Báo cáo khoa học: DNA sequence specificity of triplex-binding ligands docx

DNA sequence specificity of triplex-binding ligands
Melanie D. Keppler
1,
*, Peter L. James
1
, Stephen Neidle
2
, Tom Brown
3
and Keith R. Fox
1
1
Division of Biochemistry & Molecular Biology, School of Biological Sciences, University of Southampton, UK;
2
CRC Biomolecular
Structure Unit, Cancer Research UK, The School of Pharmacy, University of London, UK;
3
Department of Chemistry,
University of Southampton, UK
We have examined the ability of naphthylquinoline, a
2,7-disubstituted anthraquinone and BePI, a benzo[e]pyri-
doindole derivative, to stabilize parallel DNA triplexes of
different base composition.
1
Fluorescence melting studies,
with both inter- and intramolecular triplexes, show that all
three ligands stabilize triplexes that contain blocks of TAT
triplets. Naphthylquinoline has no effect on triplexes formed
with third strands composed of (TC)
n
or (CCT)

n
, but sta-
bilizes triplexes that contain (TTC)
n
. In contrast, BePI
slightly destabilizes the triplexes that are formed at (TC)
n
(CCT)
n
and (TTC)
n
. 2,7-Anthraquinone stabilizes (TC)
n
(CCT)
n
and (TTC)
n
, although it has the greatest effect on the
latter. DNase I footprinting studies confirm that triplexes
formed with (CCT)
n
are stabilized by the 2,7-disubstituted
amidoanthraquinone but not by naphthylquinoline. Both
ligands stabilize the triplex formed with (CCTT)
n
and neither
affects the complex with (CT)
n
. We suggest that BePI and
naphthylquinoline can only bind between adjacent TAT

triplets, while the anthraquinone has a broader sequence of
selectivity. These differences may be attributed to the pres-
ence (naphthylquinoline and BePI) or absence (anthraqui-
none) of a positive charge on the aromatic portion of the
ligand, which prevents intercalation adjacent to C
+
GC
triplets. The most stable structures are formed when the
stacked rings (bases or ligand) alternate between charged
and uncharged species. Triplexes containing alternating
C
+
GC and TAT triplets are not stabilized by ligands as they
would interrupt the alternating pattern of charged and
uncharged residues.
Keywords: anthraquinone; molecular beacon; naphthyl-
quinoline; triple helix; triplex-binding ligand.
The formation of intermolecular DNA triple helices offers a
means for designing agents which can bind to specific DNA
sequences [1–6]. In this approach, a third strand oligo-
nucleotide binds in the major groove of duplex DNA,
forming specific hydrogen bond contacts with substituents
on the purines of the duplex base pairs. In these structures
the third strand can run either parallel or antiparallel to the
duplex purine strand. Parallel triplexes, which have been
most widely studied, consist of TAT and C
+
GC triplets,
while the antiparallel motif contains GGC and AAT or
TAT triplets. Although triplex-forming oligonucleotides

bind to their duplex targets with considerable sequence
selectivity, their binding may not be strong. Several
strategies have therefore been used to improve their affinity,
including the use of base and backbone analogues [7–10],
and tethering DNA binding agents such as acridine [11,12]
or psoralen [13] to the end of the oligonucleotide. An
alternative strategy uses ligands which bind selectively to
triplex (not duplex) DNA and which therefore perturb the
equilibrium in the direction of triplex formation. Several
such ligands have been described (reviewed in [14]) including
3-methoxy-7H-8-methyl-11[(3¢-amino)propylamino]-benzo
[e]pyrido[4,3-b]indole
2
(BePI) and its derivatives [15–18],
coralyne [19–21], naphthylquinoline derivatives [22–26] and
bis-substituted amidoanthraquinones [27,28]. Although
most studies with these compounds have examined their
interaction with parallel triplets, they also stabilize the
antiparallel motif [24,25,29].
Although many ligands have been used to stabilize triple
helical DNA, little is known about their sequence selectivity,
in particular whether they have similar affinities for TAT
and C
+
GC triplets. Coralyne was originally thought to
possess little sequence selectivity [19], but was later shown to
be selective for TAT triplets [21]. BePI favours adjacent
TAT triplets within a parallel triplex [15], but can also
stabilize antiparallel triplexes consisting of both TAT and
GGC triplets [29]. Studies with a naphthylquinoline com-

pound (Fig. 1) indicated that at low pH this ligand stabilizes
TAT triplets in preference to C
+
GC triplets [25]. This
preference is thought to be due to the cationic charge on the
naphthylquinoline group, which hinders intercalation adja-
cent to a protonated cytosine. Other studies have shown
that isolated C
+
GC triplets impart a greater stability than
TAT triplets [30–32], although blocks of contiguous C
+
GC
triplets are destabilizing [33]. It is therefore possible that the
apparent selectivity of most ligands for TAT triplets is a
Correspondence to K. R. Fox, Division of Biochemistry & Molecular
Biology, School of Biological Sciences, University of Southampton,
Bassett Crescent East, Southampton SO16 7PX, UK.
Fax: + 44 23 80594459, Tel.: + 44 23 80594374,
E-mail:
Abbreviation: BePI, 3-methoxy-7H-8-methyl-11[(3¢-amino)propyl-
amino]-benzo[e]pyrido[4,3-b]indole.
*Present address: Department of Tumour Biology, Queen Mary’s
School of Medicine, John Vane Science Centre, Charterhouse Square,
London, EC1M 6BQ, UK.
(Received 8 September 2003, revised 23 October 2003,
accepted 25 October 2003)
Eur. J. Biochem. 270, 4982–4992 (2003) Ó FEBS 2003 doi:10.1046/j.1432-1033.2003.03901.x
consequence of the lower stability of this triplet, making it
easier to stabilize further.

