and Nucleic Acids, 24:5-7, 1101-1104, DOI: 10.1080/15257770500276866
To link to this article: http://dx.doi.org/10.1080/15257770500276866
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Nucleosides, Nucleotides, and Nucleic Acids, 24 (5–7):1101–1104, (2005)
Copyright D Taylor & Francis, Inc.
ISSN: 1525-7770 print/ 1532-2335 online
DOI: 10.1080/15257770500276866
SYNTHESIS OF A 2’-AMINO-a-L-LNA-T PHOSPHORAMIDITE
5
Patrick J. Hrdlicka, T. Santhosh Kumar, and Jesper Wengel
Nucleic Acid
Center, Department of Chemistry, University of Southern Denmark, Odense M, Denmark
5
A convergent route to 2’-amino-a-L-LNA-T phosphoramidite building block 16 has been developed.
Key steps include 1) introduction of a C2-azido group prior to nucleobase-coupling, 2) tandem
Staudinger and intramolecular nucleophilic substitution reaction, and 3) separation of a-L- and b-L-
configured intermediates.
INTRODUCTION
The high-affinity hybridizations of b-D-LNA 1 (locked nucleic acid),[1–3] 2’-
amino-b-D-LNA 2[4] (R = H) and a-L-LNA 3[5] (Figure 1) towards complementary
DNA and RNA sequences are well established. When incorporated into an
oligodeoxyribonucleotide (ODN), b-D-LNA 1 tunes duplexes towards DNA and
RNA complements towards A/B-type and A-type helix geometry, respectively.[6,7]
Conversely, when a-L-LNA 3 is incorporated into an ODN, duplexes towards DNA
and RNA adopt B-type and A/B-type helix geometries, respectively, globally similar
to unmodified duplexes.[8,9] N-substituted 2’-amino-b-D-LNA monomers have
recently been introduced as building blocks to generate functional nucleic acid
architectures with groups at the brim of the minor groove capable of signalling
assembly processes.[10–12] In contrast, the secondary amine group of a 2’-amino-a-L-
LNA 4 (Figure 1) would allow introduction of functional groups that are
predictably positioned in the major groove of nucleic acid duplexes having similar
global duplex geometries as unmodified DNA:DNA or DNA:RNA duplexes. Due
to the potential of using N-substituted 2’-amino-a-L-LNA monomers in bottom up
[13]
˚
Angstro¨m-scale chemical engineering
we set out to synthesize the protected
2’-amino-a-L-LNA-T phosphoramidite building block 16 (Scheme 2).
Address correspondence to Jesper Wengel, Nucleic Acid Center, Department of Chemistry, University of
Southern Denmark, Odense M DK-5230, Denmark; Fax: +45-66158780; E-mail: jwe@chem.sdu.dk
1101
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1102
P. J. Hrdlicka, T. S. Kumar, and J. Wengel
FIGURE 1
RESULTS AND DISCUSSION
Preliminary attempts to synthesize a-L-ribo-configured key intermediate 10
(Scheme 1) via an stereoselective route in which a thymine moiety was installed
diastereospecifically (via anchimeric assistance from an O2-acetyl group) during
nucleobase-coupling prior to introduction of a C2’-azido group, failed.[14] Instead,
the first successful synthesis of phosphoramidite 16 initiated from diol 5,[15] which
was converted into an anomeric mixture of methyl furanoside 6 in two steps
(Scheme 1).
Subsequent O2-triflation of the anomeric mixture followed by selective
nucleophilic displacement of the O2-triflate and acetolysis, furnished glycosyl donor
7. Glycosylation of 7 with persilylated thymine using modified Vorbru¨ggen
conditions, furnished an inseparable anomeric mixture of nucleosides 8 which was
reacted further in a tandem Staudinger and intramolecular nucleophilic substitution
reaction to afford a separable mixture of b-L-ribo-configured nucleoside 9 and a-L-
ribo-configured nucleoside 10 (a:bꢀ1:2).
SCHEME 1

P. J. Hrdlicka, T. S. Kumar, and J. Wengel
1103
SCHEME 2
Displacement of the O5’-methanesulfonyl group of nucleoside 10 necessitated
protection of the 2’-amino group as a trifluoroacetamide (TFA) since tricyclic
products, resulting from Michael addition of the C2’-amino group to C-6, were
otherwise formed. Remarkably, deacylation using basic conditions did not cleave
the TFA group but rather furnished nucleoside 11 (Scheme 2). However,
nucleoside 11 could readily be converted into amino alcohol 12 using mildly
reducing conditions. After chemoselective O5’-DMT protection to give nucleoside
13, transfer hydrogenolysis afforded nucleoside 14 that constitutes a suitable
intermediate for N-functionalization. Standard Fmoc-protection of nucleoside 14
followed by phosphitylation of nucleoside 15 afforded 2’-amino-a-L-LNA-T
phosphoramidite 16.
Incorporation of phosphoramidite 16 into ODNs and biophysical studies
hereof are ongoing.
ACKNOWLEDGMENT
We thank The Danish National Research Foundation for financial support.
REFERENCES
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