Synchronized Chiral Induction between [5]Helicene–Spermine Ligand and B–Z DNA Transition

Article abstract of DOI:10.1002/chem.201605276

The 2,13-dimethoxy[5]helicene–spermine ligand 8 b possesses an axial chirality. The racemic 8 b was bound to B-DNA by the accompanying induction of its (P)-chirality together with the B-to-Z helicity change of the duplex DNA, [(dC-dG)₃]₂

Full text of DOI:10.1002/chem.201605276

A Journal of
Accepted Article
Title: Synchronized Chiral Induction Between [5]Helicene-Spermine
Ligand and B-Z DNA Transition
Authors: Kensuke Kawara, Genichiro Tsuji, Yosuke Taniguchi, and
Shigeki Sasaki
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To be cited as: Chem. Eur. J. 10.1002/chem.201605276
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Synchronized Chiral Induction Between [5]Helicene-Spermine
Ligand and B-Z DNA Transition
Kensuke Kawara, Genichiro Tsuji, Yosuke Taniguchi and Shigeki Sasaki*[a]
Dedication ((optional))
Abstract: The 2,13-dimethoxy[5]helicene-spermine ligand 8b
possesses an axial chirality. The racemic 8b was bound to B-DNA
by the accompanying induction of its (P)-chirality together with the B-
to-Z helicity change of the duplex DNA, [(dC-dG)3]2. The (P)-chirality
of the bound 8b, in turn, transitioned to the (M)-chirality according to
the Z-helicity of the DNA. These results have illustrated the chirality
synchronization between the DNA and the ligand.
reported for the B-Z transition [23-30] the chiral recognition[31-35]
and the DNA template-based asymmetric induction.[36-39]
We previously reported that the bisaryl-spermine ligand 1
induced the B-Z transition for the [(dC-dG)3]2.[40] It was found that
the bisaryl part of 1 was transformed into the [5]helicene 2 via
the photo-oxidative ring closing reaction. Interestingly, the (P)-
1,14-dimethyl[5]helicene ligand (P)-3 preferentially binds to B-
DNA, whereas its enantiomer (M)-3 shows a higher affinity to Z-
DNA.[41] Accordingly, we hypothesized that the chirality of the
[5]helicene ligand is induced in a “synchronized” manner with the
B- and Z-DNA helicity. A synchronized chiral induction was
expected to occur in the following order: (i) the racemic
[5]helicene ligand binds to the right-handed B-DNA with
induction of the right-handed (P)-chirality, (ii) the B-Z transition is
induced by further binding of the ligand, and (iii) the chirality of
the bound ligand is then changed to the (M)-chirality in accord
with the B-Z transition (Figure. 2). This synchronized chiral
induction system would provide a unique feature in that both the
[5]helicene substrate and the DNA template are optically flexible
molecules. Allostery is the key process in biological regulation,
in which the binding components, such as proteins and nucleic
Typical chiral induction systems consist of the combination of a
chiral template and an optically flexible molecule. Formation of a
chiral molecule can be amplified either by a chiral metal complex
or by an organocatalyst.[1,2] Very interesting induction systems
have been demonstrated for the helicity of polymers; the helicity
of a polymer composed of a chiral unit is switched by light,[3,4]
solvent change[5] or pressure changes.[6] The chirality of a non-
helical polymer is induced by binding with chiral small
molecules[ 7 ] or on amorphous silica.[ 8 ] Moreover, the chiral-
polymer syntheses have been developed by single-handed
circularly polarized light.[9] Importantly, the helical polymer may
behave as an opposite chiral template depending on the
external signal.[10-12] In this context, we became interested in the
duplex DNA as a chiral helical polymer.
42
]
acids, exchange the binding effect with each other.[
Accordingly, our artificial system would provide a good model for
an allosteric system, allowing natural DNA to gain a foothold in
asymmetric induction as a ligand-switchable helical polymer.
Figure 1. Structures of bis-aryl spermine ligand 1, [5]helicene ligand 2 and
(P)-1,14-dimethyl[5]helicene ligand (P)-3.