In this paper we use DNase I footprinting and fluores-
cence melting experiments to assess the effects of ligands on
triplexes of different base composition. For the footprinting
experiments we have prepared a novel fragment that can
be targeted with oligonucleotides of different base compo-
sition. TyrT(35–59) contains a 25-base pair oligopurine
tract, which can be targeted with three different oligonucle-
otides as shown in Fig. 1. Oligo 1 (CCT)
n
generates a triplex
containing pairs of adjacent C
+
GC triplets which are
separated by single T ffi AT triplets, while oligo 2 (CCTT)
n
produces pairs of adjacent TAT and C
+
GC. Oligo 3 (CT)
n
generates a triplex containing alternating TAT and C
+
GC
triplets. We would expect that AT-selective ligands should
only potentiate the binding of oligo 2, as this is the only
triplex containing adjacent TAT triplets. We have compared
the effects of two triplex-binding ligands, a naphthylquino-
line and a 2,7-disubstituted amidoanthraquinone, on each
of these triplexes. These experiments were augmented with
fluorescence melting studies with inter- and intramolecular
triplexes with different sequence arrangements. The

sequences of these fluorescently labelled oligonucleotides
are shown below
3
(Results, Fluorescence melting studies).
Materials and methods
Chemicals and enzymes
Oligonucleotides were purchased from Oswel DNA Service
(Southampton, UK). These were stored in water at )20 °C
and diluted to working conditions immediately before use.
The sequences of the intermolecular triplexes generated in
the footprinting experiments are shown in Fig. 1D, while
the synthetic oligonucleotides that were used for the
fluorescence melting studies are shown below (Results,
Fluorescence melting studies). To avoid any potential
problems with misannealing of the fluorescently labelled
intermolecular triplexes, we used intramolecular duplexes in
which the two strands were connected by a single hexa-
ethylene glycol moiety (H). The fluorophore (fluorescein)
was incorporated at the 5¢-end of the duplex DNA, and the
quencher (Methyl red) was attached at the 5¢-end of the
third strand oligonucleotide. The 15-mer sequences were
chosen so as to generate triplexes with different arrange-
ments of C
+
GC and TAT triplets and are based around
repeats of (CCT)
n
(CT)
n
(CTT)

n
,andT
n
. The symmetrical
repeating structure of each complex was deliberately broken
so as to prevent strand slippage. For the fluorescently
labelled intramolecular triplexes the three strands were also
linked with hexaethylene glycol moieties. These sequences
were chosen to produce 14-mer intramolecular duplexes
with an internal fluorescein label within the purine-rich
strand. The quencher was attached to the 5¢-end of the short
third strand which generates a six-base triplex, similar to
that used in our previous studies
4
[34]. The third strand was
shorter than the underlying duplex, to ensure that the
duplex–single-strand and triplex–duplex transitions occur at
different temperatures.
The 2,7-disubstituted amidoanthraquinone with a pyr-
rolidine end group was prepared as the water-soluble
addition salt as using standard procedures as described
previously [35,36]. The naphthylquinoline triplex-bind-
ing ligand was a gift from L. Strekowski (Department
Fig. 1. Chemical structures of the 2,7-disubstituted anthraquinone, naphthylquinoline and sequences of the 110-base pair fragment from tyrT(35–59)
and the 25-base pair oligopurine tract together with the four oligonucleotides used. (A) Chemical structures of the 2,7-disubstituted anthraquinone. (B)
Chemical structure of the naphthylquinoline. (C) Sequence of the 110-base pair fragment from tyrT(35–59). The 25-base pair oligopurine tract is
underlined. In all these studies the fragment was labelled at the 3¢-end of the lower strand. (D) Sequence of the 25 base pair oligopurine tract (boxed)
together with the four oligonucleotides which are targeted to different regions.
Ó FEBS 2003 Triplex-binding ligands (Eur. J. Biochem. 270) 4983
Chemistry, Georgia State University, Atlanta, USA). This

was stored at a stock concentration of 20 m
M
in dimethyl-
sulfoxide. BePI was from Sigma.
DNA fragment for footprinting studies
For the footprinting studies, we prepared a novel derivative
of the tyrT DNA fragment which contains a 25-base
oligopurine tract. This fragment [designated tyrT(35–59)]
was derived from tyrT(43–59) by PCR site-directed muta-
genesis, and was designed so that different parts of the tract
contain (CCT)
n
(CCTT)
n
and (TC)
n
repeats. The sequence
of this fragment is shown in Fig. 1, together with the four
9-mer oligonucleotides which form specific triplexes with
different regions of this target. The radiolabelled DNA
fragment was prepared by digesting the plasmid with EcoRI
and AvaIandwaslabelledatthe3¢-end of the EcoRI site
using reverse transcriptase and [
32
P]dATP[aP]. The labelled
110-base pair DNA fragment was separated from the
remainder of the plasmid DNA on an 8% (w/v) nondena-
turing polyacrylamide gel. The isolated DNA was dissolved
in 10 m
M

Tris/HCl pH 7.5 containing 0.1 m
M
EDTA to
give about 10–20 c.p.s.ÆlL
)1
as determined on a hand held
Geiger counter (< 10 n
M
). For quantitative footprinting
experiments, the absolute DNA concentration is not
important so long as it is lower than the dissociation
constant of the DNA binding compound.
DNase I footprinting
Radiolabelled DNA (1.5 lL) was mixed with 1.5 lL
oligonucleotide and 1.5 lL triplex binding ligand. The
ligand and oligonucleotide were both dissolved in 50 m
M
sodium acetate (pH 5.0) containing 10 m
M
MgCl
2
.The
concentrations refer to conditions in the final reaction
mixture. These mixtures were equilibrated at 20 °Cforat
least 2 h. The samples were digested by adding 2 lL
DNase I (typically 0.01 UÆmL
)1
) dissolved in 20 m
M
NaCl

containing 2 m
M
MgCl
2
and 2 m
M
MnCl
2
. The reaction
was stopped after 1 min by adding 5 lL 80% formamide
containing 10 m
M
EDTA, 10 m
M
NaOH and 0.1% (w/v)
Bromophenol blue.
Gel electrophoresis
The products of digestion were separated on 9% polyacryl-
amide gels containing 8
M
urea. Samples were heated to
100 °C for 3 min, before rapidly cooling on ice and loading
onto the gel. Polyacrylamide gels (40 cm long, 0.3 mm
thick) were run at 1500 V for about 2 h and then fixed in
10% (v/v) acetic acid. These were transferred to Whatman
3MM paper and dried under vacuum at 80 °C. The dried
gels were either exposed to X-ray film at )70 °Cusingan
intensifying screen, or were subjected to phosphorimaging
using a Molecular Dynamics STORM phosphorimager.
Fig. 2. DNase I footprints showing the interaction of oligo 1 (5¢-TCCTCCTCC) with its target site on tyrT(35–59). The first panel (Left) shows the

