2,6-Dimercuriphenol as a Bifacial Dinuclear Organometallic Nucleobase

Article abstract of DOI:10.1002/anie.201809398

A C-nucleoside having 2,6-dimercuriphenol as the base moiety has been synthesized and incorporated into an oligonucleotide. NMR and UV melting experiments revealed the ability of this bifacial organometallic nucleobase surrogate to form stable dinuclear H

Full text of DOI:10.1002/anie.201809398

A Journal of the Gesellschaft Deutscher Chemiker
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Accepted Article
Title: 2,6-Dimercuriphenol as a Bifacial Dinuclear Organometallic
Nucleobase
Authors: Dattatraya Uttam Ukale and Tuomas Lönnberg
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10.1002/anie.201809398
Angewandte Chemie International Edition
2,6-Dimercuriphenol as a Bifacial Dinuclear Organometallic Nucleobase
Dattatraya Uttam Ukale and Tuomas Lönnberg
Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland
Email: tuanlo@utu.fi
A C-nucleoside having 2,6-dimercuriphenol as the base moiety has been synthesized and incorporated
into an oligonucleotide. NMR and UV melting experiments revealed the ability of this bifacial
organometallic nucleobase surrogate to form stable dinuclear Hg(II)-mediated base triples with
adenine, cytosine and thymine (or uracil) in solution as well as within a triple-helical oligonucleotide.
A single Hg(II)-mediated base triple between 2,6-dimercuriphenol and two thymines increased both
Hoogsteen and Watson-Crick melting temperatures of a 15-mer pyrimidine•purine*pyrimidine triple
helix by more than 10 °C relative to an unmodified triple helix of the same length. This novel binding
mode could be exploited in targeting certain pathogenic nucleic acids as well as in DNA
nanotechnology.
Keywords: base triple; hybridization; oligonucleotide; mercury; organometallic
Metal-mediated base pairing can substantially promote hybridization of oligonucleotides.[1]
Harnessing the high stability of metal-mediated base pairs under the metal-deficient conditions of the
intracellular medium can, in principle, be achieved with either coordination complexes of kinetically
inert metal ions, such as Pt(II)[2] or Ru(II)[3] or organometallic complexes of more labile metal ions, such
as Hg(II) or Pd(II). We have recently become interested in the latter approach and reported on metal-
mediated base pairing by covalently mercurated[4, 5] and palladated[6] nucleobase surrogates. As could
be expected, dinuclear metal-mediated base pairs can increase the stability of a double helix even
more than their mononuclear counterparts.[7] In these structures the two bridging metal ions are both
coordinated on the “Watson-Crick” face of an appropriately modified nucleobase and converge on a
single nucleobase on the complementary strand. On the other hand, bridging metal ions on both the
“Watson-Crick” and the “Hoogsteen” face of a nucleobase should allow formation of a dinuclear
metal-mediated base triple and thus promote both Watson-Crick and Hoogsteen hybridization within
a triple helix. The viral transcript polyadenylated nuclear (PAN) RNA[8] offers an example of a naturally
occurring pathogenic nucleic acid that could be targeted utilizing such a binding mode. In the present
article we describe the synthesis and base pairing properties of a 2,6-dimercuriphenol C-nucleoside,
as well as a correspondingly modified oligonucleotide. To the best of our knowledge, this is the first
example of a dinuclear covalently metalated nucleobase surrogate to be incorporated into an
oligonucleotide.
Synthesis of the phenol C-nucleoside 1 and the respective phosphoramidite building block 2
is described in Scheme 1. First, compound 3 was prepared Heck coupling between {(2R,3S)-3-[(tert-
butyldimethylsilyl)oxy]-2,3-dihydrofuran-2-yl}methanol and 4-iodophenyl benzoate. Desilylation of 3
gave the ketone intermediate 4 and subsequent reduction the benzoyl-protected C-nucleoside 5.