The duplex DNA generally adopts right-handed helices under
physiological conditions and may change to left-handed helices
depending on the sequence and medium conditions (B-Z
transition).[13,14] The B-Z transition is supposed to play a role in
the gene expression pathway,[15] and is applied to a molecular
switch of a nanodevice.[ 16 - 22 ] A variety of ligand has been
Figure 2. The concept of synchronized chiral induction.
Chiral induction of both the DNA and the [5]helicene ligand is
observed by CD measurements. As the CD bands of DNA
change in the range of 250-300 nm according to the B-Z
transition, the [5]helicene unit was designed to have CD bands
at a wavelength longer than 300 nm to avoid overlapping.
Among the several synthesized compounds, we adopted the
2,13-dimethoxy-[5]helicene-spermine ligand 8 to check our
proposal.
[a] Kensuke Kawara, Genichiro Tsuji, Yosuke Taniguchi, Shigeki Sasaki
Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1
Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
E-mail: sasaki@phar.kyushu-u.ac.jp
Supporting information for this article is given via a link at the end of the
document.((Please delete this text if not appropriate))
The ligands 8 were synthesized according to a previously
described method (Scheme 1). The dibromomaleimide
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derivatives 4 were coupled with 7-methoxy-2-borate derivatives
5 by the Suzuki-Miyaura cross-coupling reaction to produce the
bisaryl derivatives 6. The [5]helicene compounds 7 were
obtained by photocyclization under visible light and oxidation in
the presence of iodine. When this photocylization was performed
in THF, acetone, or toluene,[43,44] the benzo[a]tetraphene isomer
was formed as the major isomer. In contrast, the reaction in
changing points at 327 nm and 306 nm (Figure. 3). The
difference in the CD spectra between 8a and 8b may arise from
the difference in their UV spectra, in which 8b shows a UV
absorbance at a wavelength longer than 8a (Figure. S4).
Figure 4. CD spectral changes induced by the titration of 8b into a solution of
20 µM [(dC-dG)3]2 in the buffer containing 5 mM sodium cacodylate, 100 mM
NaCl at pH 7.0 and 25°C. The arrows represent the direction of the changes
by the addition of the ligand 8b. The inset shows the expanded CD spectra
methanol produced the [5]helicene derivatives
7 as the
predominant isomer in 96% isolated yield. The crystal structure
of the 2,13-dimethoxy[5]helicene derivatives 7b were analyzed
by X-ray analysis to show that the methyl groups are in close
contact with each other. The [5]helicene derivatives 7 were
transformed into the spermine conjugates 8 by a sequence of
reactions including hydrolysis of the maleimide, formation of the
anhydride, conjugation of the tri-N-Boc spermine, and finally,
deprotection of the Boc groups.
after smoothing the raw data.
To evaluate the B-Z transition by the ligand, The CD spectrum
was measured using 20 M [(dC-dG)3]2 as the B-DNA in 5 mM
sodium cacodylate buffer containing 100 mM NaCl at 25 °C and
pH 7.0. (Figure. 4. Arrows represent the direction of the
changes). The CD of [(dC-dG)3]2 alone indicated a positive band
at 278 nm and a negative band at 250 nm, representing a typical
right-handed B-DNA. By the addition of rac.8b, the negative
bands at 250 nm decreased and the positive bands at 278 nm
shifted to a shorter wavelength, and the negative bands at 295
nm appeared. The negative bands at 295 nm are suggestive of
the B-Z transition, because 8b has a small induced CD band
around 300 nm. In contrast, 8a did not induce the B-Z transition,
meaning that the methyl groups of 8b are important for induction
of the Z-DNA due to the hydrophobicity. The inset in Figure. 4
shows the selected CD spectra in the range of 270-370 nm
observed by the addition of 2, 6 and 10 equivalences of 8b.
Noteworthy, the positive bands around 340 nm appeared by the
low equivalences of 8b in the complexes with B-DNA, and the
further addition of 8b induced the negative bands around 340
nm. These induced CD bands suggest a chirality change from
(P)- to (M)-8b. These spectra are slightly different from the CD
spectra shown in Figure. 3B.