pattern produced by the ligand alone; the second and third panels show the pattern in the presence of 3 and 1 l
M
naphthylquinoline, while the last
two panels show the pattern in the presence of 3 and 1 l
M
2,7-anthraquinone. The bracket shows the position of the 25-base oligopurine tract, while
the filled boxes show the location of the 9-base target site for this oligonucleotide. The track labelled GA is a Maxam–Gilbert marker specific for
purines. Oligonucleotide concentrations (l
M
)areshownatthetopofeachgellane.
4984 M. D. Keppler et al. (Eur. J. Biochem. 270) Ó FEBS 2003
Quantitative analysis of footprinting data
The intensity of bands within each footprint was estimated
using
IMAGEQUANT
software. These were normalized by
comparison with a region for which DNase I cleavage was
not affected. Footprinting plots [37] were constructed from
these data and C
50
values, indicating the oligonucleotide
concentration which reduces the band intensity by 50%,
were calculated by fitting a simple binding curve to the data.
Fluorescence melting studies
Fluorescence melting profiles were determined by using a
Roche LightCycler as described previously [34]. The prin-
ciple of these experiments is that when a triplex is formed
the fluorophore and quencher are in close proximity and the
fluorescence is quenched. On denaturing the complex, the
fluorophore and quencher are separated and there is a large

increase in fluorescence. We have previously used this
method for examining the properties of DNA triplexes
[34,38] and quadruplexes [39]. This method is especially
useful for studying triplex formation as only the triplex–
duplex transition is observed, and the analysis is not
complicated by the melting of the underlying duplex.
Samples were prepared in 50 m
M
sodium acetate pH 5.0
containing 150 m
M
NaCl. For the intermolecular triplexes
each sample (20 lL) contained 0.25 l
M
duplex DNA and
4 l
M
triplex forming oligonucleotide, while for the intra-
molecular triplexes the strand concentration was 0.25 l
M
.
The complexes were denatured by heating to 95 °Catarate
of 0.1 °CÆs
)1
and maintained at this temperature for 5 min
before cooling to 30 °Cat0.1°CÆs
)1
.Sampleswerethen
held at 30 °C for 5 min before melting again by heating to
95 °Cat0.1°CÆs

)1
. The fluorescence was recorded during
both melting and annealing phases. The LightCycler excites
the samples at 488 nm, and the emission was measured at
520 nm. T
m
values were determined from the first deriva-
tives of the melting profiles using the Roche
LIGHTCYCLER
software and were reproducible to within 0.5 °C. Unless
otherwise stated the T
m
values quoted refer to the second
melting transition. The properties of the intermolecular
triplexes have been described previously [38].
Fig. 3. Footprinting plots showing the concen-
tration dependence of the footprints obtained
with the three oligonucleotides at their target
sites in tyrT(35–59), in the presence and absence
of triplex-binding ligands. (A) Oligo 1 plus
naphthylquinoline: d, oligonucleotide alone
with no added ligand; s,3 l
M
ligand; ,,1l
M
ligand. (B) Oligo 1 plus 2,7 anthraquinone: n,
10 l
M
ligand; s,3l
M

ligand; ,,1l
M
ligand.
(C) Oligo 2 plus naphthylquinoline: n,10l
M
ligand; s,3l
M
ligand; ,,1l
M
ligand. (D)
Oligo 2 plus 2,7-anthraquinone: d,oligo-
nucleotide alone with no added ligand; n,
10 l
M
ligand; s,3l
M
ligand; ,,1l
M
ligand.
(E) Oligo 3: d, oligonucleotide alone with no
added ligand; n,3l
M
anthraquinone; s,
3 l
M
naphthylquinoline. (F) Oligo 4: d
oligonucleotide alone with no added ligand;
n,3l
M
anthraquinone, s,3l

M
naphthyl-
quinoline.
Ó FEBS 2003 Triplex-binding ligands (Eur. J. Biochem. 270) 4985
Results
DNase I footprinting
Oligo 1. Fig. 2 shows the interaction of oligo
1(TCCTCCTCC) with its target site on tyrT(35–59) in the
presence and absence of the two triplex-binding ligands.
These experiments were performed at pH 5.0 to ensure
protonation of the third strand cytosines. As this triplex
does not contain any adjacent TAT triplets it should not be
stabilized by AT-selective triplex-binding ligands. The
oligonucleotide alone (left panel) produces a clear footprint
at its target site, which extends to an oligonucleotide
concentration of about 5 l
M
. This footprint extends a few
bases beyond the 5¢-(upper) end of the target site and is
accompanied by enhanced cleavage at the 3¢-(lower) end,
coincident with the triplex–duplex junction. Quantitative
analysis of the concentration dependence of the footprint
yielded a C
50
value of 2.8 ± 0.6 l
M
.
Similar experiments were performed in the presence of 1,
3and10l
M

of the naphthylquinoline and the 2,7-disubsti-
tuted anthraquinone triplex-binding ligands. The second
and third panels of Fig. 2 show the footprints obtained in
the presence of 3 and 1 l
M
of the naphthylquinoline triplex-
binding ligand, respectively. In each case the oligonucleotide
produces a clear footprint which is evident only at
concentrations above 2 l
M
. Quantitative analysis of these
patterns yields the footprinting plots shown in Fig. 3A,
generating the C
50
values presented in Table 1. It can be
seen that these values are very similar to that for the
oligonucleotide alone, suggesting that the ligand does not
significantly stabilize this triplex (even at a concentration of
10 l
M
).
The final two panels of Fig. 2 show the footprinting
patterns obtained in the presence of 3 and 1 l
M
of the
2,7-anthraquinone. Once again clear footprints are evident
at the target site, but require lower oligonucleotide concen-
trations than in the absence of ligand. In the presence of 3
and 1 l
M

of the anthraquinone the footprints extend to
oligonucleotide concentrations of 0.4 and 1 l
M
, respect-
ively. Footprinting plots derived from these data are shown
in Fig. 3B yielding the C
50
values which are presented in
Table 1. From these data it appears that the 2,7-dis-
ubstituted anthraquinone stabilizes this triplex in a concen-
tration-dependent manner, whereas the naphthylquinoline
does not affect the interaction with the oligonucleotide.
Oligo 2. Fig. 4 shows the interaction of oligo 2
(CTTCCTTCC) with its target site on tyrT(35–59) in the
presence and absence of the two triplex-binding ligands.
This oligonucleotide should generate a triplex containing
two blocks of adjacent TAT triplets, which might provide a
binding site for AT-selective ligands. The first panel shows
the interaction with the oligonucleotide alone and shows a
footprint at the target site. Quantitative analysis of the
concentration dependence of this footprint (Fig. 3D, d)
yields a C
50
value of 1.0 ± 0.2 l
M
. Similar experiments in
the presence of the triplex-binding ligands are shown in the
other panels of Fig. 4, while footprinting plots derived
from these data are shown in Fig. 3C and D. The footprints
in the presence of 3 and 1 l

