Fluorinated peptide nucleic acid

Article abstract of DOI:10.1081/NCN-120022833

The fluorinated olefinic peptide nucleic acid analogue (F-OPA) monomer containing the base thymine was synthesised in 13 steps. PNAs containing this unit were prepared and their pairing properties assessed by means of UV-melting experiments.

Full text of DOI:10.1081/NCN-120022833

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Fluorinated Peptide Nucleic Acid
Marcel Hollenstein a b , Daniel Gautschi a & Christian J. Leumann a
a Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
b Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012,
Bern, Switzerland
Version of record first published: 31 Aug 2006.
To cite this article: Marcel Hollenstein, Daniel Gautschi & Christian J. Leumann (2003): Fluorinated Peptide Nucleic Acid,
Nucleosides, Nucleotides and Nucleic Acids, 22:5-8, 1191-1194
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NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS
Vol. 22, Nos. 5–8, pp. 1191–1194, 2003
Fluorinated Peptide Nucleic Acid
*
Marcel Hollenstein, Daniel Gautschi, and Christian J. Leumann
Department of Chemistry and Biochemistry, University of Bern,
Bern, Switzerland
ABSTRACT
The fluorinated olefinic peptide nucleic acid analogue (F-OPA) monomer
containing the base thymine was synthesised in 13 steps. PNAs containing this
unit were prepared and their pairing properties assessed by means of UV-melting
experiments.
Polyamide or peptide nucleic acids 1, first described in 1991, are DNA analogues
entirely based on an achiral polyamide backbone.[1] The PNAs undergo sequence-
specific and efficient Watson-Crick base pairing with complementary DNA and
RNA.[2,3] One structural feature of PNA is the central amide linker connecting the
base to the backbone. The carbonyl oxygens of this unit, uniformly point towards
the carboxy termini in PNA=DNA,[4,5] PNA=RNA[6] and PNA=PNA[7] complexes,
whereas both rotameric forms co-exist in the free monomer. In order to elucidate this
structural ambiguity, the olefinic peptide nucleic acids (OPAs) have been synthesised
and studied (Fig. 1).[3] Fully modified OPA oligoamides resulted in a marked
decrease in affinity towards complementary DNA, compared to PNA. In order to
investigate the effect of the dipole moment of the linker carboxy group while
*Correspondence: Marcel Hollenstein, Department of Chemistry and Biochemistry,
University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland; E-mail: hollenstein@ioc.
unibe.ch.
1191
DOI: 10.1081/NCN-120022833
Copyright # 2003 by Marcel Dekker, Inc.
1525-7770 (Print); 1532-2335 (Online)
www.dekker.com

1192
Hollenstein, Gautschi, and Leumann
Figure 1. Chemical structure of the monomeric units of the different peptide nucleic acids.
maintaining the geometry of the C¼C double bond, (Z) -t-F-OPA 4 was synthesised
and incorporated into PNA.
The synthesis of the monomeric unit 4 containing the base thymine is outlined in
Sch. 1.
Scheme 1. i) LiAlH4, THF, RT, 3 h. ii) MMTrCl, Pyridine, RT, overnight. iii) TBDMSCl,
Pyridine, RT, overnight. iv) IBX, THF=DMSO 1=1, RT, 6 h. v) 1) n-BuLi, (EtO)2P(O)-
CHFCO2Et, THF, ꢀ78ꢁC, 2 h. 2) Ketone, ꢀ78ꢁC to RT, 4 h. vi) LiAlH4, Et2O, RT, 2 h.
vii) TBz, PPh3, DIAD, THF, RT, overnight. viii) 1) BCl3, CH2Cl2, ꢀ40ꢁC, 30 min. 2) LiN3,
PPh3, CBr4, DMF, RT, overnight. 3) TBAF, THF, RT, overnight. ix) 1) TBAF, THF, RT,
5 h. 2) LiN3, PPh3, CBr4, DMF, RT, overnight. 3) BCl3, CH2Cl2, ꢀ40ꢁC, 30 min. x) 1)
Dess-Martin, CH2Cl2, RT. 2) NaClO2, NaH2PO4, 2-methyl-2-butene, t-BuOH. xi) 1) Lindlar
catalyst, H2, RT. 2) MMTrCl, Pyridine, RT.

Fluorinated Peptide Nucleic Acid
1193
Table 1. Mass spectrometry data and Tm values [ꢁC] (UV-melting curves, 260 nm) of PNA
sequences containing (E)-t-OPA, (Z)-t-OPA or (Z)-t-F-OPA units with parallel and antipar-
allel DNA (c ¼ 4 mM in 100 mM NaCl, 10 mM Na2HPO4, pH 7.0). Lowercase letters: PNA
units; tZ ¼ (Z)-t-OPA, tE ¼ (E)-t-OPA and tF ¼ (Z)-t-F-OPA.
m=z
m=z found
Tm
Tm
calcd (ESIþ-TOF) (antiparallel DNA)a (parallel DNA)b
15 Lys-ttttaatata-Gly-NH2 2900.9
16 Lys-ttttaatEata-Gly-NH2 2883.9
17 Lys-ttttaatZata-Gly-NH2 2883.9
18 Lys-ttttaatFata-Gly-NH2 2901.9
19 Lys-ttttEaatata-Gly-NH2 2883.9
20 Lys-tttEtaatata-Gly-NH2 2883.9
2900.10
2883.30
2883.32
2901.26
2883.17
2883.19
33.2
36.7
28.0
35.6
30.0
28.1
< 0
n.d.c
< 0
n.d.
11.0, 34.0
n.d.
ad(AAAATTATAT).
bd(TATATTAAAA).
cNot determined.
In order to study the pairing properties, oligomers 15–20 were prepared and the
stability of the duplexes formed with anti-parallel and parallel DNA was assessed by
means of UV-melting curves (Table 1). Introduction of the modified units leads to a
marked difference in Tm as a function of the position of the modification in the
sequence. Indeed, positioning of a (E)-t-OPA unit between 2 purine bases leads to
a stabilisation of the duplex (DTm ¼ þ3.5ꢁC), while introduction of this unit between
2 pyrimidine units leads to a marked destabilisation (DTm ¼ ꢀ5.1ꢁC). Positioning
between one pyrimidine and one purine base leads, as expected, to an intermediate
value (DTm ¼ ꢀ3.2ꢁC). The (Z)-t-F-OPA modification leads to a stabilisation
comparable to the one observed for (E)-t-OPA (DTm ¼ þ2.4ꢁC), whereas a substan-
tial decrease of duplex stability is observed for the (Z)-t-OPA unit (DTm ¼ ꢀ5.2ꢁC).
The introduction of the fluorine atom at that location could alter the electro-
static properties and result in a reduced stacking ability. This could account for
the lower Tm value obtained for oligomer 18 compared to the one for oligomer
16. However, the effect on the dipole moment on the whole oligomer is yet unknown,
and only a fully modified (Z)-t-F-OPA strand could provide with an answer.
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