Scheme 1. Synthesis of the 2,13-disubstituted[5]helicene
8 and X ray
structure of the [5]helicene skeleton 7b. a) [1,1-Bis(diphenylphosphino)-
ferrocene]dichloropalladium (II), K3PO4, 1,4-Dioxane-H2O, 90 °C, 12 h. b) I2,
THF, MeOH-toluene, r.t., 40 min irradiation. C) (1) 5 M aqueous KOH, 55 °C,
18 h, then 6 M aqueous HCl aq. rt, 1.5 h, 2) TriBoc-spermine, DMF, toluene, at
110°C, 15h. 3) TFA, CH2Cl2, rt. 30 min.
Figure 3. A) CD spectra of (P)- and (M)-8a. B) CD spectra of (P)- and (M)-8b.
Enantiomers were separated by HPLC equipped with a chiral column, and the
separated peaks were transferred to a CD detector.
The enantiomers of the [5]helicene-spermine ligands 8a and 8b
were separated using an HPLC system equipped with a chiral
column and CD detector. The CD spectrum of (P)-8a shows
positive bands at around 325 nm and negative bands at around
280 nm with 296 nm as the changing point. In contrast, the CD
of (P)-8b represents two positive bands at around 340 nm and
280 nm and negative bands at around 320 nm, with two
The UV absorbance of 8b at 320 nm decreased to 16% with the
accompanying red-shifts by the DNA binding (Figure S6, A),
which are suggestive of the stacking interactions between the
[5]helicene part of the ligand and the base pair at the terminal of
the B-DNA or Z-DNA duplex. This hypochromism might affect
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the induced CD spectra in this region. To clarify the relationship
between the binding stoichiometry and the chiral induction, the
CD changes at 295 nm and 340 nm are plotted versus the
added equivalence of the ligand to DNA. The former changes
indicate the B-Z transition (Figure. 5A) and the latter changes
imply that the positive values are due to the (P)-chirality and the
negative ones are the (M)-chirality of the ligand (Figure. 5B).
Figure. 5A indicates that the B-Z transition is complete by the
addition of 4 equivalences of 8b. Figure. 5B shows a remarkable
contrast; the positive bands initially increased, then the negative
bands increased in intensity by the addition of more than 3
equivalences of 8b. In the UV-titration experiments when B-DNA
was added to a solution of 8b, the UV absorbance of 8b
decreased until the 8b:B-DNA=1:1 (Figure. S6, B). Accordingly,
these results have clearly indicated that the (P)-chirality of 8b is
initially induced by binding with B-DNA, and that further binding
of 8b induced the B-Z transition, then the (M)-chirality of 8b is
induced by the influence of the Z-DNA. The further bound ligand
may bind around the DNA and contribute to dehydration of the
DNA.
solution containing [(dC-dG)3]2. The observed heat areas were
well fitted with the simulated curve method using three
independent fitting curves, which include one endothermic and
two exothermic processes (Figure. 6A). These processes were
interpreted and compared to the CD titration data in Figure. 5.
Curve 1 may represent the first binding step with an approximate
ligand:DNA=1:1 ratio. Curve 2 continued until the addition of 2
equivalences of 8b, which is different from the CD change at
295 nm due to the B-Z transition (Figure. 5A). In our previous
study, an endothermic process associated with the ligand
binding to B-DNA was assigned to an intermediate-DNA
conformation prior to the transit to the Z-DNA. In a similar sense,
curve 2 may imply the formation of the intermediate-DNA
associated with the 8b binding. The change in curve 3 was
completed before the addition of 2 equivalences of 8b. In the
meantime, the (P)-chirality induction of 8b reached a maximum
at around 2 equivalences (Figure. 5B). Curve 3 arose after the
end of curve 1, indicating that the second binding of 8b takes
place with the intermediate-DNA. As the CD change at 295 nm
reached a plateau by the addition of more than 4 equivalences
of the 8b (Figure. 5A), excess binding of 8b is needed for the full
transition to the Z-DNA from an intermediate-DNA. Interestingly,
the (M)-chirality induction took place by excess ligand binding
after a full transition to the Z-DNA. Based on the CD and ITC
experiments, binding phenomena are interpreted as follows.
