DNA containing phenanthroline- and phenanthrene-derived, non-nucleosidic base surrogates

Article abstract of DOI:10.1016/j.tetlet.2004.10.068

Simple, non-nucleosidic phenanthroline- and phenanthrene derivatives have been synthesised and incorporated into oligodeoxynucleotides. Complementary strands containing the modified building blocks in opposite positions form stable hybrids. Thermal denaturation experiments show that the double strands containing the phenanthroline derivatives are more stable than the ones with the corresponding phenanthrenes. Furthermore, it was found that duplex stability is considerably decreased if the linkers of the modified building blocks are too short.

Full text of DOI:10.1016/j.tetlet.2004.10.068

Tetrahedron
Letters
Tetrahedron Letters 45 (2004) 9273–9276
DNA containing phenanthroline- and phenanthrene-derived,
non-nucleosidic base surrogates
Simon M. Langenegger and Robert Ha¨ner*
Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
Received 24 August 2004; revised 11 October 2004; accepted 12 October 2004
Available online 28 October 2004
Abstract—Simple, non-nucleosidic phenanthroline- and phenanthrene derivatives have been synthesised and incorporated into
oligodeoxynucleotides. Complementary strands containing the modified building blocks in opposite positions form stable hybrids.
Thermal denaturation experiments show that the double strands containing the phenanthroline derivatives are more stable than the
ones with the corresponding phenanthrenes. Furthermore, it was found that duplex stability is considerably decreased if the linkers
of the modified building blocks are too short.
Ó 2004 Elsevier Ltd. All rights reserved.
Besides their importance as the genetic material, nucleic
acids are increasingly gaining interest as nanometer-
sized, functional matter.1–4 Due to the repetitive, well-
defined arrangement of their building blocks, nucleic
acids and related types of oligomers5–8 are ideal objects
for the designed construction of larger assemblies. Thus,
they have been used for the spatially well-defined
arrangement of gold nanoparticles9,10 or for the genera-
tion of larger molecular assemblies and architectures.11–14
Furthermore, they may find applications as molecular
metal wires15–19 and even as molecular computers20,21 or
machines.22,23 The combination of nucleotides with non-
natural building blocks enhances the number of possible
constructs and their potential applications even further.
Recently, we reported the synthesis and properties of a
non-nucleosidic, phenanthrene-derived building block
and its incorporation into double stranded DNA
(Scheme 1, A).24,25 This simple building block can serve
as a base surrogate without destabilising the DNA
duplex nor altering its overall B-DNA structure. Based
on the data obtained, a model of interstrand-stacked
phenanthrenes was proposed.24 Since p-stacking interac-
tions should be favoured by heteroaromatic deriva-
tives,26 we investigated the effect of the phenanthroline
analogues (Scheme 1, B). Here, we report that the phen-
anthroline derivatives gives rise to more stable hybrids
than the analogous phenanthrenes and that the length
of the non-nucleosidic linker plays an important role.
The building blocks required for the synthesis of the
modified oligonucleotides are shown in Scheme 2. The
phenanthrene derivatives 1a–c were prepared as
Scheme 1. Non-nucleosidic phenanthrene- and phenanthroline-derived building blocks.
Keywords: Phenanthrene; Phenanthroline; DNA; Duplex; Stacking.
*
Corresponding author. Tel.: +41 31 631 4382; fax: +41 31 631 8057; e-mail: robert.haener@ioc.unibe.ch
0040-4039/$ - see front matter Ó 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2004.10.068

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S. M. Langenegger, R. Ha¨ner / Tetrahedron Letters 45 (2004) 9273–9276
Scheme 2. Synthesis of the required phosphoramidites. Reagents and conditions: (a) H N(CH ) OH/H N(CH ) ODMT (1:1), HunigÕs base, BOP;
¨
2
2 n
2
2 n
(b) 2-cyanoethyl diisopropylamidochloridophosphite, HunigÕs base.
¨
described previously.25,27 In addition, 1d was prepared
according to the same procedures. Synthesis of the
phenanthroline-derived compounds started from the
known 2.28 Attachment of the different 4,40-dimethoxy-
tritylated linkers and subsequent phosphitylation
yielded the phosphoramidite compounds 3a–d.29 Build-
ing blocks 2a–d and 3a–d were then used for the synthe-
sis of the oligonucleotides shown in Table 1. Assembly
of the oligomers involved standard automated oligonu-
cleotide synthesis.30,31 The crude oligomers were purified
by reverse phase HPLC and their identity was verified
by mass spectrometry. The oligonucleotides are sets of
complementary 21mers containing a modified building
block in the central position of each strand. Pn or Qn
Table 1. Influence of phenanthrene and phenanthroline nucleotide surrogates on the thermal stability of duplex DNA
Entry
1
Duplex
Tm (°C)a,b
DTm (°C)c
(50) AGC TCG GTC A T C GAG AGT GCA
(30) TCG AGC CAG T A G CTC TCA CGT
(50) AGC TCG GTC A P2C GAG AGT GCA
(30) TCG AGC CAG T P2G CTC TCA CGT
(50) AGC TCG GTC A P3C GAG AGT GCA
(30) TCG AGC CAG T P3G CTC TCA CGT
(50) AGC TCG GTC A P4C GAG AGT GCA
(30) TCG AGC CAG T P4G CTC TCA CGT
(50) AGC TCG GTC A P5C GAG AGT GCA
(30) TCG AGC CAG T P5G CTC TCA CGT
(50) AGC TCG GTC A Q2C GAG AGT GCA
(30) TCG AGC CAG T Q2G CTC TCA CGT
(50) AGC TCG GTC A Q3C GAG AGT GCA
(30) TCG AGC CAG T Q3G CTC TCA CGT
(50) AGC TCG GTC A Q4C GAG AGT GCA
(30) TCG AGC CAG T Q4G CTC TCA CGT
(50) AGC TCG GTC A Q5C GAG AGT GCA
(30) TCG AGC CAG T Q5G CTC TCA CGT
68.0
––
2
3
4
5
6
7
8
9
61.3
68.3
67.3
68.7
65.6
71.1
70.6
70.2
ꢀ6.7
0.3d
ꢀ0.7
0.7
ꢀ2.4
3.1
2.6
2.2
Pn (phenanthrene)
2
2
n = 2
P ,Q :
: n = 3
: n = 4
: n = 5
3
3
4
5
P ,Q
4
P ,Q
5
P ,Q
Qn (phenanthroline)
a Conditions: Oligomer concentration 1.0lM, 10mM Tris–HCl, 100mM NaCl, pH7.4; temperature gradient: 0.5°C/min.
b Melting temperatures were determined from the maximum of the first derivative of the melting curve (A260 against temperature); each Tm is the
average of three independent experiments; exptl. error: 0.5°C.
c Difference in Tm relative to the control duplex (entry 1).
d Value taken from the literature.24