M
anthraquinone persist to
about 0.2 and 0.4 l
M
, respectively, yielding C
50
values of
0.12 and 0.38 l
M
. Similarly the footprints in the presence of
3and1l
M
naphthylquinoline persist to 0.6 and 1 l
M
,
yielding C
50
values of 0.43 and 0.73 l
M
.EvenlowerC
50
are
generated in the presence of 10 l
M
ligands (Table 1).
Oligos 3 and 4. Fig. 5 shows the interaction of oligo 4
(TCTCTCTCT) with its target site on tyrT(35–59) in the
presence and absence of the two triplex-binding ligands.
This oligonucleotide should generate a triplex which consists
of alternating TAT and C

+
GC triplets. Robert and
Crothers [40] predicted that such CT repeats should
generate the most stable triplexes. It can be seen that this
oligonucleotide generates a stable triplex at pH 5.0 in the
absence of the ligands. This footprint, which is accompanied
by enhanced cleavage at the 3¢-(lower) end of the target site,
persists to an oligonucleotide concentration between 0.2 and
0.1 l
M
. The footprinting plot for this interaction yields a
C
50
value of 0.14 ± 0.04 l
M
. Addition of either 3 l
M
of
naphthylquinoline or anthraquinone has little effect on the
apparent affinity for the third strand. Clear footprints are
still visible which persist to very similar concentrations to
those in the absence of ligand. The footprinting plots for this
interaction are shown in Fig. 3E, yielding the C
50
values
shown in Table 1. From these values it can be seen that
neither of these ligands significantly affects the triplex
stability.
As oligo 3 binds tightly in the absence of ligand, we were
concerned that the inherent stability of the complex might

mask any effects due to the triplex-binding ligands. We
therefore tested the interaction with a shorter 7-mer
Table 1. C
50
and K
L
values for the interaction of the various triplex
forming oligonucleotides with their target sites on tyrT (35–59). C
50
values (l
M
), corresponding to the oligonucleotide concentration which
reduces the intensity of bands within the target site by 50%, were
determined as described in Methods.
Oligo Ligand C
50
(l
M
)
Oligo 1 No ligand 2.8 ± 0.6
10 l
M
AQ 0.09 ± 0.02
3 l
M
AQ 0.25 ± 0.07
1 l
M
AQ 0.45 ± 0.09
10 l

M
NQ 2.1 ± 0.5
3 l
M
NQ 1.5 ± 0.3
1 l
M
NQ 2.0 ± 0.4
Oligo 2 No ligand 1.0 ± 0.2
10 l
M
AQ 0.06 ± 0.02
3 l
M
AQ 0.12 ± 0.05
1 l
M
AQ 0.38 ± 0.08
10 l
M
NQ 0.12 ± 0.03
3 l
M
NQ 0.43 ± 0.14
1 l
M
NQ 0.73 ± 0.23
Oligo 3 No ligand 0.14 ± 0.04
3 l
M

AQ 0.10 ± 0.04
1 l
M
AQ 0.14 ± 0.07
3 l
M
NQ 0.12 ± 0.04
1 l
M
NQ 0.12 ± 0.04
Oligo 4 No ligand 0.9 ± 0.2
3 l
M
AQ 0.6 ± 0.2
3 l
M
NQ 0.7 ± 0.2
4986 M. D. Keppler et al. (Eur. J. Biochem. 270) Ó FEBS 2003
oligonucleotide (oligo 4), which lacks the two terminal
thymine bases of oligo 3. We would expect oligo 4 to possess
a lower triplex affinity than oligo 3 as a result of its shorter
length. We avoided the use of even shorter oligos as these
would be able to bind in more than one position.
Footprinting experiments with this oligonucleotide (data
not shown) confirmed that it bound less well than oligo 3,
generating the footprinting plot shown in Fig. 3F (d),
yielding a C
50
value of 0.9 ± 0.2 l
M

. This is still a high
affinity for such a short oligonucleotide and confirms
the unusually high affinity of triplexes which consist of
alternating TAT and C
+
GC triplets. Addition of either
ligand failed to affect the concentration dependence of the
footprints (Fig. 3F), yielding very similar C
50
values
(Table 1). It therefore appears that neither ligand binds to
tracts of alternating TAT and C
+
GC triplets.
Fluorescence melting studies
We further examined the sequence specificity of these
ligands by performing DNA melting experiments with
fluorescently labelled synthetic oligonucleotides (Fig. 6). In
these oligonucleotides the fluorophore and quencher are
positioned so that they are in close proximity when a triplex
is formed, and the fluorescence is quenched. When the
triplex melts these groups are separated and there is large
increase in fluorescence. Fluorescence melting curves show-
ing the effects of naphthylquinoline, anthraquinone and
BePI on the melting transitions of these triplexes are shown
in Figs 7–9. Looking first at the results for the intramole-
cular triplexes (upper panels) it can be seen that, in the
absence of added ligand, these all show unusual biphasic
melting profiles in which the initial increase in fluorescence is
followed by a decrease at higher temperatures. This second

transition is less pronounced for the more stable triplexes
(those containing C
+
GC triplets) and is not observed with
the intermolecular triplexes (see below). We have suggested
previously that this second transition arises from melting of
the underlying duplex [34], since the time-averaged distance
between the fluorophore and quencher is greater for the
partially melted triplex than for the fully melted random
coil. When the third strand dissociates the remaining duplex
will be relatively rigid and hold the fluorophore and
quencher apart. The T
m
values for these transitions are
presented in Table 2. It can be seen that the T
m
of the
second transition increases with increasing GC-content, as
expected for melting of a DNA duplex, and is maximal for
(CCT)
2
. In contrast the first melting transition is highest
for (TC)
3
, consistent with the suggestion that regions of
alternating C
+
GC and TAT triplets are unusually stable
[40], and is similar to our previous work with intermolecular
triplexes [38].