Curve 1 indicates a process of 1:1 ligand:DNA binding, probably
at the end of the duplex. The initial 1:1 binding induces the
conformational change of B-DNA to an intermediate-DNA, which
is reflected in curve 2. The second binding of 8b occurs with the
intermediate-DNA, which is shown by curve 3. During the
binding to the B-DNA duplex, the (P)-chirality of 8b is induced.
No thermodynamic behavior was observed for more than 2
equivalences of 8b by the ITC experiments, although the full B-Z
transition of the DNA was achieved at about 4 equivalences of
8b (Figure. 5A). As the ITC method is applicable for the rapid
reaction, the transition from the intermediate-DNA to the Z-DNA
is too slow to be detected by ITC analysis. After the B-DNA was
fully transformed into the Z-DNA, the induction of the (M)-
chirality of 8b increased depending on the amount of 8b (Figure.
5B). Similar to preferences of (P)-3 for the B-DNA and that of
(M)-3 for the Z-DNA, it is conceivable that (P)-8b preferentially
binds the B-DNA and (M)-8b binds the Z-DNA.
Figure 5. Plot of CD band intensity versus ligand 8b equivalence to DNA [(dC-
dG)3]2. (A) Plot of CD values at 295 nm, an indication of Z-DNA. (B) Plot of CD
values at 295 nm, indicating (P)- to (M)-chirality shift.
Attempts for isolation of 8b from the DNA complex to directly
determine the (P)- or (M)-chirality were unsuccessful. It is of
particular interest that (P)- and (M)-8b, which were isolated by a
chiral column, and racemized at different rates depending on the
concentrations and the B- or Z-chirality of the bound DNA. (P)-
8b more rapidly racemized in the presence of the B-DNA than
the absence or in the presence of the Z-DNA (Figure. 7A, red
marks). On the other hand, the racemization rates of (M)-8b in
the presence of either the B-DNA or Z-DNA were almost the
same, although they were faster than that in the absence of
DNA (Figure. 7A, blue marks). Figure. 7B shows that the CD
intensity of (P)- and (M)-8b did not significantly change at their
high concentrations.
Figure 6. (A) The integrated data and the fitting curves. (B) The
thermodynamic data of the fitting curves. A solution of 8b was added to a
solution of 17.8 M [(dC-dG)3]2 in the buffer containing 5 mM Na cacodylate
and 100 mM NaCl at pH 7.0 and 20 °C. The concentration of 8b was
increased by 3.56 M (0.2 equivalences to DNA) after each addition.
To obtain further insight into the relationship between the ligand
binding, chirality change and the B-Z transition, the
thermodynamic parameters were obtained by isothermal
calorimetric titration (ITC). The solution of 8b was added to a
Figure 7. Racemization rates of (P)- and (M)-8b in the presence or the
absence of 10 M of DNA. (A) 5 M 8b, (B) 40 M 8b in the buffer containing
1 mM Na cacodylate and 100 mM NaCl at pH 7.0 and 25°C.
