Synthesis and hybridization of novel chiral pyrrolidine based PNA analogue

Article abstract of DOI:10.1081/NCN-100002559

Four different PNA fragments containing units of either the R- or S- isomer of N-(2-pyrrolidine-methyl)-N-(thymine-1-acetyl)-glycine (Pmg) were synthesized on a solid support. UV thermal melting experiments with complementary RNAs were performed and it was found that R-Pmg containing PNAs bind better to RNA than those containing the S-Pmg units.

Full text of DOI:10.1081/NCN-100002559

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SYNTHESIS AND HYBRIDIZATION OF NOVEL CHIRAL
PYRROLIDINE BASED PNA ANALOGUE
Andis Slaitas a & Esther Yeheskiely b
a Division of Organic and Bioorganic Chemistry, MBB , Scheele Laboratory, Karolinska
Institute , Stockholm, S-17177, Sweden
b Division of Organic and Bioorganic Chemistry, MBB , Scheele Laboratory, Karolinska
Institute , Stockholm, S-17177, Sweden
Published online: 07 Feb 2007.
To cite this article: Andis Slaitas & Esther Yeheskiely (2001) SYNTHESIS AND HYBRIDIZATION OF NOVEL CHIRAL
PYRROLIDINE BASED PNA ANALOGUE, Nucleosides, Nucleotides and Nucleic Acids, 20:4-7, 1377-1379, DOI: 10.1081/
NCN-100002559
To link to this article: http://dx.doi.org/10.1081/NCN-100002559
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NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS, 20(4–7), 1377–1379 (2001)
SYNTHESIS AND HYBRIDIZATION OF NOVEL
CHIRAL PYRROLIDINE BASED PNA ANALOGUE
Andis Slaitas and Esther Yeheskiely∗
Division of Organic and Bioorganic Chemistry,
MBB, Scheele Laboratory, Karolinska Institute,
S-17177 Stockholm, Sweden
ABSTRACT
Four different PNA fragments containing units of either the R- or S- isomer of N-
(2-pyrrolidine-methyl)-N-(thymine-1-acetyl)-glycine (Pmg) were synthesized
on a solid support. UV thermal melting experiments with complementary RNAs
were performed and it was found that R-Pmg containing PNAs bind better to
RNA than those containing the S-Pmg units.
INTRODUCTION
Amino acid based oligonucleotide analogues can form stable duplexes with
complementary DNA (RNA) (1). Many factors influence the stability of these du-
plexes, e.g., it is dependent on the rigidity and bulkiness of the backbone and on
whether it contains the D or the L amino acid (1).
OurobjectivewastoprepareandinvestigatethepropertiesofanewchiralPNA
analogue, the backbone of which contains N-[(2R-pyrrolidine)methyl]-glycine (R-
Pmg)orthe2Sisomer(S-Pmg). Wereasonedthatthepyrrolidinemoiety(Fig. 1)will
introduce rigidity and chirality, while the backbone will still contain the requisite
six covalent bonds as in PNA monomers (2).
∗Corresponding author.
1377
ꢀ
C
Copyright 2001 by Marcel Dekker, Inc.
www.dekker.com

ORDER
REPRINTS
1378
SLAITAS AND YEHESKIELY
Figure 1. Structure of thymine-Pmg PNA.
RESULTS AND DISCUSSION
Construction of the Pmg backbone starting from prolinol involves the fol-
lowing steps: The amino function of prolinol 1 (Scheme 1) was protected with the
t-butoxycarbonyl group (Boc) and the primary alcohol of 2 was then mesylated.
Nucleophilic substitution of the mesylate 3 with azide ion in DMF and subsequent
reduction of compound 4 afforded 2-(aminomethyl)-N-Boc-pyrrolidine 5 in 81%
overall yield (3). Alkylation with allyl bromoacetate and 2-(benzotriazol-1-yl)-
1,1,3,3-tetramethyluronium hexafluoro-phosphate (HBTU) mediated acylation of
the resulting secondary amino function of the backbone 6 with thymine-1-acetic
acid (7) gave the fully protected monomeric unit 8 (4). Finally, Pd-catalyzed cleav-
age of the allyl ester (5) afforded the T-Pmg building block 9 in a form suitable for
solid phase synthesis.
Scheme 1. Synthesis of T-Pmg monomer.

ORDER
REPRINTS
CHIRAL PYRROLIDINE BASED PNA ANALOGUE
Table 1. UV Thermal Melting Data
1379
#
Sequence
Tm,† ◦
C
ꢀTm/mod.,‡ ◦
C
ꢀTm (R–S)/mod.
1.
H-Lys2-tcacttccat
53.0
R
S
S
R
2.
3.
H-Lys2-tcacttccat
H-Lys2-tcacttccat
39.0
27.0
44.0
36.0
−14.0
−9.0
+5.0
+4.5
−13.0
−8.5
†Measured with the complementary (antiparallel) RNA strand in 100 mM NaCl.
‡Compared to Tm of entry 1.
PNA sequences ‘H-(Lys)2-tcacttccat-Gly-NH2’ containing one or two S- or
R- T-Pmg units were synthesized on a solid support using mixed Fmoc/MMT/Boc
strategy [Nα-Fmoc-Nε-Boc-L-lysine, N-MMT-AEG-PNA and N-Boc-Pmg-PNA
monomers] and HBTU as condensation agent. The coupling yields were up to 99%
per step. The PNAs were purified on reverse-phase HPLC and their authenticity
confirmed by MALDI-TOF mass spectrometry.
The ability of the above-mentioned oligomers to form stable duplexes with
RNA was evaluated by UV thermal melting experiments (reference: PNA-RNA
duplex). The values for S-Pmg fragments indicated decrease of Tm (14◦C/mod.),
while the R-Pmg containing PNA showed decrease of 8.5◦C/mod (See Table 1).
CONCLUSIONS
Both S- and R- T-Pmg units were prepared in good yields and incorporated into
four individual PNA decamers the hybridization properties of which were investi-
gated. All modified sequences showed decreased thermal stability. At the moment
we are engaged in the synthesis and study of fully modified R-Pmg decamers.
ACKNOWLEDGMENT
We wish to thank the Swedish Natural Science Research Council (NFR) for
financial support.
REFERENCES
1. Laan, A.C. van der.; Amsterdam, I. van.; Tesser, G.I.; Boom, J.H. van.; Kuyl-Yeheskiely,
E. Nucleosides & Nucleotides 1998, 17, 219–232.
2. Nielsen, P.E.; Egholm, M.; Berg, R.M.; Buchardt, O. Science 1991, 254, 1497–1500.
3. Soth, M.J.; Nowick, J.S. J. Org. Chem. 1999, 64, 276–281.
4. Laan, A.C. van der.; Brill, R.; Kuimelis, R.G.; Kuyl-Yeheskiely, E.; Boom, J.H. van.;
Andrus, A.; Vinayak, R. Tetrahedron Lett. 1997, 38, 2249–2252.
5. Dangles, O.; Guibe, F.; Balavoine, G.; Lavielle, S.; Marquet, A. J. Org. Chem. 1987,
52, 4984–4993.

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