Fig. 4. DNase I footprints showing the interaction of oligo 2 (5¢-CTTCCTTCC) with its target site on tyrT(35–59). The first panel (Left) shows the
pattern produced by the ligand alone; the second and third panels show the pattern in the presence of 3 and 1 l
M
2,7-anthraquinone, while the last
two panels show the pattern in the presence of 3 and 1 l
M
naphthylquinoline. The bracket shows the position of the 25-base oligopurine tract, while
the filled boxes show the location of the 9-base target site for this oligonucleotide. Tracks labelled GA are Maxam–Gilbert markers specific for
purines. Oligonucleotide concentrations (l
M
)areshownatthetopofeachgellane.
Ó FEBS 2003 Triplex-binding ligands (Eur. J. Biochem. 270) 4987
Figure 7 shows the effect of naphthylquinoline on these
melting transitions and the DT
m
s induced by 10 l
M
ligand
are shown in Table 2. It can be seen that the ligand increases
the melting temperature of triplexes that contain only TAT
triplets (T
6
) and has little effect on the other triplexes. This
effect is most pronounced in the absence of magnesium for
which 10 l
M
ligand increases the melting temperature of the
intramolecular complex by 17.9 °C. The intermolecular
triplex that contains mainly TAT triplets (TTT) is unstable
in the absence of ligand, and melts below 30 °C; addition of

naphthylquinoline raises this T
m
to 64.7 °C. The ligand has a
much smaller effect on the more stable triplexes, and has no
effect on triplexes that contain repeats of CCT and CTCT,
though it stabilizes the intermolecular triplex CTT by the
same amount as TTT in the presence of magnesium.
Figure 8 shows the results of similar experiments with the
2,7-anthraquinone. The overall pattern of these results is
very similar to that seen with the naphthylquinoline and the
greatest effect is again produced with the triplexes that
contain TAT triplets. However, this ligand also produces a
small, though significant, stabilization of CCT and CTCT
triplexes.
Fig. 5. DNase I footprints showing the interaction of oligo 3 (5¢-TCTCTCTCT) with its target site on tyrT(35–59). The first panel (Left) shows the
pattern produced by the ligand alone (left hand lanes) and in the presence of 1 l
M
naphthylquinoline. The second panel shows the pattern in
thepresenceof3l
M
naphthylquinoline, while the last panel shows the pattern in the presence of 3 l
M
2,7-anthraquinone. The bracket shows the
position of the 25-base oligopurine tract, while the filled boxes show the location of the 9-base target site for this oligonucleotide. The track labelled
GA is a Maxam–Gilbert marker specific for purines. Oligonucleotide concentrations (l
M
)areshownatthetopofeachgellane.
Fig. 6. Sequences of the fluorescently labelled inter- and intramolecular
triplexes. Fluorescein (F) was incorporated as Fam-cap-dU, while the
quencher methyl red (Q) was Methyl-Red-dR. H indicates the hexa-

ethylene glycol joining the two duplex strands. In each case the Hoo-
gsteen strand is shown in italics.
4988 M. D. Keppler et al. (Eur. J. Biochem. 270) Ó FEBS 2003
For comparison we also examined the effect of BePI on
melting of these fluorescently labelled triplexes, and the
results are shown in Fig. 9 and Table 2. This ligand is one
of the best characterized triplex-binding ligands and is well
known to bind to triplexes that are rich in TAT triplets.
It can be seen that BePI strongly stabilizes the TAT-
containing triplets and is the most potent ligand at the
intramolecular triplex T
6
. This activity is reduced on
addition of magnesium, but is still greater than the other
ligands under these conditions. BePI has a small stabil-
izing effect on the intermolecular triplex CTT. However, it
destabilizes the intermolecular and intramolecular triplexes
Fig. 7. Effect of the naphthylquinoline triplex-binding ligand on the fluorescence melting curves of the inter- and intramolecular triplexes. The upper
panels show the results for the intramolecular triplexes, while the lower panels correspond to the intermolecular triplexes. The experiments were
performed in 50 m
M
sodium acetate (pH 5.0) containing 150 m
M
sodium chloride, except for those labelled Ô+MgÕ where 50 m
M
MgCl
2
was also
included. In each case, the solid lines correspond to melting of the oligonucleotide alone, in the absence of added ligand, while the circles show the
transitions in the presence of 10 l

M
ligand. For the triplexes that contain only TAT triplexes (first panel in each row), the curves shown correspond
to ligand concentrations of 1, 2, 5 and 10 l
M
(intramolecular triplex T
6
) and 0.5, 1, 2, 5 and 10 l
M
(intermolecular triplex TTT), in each case the
concentrations increase from left to right. The curves have been normalized to the same final fluorescence.
Fig. 8. Effect of the 2,7-disubstituted anthraquinone on the fluorescence melting curves of the inter- and intramolecular triplexes. The upper panels
show the results for the intramolecular triplexes, while the lower panels correspond to the intermolecular triplexes. The experiments were performed
in 50 m
M
sodium acetate (pH 5.0) containing 150 m
M
sodium chloride, except for those labelled Ô +MgÕ,where50 m
M
MgCl
2
was also included. In
each case the solid lines correspond to melting of the oligonucleotide alone, in the absence of added ligand, the circles show the transitions in the
presence of 10 l
M
ligand. For the triplexes that contain only TAT triplexes (first panel in each row) the curves shown correspond to ligand
concentrations of 0.5, 2, 5 and 10 l
M
ligand; in each case the concentrations increase from left to right. The curves have been normalized to the same
final fluorescence.
Ó FEBS 2003 Triplex-binding ligands (Eur. J. Biochem. 270) 4989

that contain repeats of CT or CCT, producing melting
curves that are unusually shallow. These results suggest
that BePI cannot bind adjacent to C
+
GC triplets and are
consistent with previous observations that the effect of
BePI decreases as the proportion of C
+
GC triplets
increases.
Discussion
The results presented in this paper confirm that naphthyl-
quinoline, anthraquinone and BePI, triplex-binding ligands,
are much more effective at stabilizing triplexes that are rich
in TAT triplets. This preference is most pronounced for
Fig. 9. Effect of BePI on the fluorescence melting curves of inter- and intramolecular triplexes. The upper panels show the results for the intra-
molecular triplexes, while the lower panels correspond to the intermolecular triplexes. The experiments were performed in 50 m
M
sodium acetate
(pH 5.0) containing 150 m
M
sodium chloride, except for those labelled Ô+MgÕ,where50m
M
MgCl
2
was also included. In each case the solid lines
correspond to melting of the oligonucleotide alone, in the absence of added ligand, while the circles show the transitions in the presence of 10 l
M
ligand. For the triplexes that contain only TAT triplexes (first two panels in each row) the curves shown correspond to ligand concentrations of 0.2,
0.5, 1, 2, 5 and 10 l