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2-(7-Methoxynaphthalen-2-yl)-4,4,5,5-tetramethyl-1,3,2-dioxaborolane
(5b)
CH3I (2.1 mL, 33.7 mmol) was added to a solution of 7-bromo-2-naphthol
(1 g, 4.48 mmol) and K2CO3 (2.22 g, 13.4 mmol) in DMF (300 mL), then
the mixture was stirred at room temperature for 3 h. The reaction was
quenched with saturated aqueous NH4Cl and extracted with AcOEt. The
organic layers were washed with brine and dried over Na2SO4, then
evaporated. The residue was chromatographed (silica gel, n-hexane
only) to give 2-bromo-7-methoxy naphthalene (1.01 g, 95 %) as a white
powder. 1H-NMR (400 MHz, CDCl3) ppm, 7.88 (1H, d, J=1.5 Hz), 7.67
(1H, d, J=9.2 Hz), 7.60 (1H, d, J=8.9 Hz), 7.38 (1H, dd, J=1.8 Hz, 8.5 Hz),
7.13 (1H, dd, J=2.4 Hz, 8.9 Hz), 7.01 (1H, d, J=2.4 Hz), 3.90 (3H, s); IR
(cm-1) 1623; ESI-MS (m/z) 236.04 ([M+H]+). This compound (81.3 mg,
0.343 mmol), bis(pinacolato)diboron (130.8 mg, 0.515 mmol) and [1,1′-
bis(diphenylphosphino)ferrocene]dichloropalladium(II) (33.6 mg, 0.0412
mmol) and KOAc (117.8 mg, 1.20 mmol) were dissolved in degassed
1,4-dioxane (3.4 mL). The mixture was stirred at 90 °C for 15 h. The
reaction mixture was diluted with AcOEt and filtered using celite, then
saturated aqueous NH4Cl was added to the filtrate and extracted with
AcOEt. The organic layers were washed with water, brine, and dried over
Na2SO4, then evaporated. The residue was chromatographed (silica gel,
n-hexane:AcOEt = gradient 50:1 to 20:1) to give 5b (83.0 mg, 85 %) as a
pale brown powder. 1H-NMR (500 MHz, CDCl3)  ppm, 8.29 (1H, s),
7.77-7.71 (3H, m), 7.20-7.17 (2H, m), 3.91 (3H, s), 1.38 (12H, s); 13C-
NMR (500 MHz, CDCl3)  ppm, 157.60, 135.16, 134.03, 130.75, 129.31,
128.44, 126.88, 119.94, 106.52, 84.00, 55.38, 25.06; IR (cm-1) 2978,
1605, 1463; ESI-HRMS (m/z) Calcd. for 285.1660 ([M+H]+), Found
285.1640.
It was shown in our previous study that the (P)- or (M)-
[5]helicene ligand was preferentially bound to the B- or Z-DNA,
respectively. Figure. 7 suggests that 8b rapidly racemizes only
in the complex with the DNA and that the ligand with the
preferable chirality for the corresponding B- or Z-DNA would
become relatively dominant. Most probably, the orientation of
the methoxy groups, which should be a major racemization
barrier of 8b as shown in the X-ray structure (Scheme 1), may
be aligned in a different direction in the complex with the DNA,
resulting in a decreased racemization barrier. Accordingly, the
chirality induction observed in the CD changes shown in Figure.
4 can be interpreted as the result of the chiral induction of part of
the ligand bound to the DNA.
In conclusion, we have successfully demonstrated
a
synchronized chiral induction system using the 2,13-dimethoxy
[5]helicene-spermine ligand 8b and the template DNA duplex.
This synchronized chiral induction system provides a unique
feature in that the chirality of both the ligand and template is
mutually induced by their binding, and would draw attention to
the natural DNA as a ligand-switchable helical polymer.
Experimental Section
Bisnaphthol-benzylmaleimide intermediate (6a)
tert-Butyldimethyl((7-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-