Finally, compound 5 was either debenzoylated to give the unprotected C-nucleoside 1 or 5´-tritylated
and 3´-phosphitylated to give the phosphoramidite 2. Compound 5 has been prepared previously by
organolithium chemistry[9] but the method presented herein is significantly more b-stereoselective.
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OBz
OBz
HO
O
HO
HO
a
b
O
O
OTBDMS
OTBDMS
O
3
4
OBz
OBz
OBz
HO
DMTrO
DMTrO
c
d
e
O
O
O
OH
OH
O
P
CN
5
6
N
O
f
2
OH
OH
AcOHgII
HO
HgIIOAc
HO
g
O
O
OH
OH
1-Hg2
1
Scheme 1. Synthesis of the phenol C-nucleoside 1, its dimercurated derivative 1-Hg2 and
phosphoramidite building block 2. Reagents and conditions: a) Pd(OAc)2, P(C6F5)3, 4-iodophenyl
benzoate, Ag2CO3, CHCl3, Ar atmosphere, 70 °C, 12 h; b) Et3N•3HF, THF, Ar atmosphere, 25 °C, 15 min;
c) NaBH(OAc)3, AcOH, MeCN, Ar atmosphere, 0 °C, 15 min; d) DMTrCl, pyridine, 25 °C, 16 h; e) 2-
cyanoethyl-N,N-diisopropylchlorophosphoramidite, Et3N, CH2Cl2, N2 atmosphere, 25 °C, 3 h; f) NH3,
MeOH, H2O, 25 °C, 16 h; g) Hg(OAc)2, MeOH, 25 °C, 16 h.
Dimercuration of the phenol C-nucleoside 1 was carried out by overnight treatment with
Hg(OAc)2 in MeOH at 25 °C (Scheme 1). 1H NMR spectrum of the product showed loss of H2 and H6,
consistent with exchange of these protons for Hg. Formation of the desired dimercurated product 1-
Hg2 was further verified by 199Hg NMR and HRMS. For reference, 2´-deoxyadenosine was subjected to
the same conditions and found to be unreactive.
Sequences of the oligonucleotides used in the present study are summarized in Table 1.
Homoadenine and homothymine sequences were chosen to allow pyrimidine•purine*pyrimidine
triple helix formation under physiological conditions. The modified oligonucleotide ON1f, bearing a
single phenol residue in the middle of the chain, was assembled on an automated DNA synthesizer by
the conventional phosphoramidite strategy, employing an extended time for coupling of building
block 2. Dimercuration of ON1f was accomplished by overnight treatment with Hg(OAc)2 in aqueous
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10.1002/anie.201809398
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NaOAc at 70 °C (Scheme 2). The product ON1f-Hg2 was purified by sequential IE- and RP-HPLC. Both
ON1f and ON1f-Hg2 were characterized mass spectrometrically and quantified UV
spectrophotometrically. Finally, the site of mercuration in ON1f-Hg2 was verified by mass
spectrometric analysis of the product mixture after digestion by P1 nuclease.
Table 1. Oligonucleotides used in the present study.
Oligonucleotide
ON1f
ON1f-Hg2
ON1a
ON2a
ON2c
Sequence[a]
5´-AAA AAA AFA AAA AAA -3´
5´-AAA AAA AFHg2A AAA AAA -3´
5´-AAA AAA AAA AAA AAA -3´
5´-TTT TTT TAT TTT TTT-3´
5´-TTT TTT TCT TTT TTT-3´
5´-TTT TTT TGT TTT TTT-3´
5´-TTT TTT TTT TTT TTT-3´
5´-TTT TTT TST TTT TTT-3´
ON2g
ON2t
ON2s
[a]
F S to an abasic site (2-
refers to phenol, FHg2 to 2,6-dimercuriphenol and
(hydroxymethyl)tetrahydrofuran-3-ol spacer). In each sequence, the residue varied in the
hybridization studies has been underlined.