M
5
(intramolecular triplex T
6
), 2, 5 and 10 l
M
(intramolecular triplex T
6
+Mg),0.5,1,2,5and10l
M
(intermolecular triplex
TTT) and 2, 5 and 10 l
M
(intermolecular triplex TTT + Mg). In each case the concentrations increase from left to right. The curves have been
normalized to the same final fluorescence.
Table 2. Effects of triplex-binding ligand on the melting of intramolecular and intermolecular triplexes. The experiments were performed in 50 mm
sodium acetate (pH 5.0) containing 150 mm NaCl. The concentration of the intramolecular triplexes was 0.25 lm. For the intermolecular triplexes
hairpin duplex concentration was 0.25 lm, with 4 lm third strand. In each case the ligand concentration was 10 lm. For the intramolecular
triplexes two melting transitions were observed: T
m1
corresponds to triplex fi duplex, and T
m2
corresponds to duplex fi single strands. DT
m
is
equal to the T
m
in the presence of ligand minus the T
m
in its absence. Since the intermolecular TTT melts below 30 °C under these conditions the

actual T
m
values in the presence of ligands are shown. In the presence of BePI some melting transitions were unusually broad and are indicated by
an asterisk (*).
Sequence
No ligand Naphthylquinoline Anthraquinone BePI
T
m1
T
m2
DT
m1
DT
m2
DT
m1
DT
m2
DT
m1
DT
m2
Intra-
T
6
36.1 69.0 17.9 2.2 16.1 2.1 26.7 7.9
T
6
+ Mg 57.9 72.6 4.9 0.4 2.2 0.2 6.3 2.0
(CTT)

2
60.2 76.0 0.9 0 6.3 2.8 )1.9 5.1
(TC)
3
67.2 79.6 0.6 0.6 3.1 1.4 )7.7* 4.9
(CCT)
2
64.7 81.2 1.3 1.3 3.6 1.2 )5.8* 5.5
T
m
DT
m
DT
m
DT
m
Inter-
TTT < 30 T
m
¼ 64.7 T
m
¼ 51.0 T
m
¼ 64.2
TTT + Mg 53.2 5.0 4.6 13.7
CTT 68.2 5.0 3.7 1.8
CTCT 75.2 0.9 1.3 )4.2
CCT 74.6 )0.4 0.4 )5.3*
4990 M. D. Keppler et al. (Eur. J. Biochem. 270) Ó FEBS 2003
BePI as the melting experiments showed a small destabil-

ization of complexes containing a high proportion of
C
+
GC triplets. Naphthylquinoline stabilizes only triplexes
that contain adjacent TAT triplets and has no effect on the
complexes that are formed with (CCT)
n
or (CT)
n
.In
contrast, although the 2,7-disubstituted anthraquinone is
most effective at stabilizing sequences that are rich in TAT
triplets, it produces a small stabilization of all the triplexes
examined, except those formed with oligos 3 and 4 in the
footprinting experiments (generating triplexes that contain
alternating TAT and C
+
GC triplets).
In general, all of these ligands are less effective at the more
stable triplexes and DT
m
values with complexes TTT and
T
6
are much lower in the presence of magnesium, which
selectively stabilizes the TAT triplet [38,41,42]. Nonetheless
both naphthylquinoline and BePI still produce appreciable
stabilization of this triplex in the presence of high concen-
trations of magnesium. It should be noted that these
experiments were all performed at low pH in order to ensure

cytosine protonation. We have previously reported the pH
dependency of these triplexes [38] and have shown that,
except for the complexes that contain only TAT triplets,
they are not stable above pH 6.5. None of these ligands
promotes triplex formation with C
+
GC-containing tri-
plexes at pH 7.0. However, it will be interesting to discover
whether they facilitate triplex formation at physiological pH
with third strands containing cytosine analogues which have
elevated pK values.
The quantitative DNase I footprinting experiments with
oligo 1 (CCTCCTCCT), and the melting experiments with
CCT and (CCT)
2
clearly indicate that the naphthylquinoline
ligand fails to stabilize this triplex. In contrast, the 2,7-
disubstituted anthraquinone increases the melting temper-
atures, and lower the concentrations that are required to
generate DNase I footprints. The inability of the naphthyl-
quinoline ligand to stabilize these triplexes is not surprising
as it has previously been shown to be selective for triplexes
containing TAT triplets [25]. The triplex formed with these
oligonucleotides do not contain any adjacent TAT triplets
and every potential intercalation site contains protonated
cytosines on either the 3¢-or5¢-side. We presume that the
positive charges on the third strand cytosines hinder
intercalation of the charged naphthylquinoline ring. By
contrast the disubstituted anthraquinones have neutral ring
systems, although they possess positively charged side

groups. We suggest that this is because intercalation of the
uncharged anthraquinone ring system between the adjacent
protonated cytosines generates a stack of alternating
charged and uncharged residues, separating the charged
C
+
GC triplets from each other. This will result in superior
triplex stability in much the same way that alternating
TAT and C
+
GC triplets generate the most stable triplexes
[30–32].
By contrast the triplex formed by oligo 2 (CTTCCTTCC)
is stabilized by both ligands. This triplex contains all
possible combinations of adjacent triplets. Taken together
with the results discussed above, this suggests that the
adjacent TAT triplets form the binding site for the
naphthylquinoline ligand while the anthraquinone may be
able to bind in several different locations.
Neither ligand stabilizes the triplexes formed with oligos
3 or 4 in footprinting experiments and they do not affect
the melting of triplexes containing alternating TAT and
C
+
GC triplets. These triplexes are unusually stable, as
predicted by Roberts and Crothers [40]. In this case we
suggest that the alternation of charged and uncharged
bases generates a very stable triplex, which cannot readily
be disrupted by intercalation of any ligand into its
structure. This would interrupt the alternation of charged