yl)naphthalen-2-yl)oxy)silane (5a)
1-Benzyl-3,4-dibromopyrrole-2,5-dione 4 (8.6 mg, 0.0248 mmol), 5a
(20.0 g, 0.0520 mmol) and bis(triphenylphosphine)palladium(II)dichloride
(5.2 mg, 0.00744 mmol), benzyltriethylammonium chloride (2.8 mg,
0.0124 mmol) and Cs2CO3 (40.4 mg, 0.124 mmol) were dissolved in
degassed toluene (1.5 mL) and H2O (0.5 mL). The mixture was stirred at
tert-Butyldimethylsilyl chloride (2.19 g, 14.5 mmol), imidazole (1.97 g,
28.9 mmol), and N,N-dimethyl-4-aminopyridine (60.2 mg, 0.48 mmol)
were added to a solution of 7-bromo-2-naphthol (2.2 g, 9.86 mmol) in
DMF (40 mL), then the mixture was stirred at room temperature for 30
min. The reaction mixture was diluted and extracted with AcOEt. The
organic layers were washed with brine and dried over Na2SO4, then
evaporated. The residue was chromatographed (silica gel, n-
hexane:AcOEt = 20:1) to give the TBDMS-protected 7-bromo-2-naphthol
(3.32 g, 99 %) as a white powder. 1H-NMR (400 MHz, CDCl3)  ppm,
7.84 (1H, s), 7.67 (1H, d, J=8.6 Hz), 7.60 (1H, d, J=8.9 Hz), 7.39 (1H, d,
J=8.9 Hz), 7.08 (1H, s), 7.05 (1H, d, J=9.2 Hz), 1.01 (9H, s), 0.24 (6H, s);
IR (cm-1) 2955, 2929, 1625; ESI-MS (m/z) 338.36 ([M+H]+). This
compound (888.4 mg, 2.63 mmol), bis(pinacolato)diboron (1.00 g, 3.95
mmol) and [1,1′-bis (diphenylphosphino)ferrocene]dichloro-palladium(II)
(107.8 mg, 0.132 mmol) and KOAc (907.3 mg, 9.21 mmol) were
dissolved in degassed 1,4-dioxane (26.3 mL). The mixture was stirred at
80 °C for 12 h. The reaction mixture was diluted with AcOEt and filtered
using celite, then saturated aqueous NH4Cl was added to the filtrate and
extracted with AcOEt. The organic layers were washed with water, brine,
and dried over Na2SO4, then evaporated. The residue was
chromatographed (silica gel, n-hexane:AcOEt = gradient 100:1 to 50:1) to
give 5a (861.3 g, 85 %) as a white powder. 1H-NMR (400 MHz, CDCl3) 
ppm, 8.21 (1H, s), 7.66-7.41 (3H, m), 7.22 (1H, d, J=2.1 Hz), 7.09 (1H,
dd, J=2.4 Hz, 8.6 Hz), 1.37 (12H, s), 1.00 (9H, s), 0.22 (6H, s); 13C-NMR
(500 MHz, (CDCl3)  ppm, 153.50, 153.13, 134.06, 130.98, 129.23,
128.50, 126.84, 123.45, 115.56, 84.01, 25.87, 25.15, 25.05, -4.23; IR
(cm-1) 2977, 1602, 1510, 1460, 1380, 1126; ESI-HRMS (m/z) Calcd. for
385.2369 ([M+H]+), Found 385.2391.
°
85 C for 4 h. The reaction mixture was diluted with AcOEt and filtered
using celite, then saturated aqueous NH4Cl was added to the filtrate and
extracted with AcOEt. The combined organic layers were dried over
Na2SO4, evaporated. The residue was chromatographed (silica gel, n-
hexane:AcOEt = gradient 50:1 to 20:1) to give 6a (13.6 mg, 78%) as a
yellow amorphous form. 1H-NMR (500 MHz, CDCl3) ppm, 8.08 (2H, s),
7.65 (2H, d, J=8.9 Hz), 7.57 (2H, d, J=8.5 Hz), 7.48 (2H, d, J=8.5 Hz),
7.27-7.36 (5H, m), 7.18 (2H, s), 7.09 (2H, d, J=8.9 Hz), 4.85 (2H, s), 1.00
(18H, s), 0.22 (12H, s); 13C-NMR (500 MHz, (CD3)2CO)  ppm, 171.23,
154.98, 138.10, 137.22, 135.32, 130.39, 130.32, 130.26, 129.48, 128.90,
128.44, 128.42, 127.87, 125.53, 124.31, 116.47, 42.49, 26.07, 18.85, -
4.25; IR (cm-1) 1705; ESI-HRMS (m/z) Calcd. for 700.3278 ([M+H]+),
722.3098 ([M+Na]+), Found 700.3259, 722.3091.