OH
OH
AcOHgII
A7O
HgIIOAc
A7O
a
O
O
OA7
OA7
ON1f-Hg2
ON1f
Scheme 2. Dimercuration of oligonucleotide ON1f. Reagents and conditions: Hg(OAc)2, NaOAc, H2O,
70 °C, 16 h.
Binding affinity of the 2,6-bis(acetoxymercuri)phenol C-nucleoside 1-Hg2 for the canonical
ribonucleoside-5´-monophosphates was quantified NMR spectrometrically at 25 °C and pH 7.2. 5´-
monophosphates were used instead of their constituent nucleosides to overcome the low solubility
of 1-Hg2 in water. For the same reason, a mixture of D2O and DMSO (1:1, v/v) was used as the solvent.
Samples containing a 4 mM concentration of 1-Hg2 and an 8 mM concentration of either 5´-AMP, 5´-
CMP, 5´-GMP or 5´-UMP were prepared and gradually diluted, maintaining a constant pH and ionic
strength. A control experiment in the absence of any nucleoside monophosphate was also carried out.
At each concentration, the chemical shift of the H3 and H5 protons of 1-Hg2 was recorded (Figure 1).
Owing to the kinetic lability of Hg(II) complexes, this signal represents the average of all species in
equilibrium with each other.
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10.1002/anie.201809398
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7.26
7.24
7.22
7.20
7.18
d
7.16
7.14
7.12
0.000
0.001
0.002
0.003
0.004
c / mol L-1
Figure 1. Chemical shift of the H3 and H5 protons of 1-Hg2 as a function of concentration in a 1:2
mixture with 5´-AMP (˜), 5´-CMP (£), 5´-GMP (¢) and 5´-UMP (™), as well as in the absence of any
nucleoside monophosphate (Ï); T = 25 °C; pH = 7.2 (120 mM phosphate buffer in a mixture of D2O
and DMSO (1:1, v/v)).
A very small linear downfield shift of the H3 and H5 signal was observed on increasing
concentration of 1-Hg2 in the absence of any nucleoside monophosphate, indicating negligible
intermolecular interactions. Somewhat unexpectedly, a similar plot was obtained in the presence of
5´-GMP, known to be a good ligand for Hg(II).[10] It should be noted, however, that the main signal of
H3 and H5 was accompanied with a number of minor signals of similar chemical shifts so formation of
an intractable higher-order structure cannot be ruled out. Guanine can simultaneously coordinate
Hg(II) on both N1 and N7 and is unique among the canonical nucleobases in its ability to self-assemble
into complex structures.[11] The other nucleoside monophosphates induced more marked shifts, either
downfield (5´-UMP) or upfield (5´-AMP and 5´-CMP), with saturation at high concentration. Assuming
formation a ternary 1:2 complexes between 1-Hg2 and the nucleoside monophosphates, with equal
equilibrium constants for the two coordination steps (justification for this simplification comes from
the fact that the plots exhibit no biphasicity), the observed chemical shifts, dobs, may be expressed by
Equation (1):[12]
ꢎ
ꢎ
ꢍ
ꢆꢇ ꢉꢊꢋꢌ
ꢇ
ꢉꢏꢇ ꢋꢐ
ꢈ
ꢈ
ꢈ
ꢎ
ꢀꢁꢂꢃ = ꢀꢄ + (ꢀꢅ − ꢀꢄ)
(1)
ꢏꢋ
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10.1002/anie.201809398
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where d0 and d¥ are the H3 and H5 chemical shifts at zero and infinite concentration, respectively, Kd
is the common dissociation constant for binary and ternary complexes between 1-Hg2 and the
nucleoside monophosphate and c is the concentration of 1-Hg2. The Kd values obtained with 5´-AMP,
5´-CMP and 5´-UMP by nonlinear least-squares fitting of the experimental data to Equation (1) were
700 ± 200, 600 ± 300 and 15 ± 4 mM, respectively. In other words, complexation with 5´-UMP is
strongly favored, consistent with the ability of uracil to serve as an anionic ligand under the
experimental conditions.[10, 13] Similarly, Hg(II)-mediated base pairs are preferentially formed between
two thymine or uracil bases, with concomitant N3 deprotonation of both partners.[14]
The ability of the 2,6-dimercuriphenol-modified oligonucleotide ON1f-Hg2 to form triple
helices with unmodified oligonucleotides was studied by UV melting temperature measurements at
pH 7.4 (20 mM cacodylate buffer) and ionic strength of 0.10 M (adjusted with sodium perchlorate).