and uncharged residues and so would destabilize the
structure.
The suggestion that alternating positively charged and
neutral rings (whether from the bases themselves or from
the stabilizing ligand) generate triplexes with maximal
stability, means that both positively charged and neutral
ligands will be needed to stabilize all triplexes. Ligands with
uncharged rings, such as the disubstituted anthraquinones,
will be best suited for stabilizing C
+
GC-rich triplexes while
ligands bearing a charged ring, such as the naphthylquino-
line will be best for stabilizing TAT-rich triplexes. It appears
that regions of alternating TAT and C
+
GC may have
maximal stability and may be difficult to stabilize by adding
ligands.
Acknowledgements
This work was supported by grants from Cancer Research UK and the
European Union.
References
1. Soyfer, V.N. & Potoman, V.N. (1996) Triple-Helical Nucleic
Acids. Springer-Verlag, New York.
2. Thuong, N.T. & He
´
le
`
ne, C. (1993) Sequence specific recognition
and modification of double helical DNA by oligonucleotides.

Angew. Chem. Int. Ed. Engl. 32, 666–690.
3. Fox, K.R. (2000) Targeting DNA with triplexes. Curr. Med.
Chem. 7, 17–37.
4. Neidle, S. (1997) Recent developments in triple helix regulation of
gene expression. Anti-Cancer Drug Des. 12, 433–442.
5. Vasquez, K.M. & Wilson, J.H. (1998) Triplex-directed modifica-
tion of genes and gene activity. Trends Biochem. Sci. 23,4–9.
6. Chan, P.P. & Glazer, P.M. (1997) Triplex DNA: fundamental
advances and potential applications for gene therapy. J. Mol.
Med. 75, 267–282.
7. Lacroix, L., Arimondo, P.B., Takasugi, M., He
´
le
`
ne, C. & Mergny,
J.L. (2000) Pyrimidine morpholino oligonucleotides form a stable
triple helix in the absence of magnesium ions. Biochem. Biophys.
Res. Commun. 270, 363–369.
8. Zhou-Sun, B.W., Sun, J.S., Gryaznov, S.M., Liquier, J., Garestier,
T., He
´
le
`
ne, C. & Taillandier, E. (1997) A physico-chemical study
of triple helix formation by an oligodeoxythymidylate with
N3¢fiP5¢ phosphoramidate linkages. Nucleic Acids Res. 25,
1782–1787.
9. Cuenoud,B.,Casset,F.,Hu
¨
sken, D., Natt, F., Wolf, R.M., Alt-

mann, K.H., Martin, P. & Moser, H.E. (1998) Dual recognition of
double-stranded DNA by 2¢-aminoethoxy-modified oligonucleo-
tides. Angew. Chem. Int. Ed. Engl. 37, 1288–1291.
10. Bijapur, J., Keppler, M.D., Bergqvist, S., Brown, T. & Fox, K.R.
(1999) 5-(1-propargylamino)-2¢-deoxyuridine (U
P
): a novel
thymidine analogue for generating DNA triplexes with increased
stability. Nucleic Acids Res. 27, 1802–1809.
11. Sun, J S., Franc¸ ois, J C., Montenay-Garestier, T., Saison-
Behmoaras, T., Roig, V., Thuong, N.T. & He
´
le
`
ne, C. (1989)
Sequence-specific intercalating agents: Intercalation at specific
sequences on duplex DNA via major groove recognition by
Ó FEBS 2003 Triplex-binding ligands (Eur. J. Biochem. 270) 4991
oligonucleotide-intercalator conjugates. Proc. Natl Acad. Sci.
USA 86, 9198–9202.
12. Stonehouse, T.J. & Fox, K.R. (1994) DNase I footprinting of
triple helix formation at polypurine tracts by acridine-linked
oligopyrimidines: Stringency, structural changes and interaction
with minor groove binding ligands. Biochim. Biophys. Acta 1218,
322–330.
13. Takasugi, M., Guendouz, A., Chassignol, M., Decout, J.L.,
Lhomme, J., Thuong, N.T. & He
´
le
`

ne, C. (1991) Sequence-specific
photo-induced cross-linking of the two strands of double-helical
DNA by a psoralen covalently linked to a triple helix-forming
oligonucleotide. Proc. Natl Acad. Sci. USA 88, 5602–5605.
14. Darby, R.A.J. & Fox, K.R. (2002) Triple-helix-specific ligands. In:
Interaction of Small Molecules with DNA and RNA: from Synthesis
to Nucleic Acid Complexes (eds Demeunynck, M., Bailly, C.,
Wilson, W.D.) pp. 360–383, Wiley VCH, NJ.
15. Mergny, J.L., Duval-Valentin, G., Nguyen, C.H., Perrouault, L.,
Faucon, B., Rouge
´
e, M., Montenay-Garestier, T., Bisagni, E. &
He
´
le
`
ne, C. (1992) Triple-helix specific ligands. Science 256,
1681–1684.
16. Marchand, C., Bailly, C., Nguyen, C.H., Bisagni, E., Garestier, T.,
He
´
le
`
ne, C. & Waring, M.J. (1996) Stabilization of triple helical
DNA by a benzopyridoquinoxaline intercalator. Biochemistry 35,
5022–5032.
17. Schmitt, P., Nguyen, C.H., Sun, J.S., Grierson, D.S., Bisagni, E.,
Garestier, T. & He
´
le