2,13-Dihydroxy[5]helicene-bemzylmaleimide intermediate (7a)
Compound 6a (650 mg, 0.931 mmol) was added to MeOH (300 mL) and
any insoluble residue was filtered off. Iodine (87.7 mg, 0.380 mmol) and
THF (3 mL) were added to this saturated MeOH solution and mixture was
stirred under irradiation by a high-pressure mercury lamp (500 W) at
room temperature for 5 h. The reaction mixture was quenched with 20 %
aqueous Na2S2O3 and extracted with AcOEt. The organic layers were
washed with water, brine and dried over Na2SO4, then evaporated. This
procedure was repeated twice. The collected residue was
chromatographed (silica gel, n-hexane:AcOEt = gradient 15:1 to 9:1) to
give the TBDMS-protected [5]helicene intermediate (464 mg, 71 %) as a
yellow amorphous form. 1H-NMR (400 MHz, CDCl3)  ppm, 8.89 (2H, d,
J=8.9 Hz), 7.96 (2H, d, J=8.9 Hz), 7.81 (2H, d, J=8.9 Hz), 7.71 (2H, d,
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10.1002/chem.201605276
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COMMUNICATION
J=2.4 Hz), 7.48 (2H, d, J=7.0 Hz), 7.31-7.25 (3H, m), 7.09 (2H, dd, J=2.4,
6.4 Hz), 4.93 (2H, s). 0.83 (18H, s), -0.05, (6H, s), -0.09 (6H, s); IR (cm-1)
1704. This protected intermediate (309 mg, 0.440 mmol) was treated with
TBAF (1.5 mL, 1.32 mmol) in a THF (5 mL) solution at room temperature
for 1.5 h. Saturated aqueous NH4Cl was added to the reaction mixture
and extracted with AcOEt. The organic layers were washed with water
and brine, dried over Na2SO4, then evaporated. The residue was
chromatographed (silica gel, n-hexane:AcOEt = 2:1) to give the TBDMS-
deprotected 7a (199 mg, 97 %) as a yellow amorphous form. 1H-NMR
(400 MHz, (CD3)2CO)  ppm, 8.82 (2H, d, J=8.5 Hz), 8.05 (2H, d, J=8.9
Hz), 7.95 (2H, d, J=8.9 Hz), 7.80 (2H, d, J=2.4 Hz), 7.47 (2H, d, J=7.6
Hz), 7.33 (2H, d, J=7.3 Hz), 7.22-7.26 (3H, m), 4.92 (2H, s); 13C-NMR
(500 MHz, (CD3)2CO)  ppm, 169.98, 132.61, 131.44, 130.76, 130.50,
129.39, 128.66, 128.46, 128.46, 128.24, 127.57, 127.13, 120.09, 118.86,
117.58, 113.70, 41.87; IR (cm-1) 1735; ESI-MS (m/z) 468.30 ([M-H]-) ESI-
HRMS (m/z) Calcd. for 469.1236 ([M-H]-), Found 469.1243.
dried over Na2SO4, then evaporated. The residue was chromatographed
(silica gel, n-hexane:AcOEt = gradient 50:1 to 20:1) to give 6b (435 mg,
59 %) as a yellow amorphous form. 1H-NMR (400 MHz, CDCl3)  ppm,
8.10 (2H, s), 7.67 (2H, d, J=8.9 Hz), 7.60 (2H, d, J=8.5 Hz), 7.51-7.49
(2H, m), 7.35-7.27 (3H, m), 7.22 (2H, dd, J=1.5 Hz, 8.5 Hz), 7.17 (2H, dd,
J=2.4 Hz, 8.9 Hz), 7.11 (2H, d, J=2.4 Hz), 4.85 (2H, s), 3.88 (6H, s); 13C-
NMR (500 MHz, CDCl3)  ppm, 170.80, 158.18, 136.66, 136.10, 135.16,
134.42, 129.61, 129.35, 129.28, 129.01, 128.87, 127.90, 126.80, 124.44,
120.52, 106.80, 55.51, 25.06; IR (cm-1) 2921, 1702, 1217; ESI-HRMS
(m/z) Calcd. for 500.1856 ([M+H]+), Found 500.1894.