For reference, similar experiments were also performed with the unmercurated counterpart ON1f, as
well as the natural oligonucleotide ON1a, bearing an adenine residue in place of the phenol residue.
In each experiment, the homoadenine strand (ON1a, ON1f or ON1f-Hg2, 1.0 mM) was hybridized with
two equivalents of the homothymine strand (ON2a, ON2c, ON2g, ON2t or ON2s, 2.0 mM) and only the
central base triple was varied.
Melting profiles for ON2t•ON1a*ON2t, ON2t•ON1f*ON2t and ON2t•ON1f-Hg2*ON2t are
presented in Figure 2A (respective plots for other combinations can be found in the Supporting
Information). With ON1a and ON1f, monophasic sigmoidal curves were obtained, with melting
temperatures of 34.8 ± 0.8 and 21.5 ± 0.9 °C, respectively (Figure 3A, all Tm values are tabulated in the
Supporting Information). The melting profile of ON2t•ON1f-Hg2*ON2t, in turn, was biphasic, with
melting temperatures of 19.8 ± 0.9 and 45.7 ± 0.7 °C. Evidently a triple helix is formed only with ON1f-
Hg2 under the experimental conditions, suggesting more than a 10 °C increase in the Hoogsteen Tm
compared to ON1a (stable triplexes with the latter were, however, obtained at 10 mM Mg(II), melting
profiles presented in the Supporting Information). Increase of the Watson-Crick Tm was also
considerable, 11 °C compared to ON1a and 24 °C compared to ON1f. Even greater stabilizations were
observed with ON2a or ON2c as the complementary strand although the absolute Watson-Crick Tm
values still remained 7 – 9 °C degrees lower than with ON2t. In contrast, with ON2s, placing an abasic
site opposite to the variable residue, ON1a formed a more stable duplex than either ON1f or ON1f-
Hg2. Finally, no sigmoidal melting curve could be obtained with ON2g•ON1f-Hg2*ON2g. The results
are, hence, in good agreement with those of the NMR studies and consistent with formation of Hg(II)-
mediated base triplets between 2,6-dimercuriphenol and adenine, cytosine and, especially, thymine
(Figure 4). It also seems likely that the anomalous results with guanine in both the NMR and UV melting
studies share a common origin.
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A
1.05
1.00
0.95
0.90
0.85
0.80
0.75
0.70
0
20
40
60
80
100
T / oC
B
1.05
1.00
0.95
0.90
0.85
0.80
0.75
0.70
0
20
40
60
80
100
T / oC
Figure 2. UV melting profiles of ON2t•ON1a*ON2t (™), ON2t•ON1f*ON2t (£) and ON2t•ON1f-
Hg2*ON2t (¢) in the A) absence and B) presence of 2-mercaptoethanol; pH = 7.4 (20 mM cacodylate
buffer); [ON1a] = [ON1f] = [ON1f-Hg2] = 1.0 mM; [ON2t] = 2.0 mM; [2-mercaptoethanol] = 0 / 100 mM;
I(NaClO4) = 0.10 M.
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A
50
40
30
20
10
ON1a
ON1f
ON1f-Hg2
B
50
40
30
20
10
ON1a
ON1f
ON1f-Hg2
Figure 3. Watson-Crick melting temperatures of triplexes formed by ON1a, ON1f and ON1f-Hg2 with
ON2a (medium hash), ON2c (sparse hash), ON2g (black), ON2t (dense hash) and ON2s (white) in the
A) absence and B) presence of 2-mercaptoethanol; pH = 7.4 (20 mM cacodylate buffer); [ON1a] =
[ON1f] = [ON1f-Hg2] = 1.0 mM; [ON2t] = 2.0 mM; [2-mercaptoethanol] = 0 / 100 mM; I(NaClO4) = 0.10
M.