`
ne, C. (2000) 13H-benzo[6–7]indolo[3,2-
c]quinolines (B[6,7]IQ): optimization of their DNA triplex-specific
stabilization properties. Chem. Commun. 763–764.
18. Silver, G.C., Sun, J.S., Nguyen, C.H., Boutorine, A.S., Bisagni, E.
&He
´
le
`
ne, C. (1997) Stable triple-helical DNA complexes formed
by benzopyridoindole- and benzopyridoquinoxaline-oligonucleo-
tide conjugates. J. Am. Chem. Soc. 119, 263–268.
19. Lee,J.S.,Latimer,L.J.P.&Hampel,K.J.(1993)Coralynebinds
tightly to both TAT- and CGC
+
-containing DNA triplexes.
Biochemistry 32, 5591–5597.
20. Latimer, L.J.P., Payton, N., Forsyth, G. & Lee, J.S. (1995) The
binding of analogues of coralyne and related heterocyclics to
DNA triplexes. Biochem. Cell Biol. 73, 11–18.
21. Moraru-Allen, A.A., Cassidy, S., Alvarez, J.L.A., Fox, K.R.,
Brown, T. & Lane, A.N. (1997) Coralyne has a preference for
intercalation between TA.T triples in intramolecular DNA triple
helices. Nucleic Acids Res. 25, 1890–1896.
22. Wilson, W.D., Tanious, F.A., Mizan, S., Yao, S., Kiselyov,
A.S., Zon, G. & Strekowski, L. (1993) DNA triple-helix specific
intercalators as antigene enhancers. Biochemistry 32, 10614–
10621.
23. Chandler, S.P., Strekowski, L., Wilson, W.D. & Fox, K.R. (1995)
Footprinting studies on ligands which stabilise DNA triplexes.

Biochemistry 34, 7234–7242.
24. Cassidy, S.A., Strekowski, L., Wilson, W.D. & Fox, K.R. (1994)
Effect of a triplex-binding ligand on parallel and antiparallel DNA
triple helices using short unmodified and acridine-linked oligo-
nucleotides. Biochemistry 33, 15338–15347.
25. Cassidy, S.A., Strekowski, L. & Fox, K.R. (1996) DNA sequence
specificity of a naphthylquinoline triple helix-binding ligand.
Nucleic Acids Res. 24, 4133–4138.
26. Chaires,J.B.,Ren,J.,Henary,M.,Zegrocka,O.,Bischop,G.R.&
Strekowski, L. (2003) Triplex selective 2-(2-naphthyl) quinoline
compounds: origins of affinity and new design principles. J. Am.
Chem. Soc. 125, 7272–7283.
27. Fox, K.R., Polucci, P., Jenkins, T.C. & Neidle, S. (1995) A
molecular anchor for stabilizing triple-helical DNA. Proc. Natl
Acad. Sci. USA 92, 7887–7891.
28. Keppler, M.D., Read, M.A., Perry, P.J., Trent, J.O., Jenkins,
T.C., Reszka, A.P., Neidle, S. & Fox, K.R. (1999) Stabilization of
DNA triple helices by a series of mono- and disubstituted ami-
doanthraquinones. Eur. J. Biochem. 263, 817–825.
29. Escude
´
, C., Sun, J S., Nguyen, C.H., Bisagni, E., Garestier, T. &
He
´
le
`
ne, C. (1996) Ligand-induced formation of triple helices with
antiparallel third strands containing G and T. Biochemistry 35,
5735–5740.
30. Volker, J. & Klump, H.H. (1994) Electrostatic effects in DNA

triple helices. Biochemistry 33, 13502–13508.
31. Asensio,J.L.,Lane,A.N.,Dhesi,J.,Bergvist,S.&Brown,T.
(1998) The contribution of cytosine protonation to the stability of
parallel DNA triple helices. J. Mol. Biol. 275, 811–822.
32. Keppler, M.D. & Fox, K.R. (1997) Relative stability of triplexes
containing different numbers of T.AT and C
+
.GC triplets. Nucleic
Acids Res. 25, 4644–4649.
33. Lee, J.S., Woodsworth, M.L., Latimer, L.J.P. & Morgan, A.R.
(1984) Poly (pyrimidine) poly (purine) synthetic DNAs containing
5-methylcytosine form stable triplexes at neutral pH. Nucleic Acids
Res. 12, 6603–6614.
34. Darby, R.A.J., Sollogoub, M., McKeen, C., Brown, L., Risitano,
A.,Brown,N.,Barton,C.,Brown,T.&Fox,K.R.(2002)High
throughput measurement of duplex, triplex and quadruplex
melting curves using molecular beacons and the LightCycler.
Nucleic Acids Res. 29,e39.
35. Perry,P.J.,Gowan,S.M.,Reszka,A.P.,Polucci,P.,Jenkins,T.C.,
Kelland, L.R. & Neidle, S. (1998) 1,4- and 2,6-disubstituted
amidoanthracene-9,10-dione derivatives as inhibitors of human
telomerase. J. Med. Chem. 41, 3253–3260.
36. Perry, P.J., Reszka, A.P., Wood, A.A., Read, M.A., Gowan,
S.M., Dosanjh, H.S., Trent, J.O., Jenkins, T.C., Kelland, L.R. &
Neidle, S. (1998) Human telomerase inhibition by regioisomeric
disubstituted amidoanthacene-9,10-diones. J. Med. Chem. 41,
4873–4874.
37. Dabrowiak, J.C. & Goodisman, J. (1989) Quantitative footprint-
ing analysis of drug–DNA interactions. In: Chemistry and Physics
of DNA–Ligand Interactions (Kallenbach, N.R., ed.), pp. 143–174.

Academic Press, New York.
38. James, P.L., Brown, T. & Fox, K.R. (2003) Thermodynamic and
kinetic stability of intermolecular triple helices containing different
proportions of C
+
?GC and T?AT triplets. Nucleic Acids Res. 31,
5598–5606.
39. Risitano, A. & Fox, K.R. (2003) Stability of intramolecular DNA
quadruplexes: comparison with DNA duplexes. Biochemistry 42,
6507–6513.
40. Roberts, R.W. & Crothers, D.M. (1996) Prediction of the stability
of DNA triplexes. Proc.NatlAcad.Sci.USA93, 4320–4325.
41. Plum, G.E. & Breslauer, K.J. (1995) Thermodynamics of an
intramolecular DNA triple helix: a calorimetric and spectroscopic
study of the pH and salt dependence of thermally induced struc-
tural transitions. J. Mol. Biol. 248, 679–695.
42. Wilson, W.D., Hopkins, H.P., Mizan, S., Hamilton, D.D. & Zon,
G. (1994) Thermodynamics of DNA triplex formation in oligo-
mers with and without cytosine base. J. Am. Chem. Soc. 116,
3607–3608.
4992 M. D. Keppler et al. (Eur. J. Biochem. 270) Ó FEBS 2003