S. M. Langenegger, R. Ha¨ner / Tetrahedron Letters 45 (2004) 9273–9276
9275
symbolise a phenanthrene or a phenanthroline, respec-
tively, and n indicates the length of the alkyl linkers.
For comparison, an unmodified reference duplex was
synthesised possessing an AT-base pair in the central
position.
The influence of the aromatic base surrogates on duplex
stability was analysed by thermal denaturation experi-
ments. The melting temperatures (TmÕs, see Table 1)
reveal that the phenanthrene-modified hybrids (entries
2–5) are consistently less stable than the corresponding
hybrids containing phenanthroline and analogous lin-
kers (entries 6–9). The difference in TmÕs between the
two series is in the range of 2–4°C, always in favour
of the phenanthroline-modified duplexes. Such a differ-
ence is comparable to the contribution of an AT-base
pair to duplex stability. Furthermore, in both series
the optimal linker length is reached with n = 3, that is,
with propyl-type linkers. Duplex stability is rather insen-
sitive to a further increase in the linker length. No statis-
tically significant change (exptl. error: 0.5°C) is
observed among the derivatives containing propyl, butyl
or pentyl linkers in both series. In contrast, the stability
is considerably diminished if the linker is too short.
Thus, going from a propyl to an ethyl linker, the Tm is
reduced by 7.0 and 5.5°C in the phenanthrene and the
phenanthroline series, respectively (cf. entries 2/3 and 6/7).
Figure 2. CD spectrum of the duplex containing two non-nucleosidic
phenanthroline building blocks (d, Q3, see also Table 1, entry 7) in
comparison to the unmodified duplex (s, Table 1, entry 1).
All oligomers investigated in the study showed a single,
cooperative transition. Figure 1 shows the melting curve
of the duplex containing phenanthrolines with three
methylene groups in the linkers (i.e., Q3, see also entry
7 in Table 1). In addition, the circular dichroism spectra
(CD) of the hybrids investigated are all in agreement
with a B-form duplex. The CD spectrum of the duplex
containing the Q3 building blocks (see also Table 1,
entry 7) is shown in Figure 2 as a representative
example.
Figure 3. Illustration of
phenanthrolines with flexible, non-nucleosidic linkers.
a duplex containing interstrand-stacked
compromise the overall stability of the hybrid nor do
they substantially alter the overall B-DNA geometry.
The increase in Tm, which is observed by going from
phenanthrene to the corresponding phenanthroline
building blocks is well in agreement with the expecta-
tion, since the higher dipole moment present in the
heteroaromatic phenanthrolines should lead to stronger
stacking interactions.26
All the data obtained support a model of interstrand-
stacked, non-nucleosidic building blocks in an otherwise
regular B-DNA duplex. An illustration of interstrand-
stacked phenanthrolines is shown in Figure 3. The flex-
ible linkers connecting the polyaromatic hydrocarbons
to the phosphate backbone of the nucleic acid do not
In conclusion, non-nucleosidic phenanthrene and phen-
anthroline building blocks are well tolerated in duplex
DNA. In general, the phenanthroline derivatives give
more stable hybrids than the corresponding phenanth-
rene analogs. The difference in Tm is most likely a result
of the higher dipole moment of the heteroaromatic
phenanthroline, compared to the phenanthrene, result-
ing in stronger interstrand stacking interactions. Finally,
the stability of the hybrids is considerably decreased if
the linkers of the building blocks are too short.
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Figure 1. Representative thermal melting curve of a duplex containing
two non-nucleosidic phenanthroline building blocks (Q3, see also
Table 1, entry 7) in opposite positions.

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