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Figure 4. Proposed structures of base triples formed between 2,6-dimercuriphenol and A) adenine, B)
cytosine and C) thymine. Relative polarities of the three strands are indicated by (+) and (-) signs. The
possibility of hydrogen bonding between the phenolic hydroxy function and exocyclic amino and oxo
functions of the canonical nucleobases cannot be verified or excluded based on the data at hand. In
fact, dimercuration may substantially acidify the phenolic OH function so even its protonation state
cannot be firmly established. In the case of cytosine and adenine, coordination to the exocyclic amino
group is also a viable alternative.[15]
The UV melting experiments described above were repeated in the presence of 100 mM 2-
mercaptoethanol, a strong competing ligand for Hg(II),[16] to verify that the enhanced hybridization of
ON1f-Hg2 is indeed attributable to Hg(II)-mediated base pairing. As expected, melting temperatures
of the unmercurated triplexes were largely unaffected (Figure 2B and 3B). In contrast, melting
temperatures of the triplexes formed by ON1f-Hg2 dropped to the levels observed with the
unmercurated counterpart ON1f. Mass spectrometric analysis of the samples after several heating
and cooling cycles in the presence of 2-mercaptoethanol revealed considerable demercuration of
ON1f-Hg2 to ON1f (a representative mass spectrum is presented in the Supporting Information).
While Hoogsteen and Watson-Crick melting partially overlap in the UV melting profiles of the
dimercurated triplexes, precluding detailed thermodynamic analysis, it is evident that the thermal
denaturation is much more gradual than with the unmercurated triplexes. This observation is in line
with previous reports on similar systems[4, 17] and can be taken as a final piece of evidence for Hg(II)-
mediated base pairing. The gradual thermal denaturation translates to a relatively low entropic
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10.1002/anie.201809398
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penalty of hybridization which, in turn, has been attributed to the dehydration of Hg(II) on formation
of a Hg(II)-mediated base pair.[18]
Folding of the dimercurated triplexes to the expected pyrimidine•purine*pyrimidine
secondary structure was verified by CD spectropolarimetric analysis. The measurements were carried
out at 5 °C intervals over a temperature range of 10 – 90 °C under otherwise the same conditions as
those used for the UV melting experiments. At 10 °C, the spectra of ON2a•ON1f-Hg2*ON2a,
ON2c•ON1f-Hg2*ON2c
and
ON2t•ON1f-Hg2*ON2t
were
characteristic
of
pyrimidine•purine*pyrimidine triple helices,[19] with minima at 248 nm and maxima at 260 and 284
nm (spectra presented in the Supporting Information). As could be expected, folding into a triplex was
most evident with ON2t•ON1f-Hg2*ON2t. The spectra of ON2g•ON1f-Hg2*ON2g and ON2s•ON1f-
Hg2*ON2s, in turn, resembled that of a B-type double helix. In all cases, diminution of the minima and
maxima on increasing temperature was observed, consistent with thermal denaturation.
In summary, formation of stable dinuclear Hg(II)-mediated base triples between 2,6-
dimercuriphenol and adenine, cytosine and thymine (or uracil) has been demonstrated in solution as
well as within a triple-helical oligonucleotide. In the latter case, increases of more than 10 °C in both
Hoogsteen and Watson-Crick melting temperatures and a good selectivity for thymine were observed.
This novel binding mode could be used for targeting certain pathogenic nucleic acids, such as the viral
PAN RNA, as well for construction of new types of metalated DNA nanostructures.
Acknowledgements: We thank the Academy of Finland (decision #286478) and the Finnish National
Agency for Education (decision #TM-17-10348) for financial support of this work.
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