2,13-Dimethoxy[5]helicene-bemzylmaleimide intermediate (7b)
A solution of 6b (5.3 mg, 0.0106mmol), iodine (3.0 mg, 0.0117 mmol)
and THF (100 µL) in toluene (2.6 mL) and MeOH (2.6 mL) was stirred
under irradiation of by a high-pressure mercury lamp (500 W) at room
temperature for 40 min. The reaction mixture was quenched with 20 %
aqueous Na2S2O3 and extracted with AcOEt. The organic layers were
washed with water, brine and dried over Na2SO4, then evaporated. The
residue was chromatographed (silica gel, n-Hexane:AcOEt = 50:1) to
give 7b (5.1 mg, 96 %) as a yellow amorphous form. 1H-NMR (400 MHz,
CDCl3)  ppm, 8.97 (2H, d, J=8.9 Hz), 7.99 (2H, d, J=8.9 Hz), 7.87 (2H,
d, J=8.9 Hz), 7.66 (2H, s), 7.50 (2H, d, J=7.0 Hz), 7.32-7.20 (5H, m), 4.94
(2H, s), 3.48 (6H, s); 13C-NMR (500 MHz, CDCl3)  ppm, 169.58, 157.00,
136.90, 131.16, 130.90, 129.93, 129.58, 128.86, 128.68, 128.50, 127.90,
127.05, 126.58, 119.68, 119.57, 110.44, 68.13, 55.10; IR (cm-1) 2921,
1702, 1390, 1261; ESI-HRMS (m/z) Calcd. for 498.1700 ([M+H]+), Found
498.1708.
2,13-Dihydroxy[5]helicene-Spermine ligand (8a)
Five M aqueous KOH (8 mL) was added to a solution of 7a (193 mg,
0.411mmol) in ethanol (5 mL) and the mixture was stirred at 50 °C for 15
h, then the mixture was acidified to pH1 with 10 % aqueous HCl. After
1.5 h, the precipitates were collected and washed with water, then dried
under vacuum to give the corresponding anhydrous material as a dark
yellow amorphous form. This material was used for the next reaction
without further purification. A mixture of this anhydrous material (162 mg,
0.432 mmol) and tri-Boc spermine (256 mg, 0527 mmol) in toluene-DMF
was heated at 90 °C for 24 h. The reaction mixture was diluted and
extracted with AcOEt. The organic layers were washed with brine and
dried over Na2SO4, then evaporated. The residue was chromatographed
(silica gel, n-hexane:AcOEt = 2:1) to give the tri-Boc-spermine-2,13-
dihydrioxy[5]helicene conjugate (185 mg, 50 % in 2 steps) as an orange
amorphous form. 1H-NMR (400 MHz, (CD3)2CO)  ppm, 8.67 (2H, d,
J=8.9 Hz), 7.88 (2H, d, J=8.9 Hz), 7.82 (2H, d, J=8.6 Hz), 7.63 (2H, d,
J=2.1 Hz), 7.12 (2H, dd, J=8.5 Hz), 3.70 (2H, t, J=6.9 Hz), 3.24-3.14 (8H,
m), 2.98-2.95 (2H, m), 1.97 (2H, quint., J=7.0 Hz), 1.65-1.56 (2H, m),
1.48-1.42 (4H, m), 1.39 (9H, s), 1.36 (18H, s); IR (cm-1) 3314, 1757, 1697,
1618; ESI-MS (m/z) 866.59 ([M+H]+). This material (24.6 mg, 0.0280
mmol) was treated with 25 % TFA in CH2Cl2 (3 mL) at room temperature
for 15 min. TFA was removed by NH-silica and the target material was
eluted with a CHCl3 : MeOH= 5:1 solution. The obtained crude material
was purified by HPLC (Nacalai Tesque COSMOSIL 5C18-AR-II) (Figure
S3) to give the 2,13-hydroxy[5]helicene-spermine ligand 8a (7.53 mg as
tri-acetate, 36 %) as a yellow solid. 1H-NMR (500 MHz, CD3OD)  ppm,
9.39 (2H, d, J=8.5 Hz), 8.83 (2H, d, J=8.5 Hz), 8.43 (2H, d, J=8.9 Hz),
7.93 (2H, d, J=8.6 Hz), 3.97 (2H, t, J=6.7 Hz), 3.30-3.02 (10H, m), 2.69
(2H, s), 2.20 (2H, t, J=7.9 Hz), 2.06 (2H, t, J=7.9 Hz), 1.80 (4H, m); 13C-
NMR (500 MHz, (CD3)2SO)  ppm, 169.25, 155.59, 131.40, 129.85,
129.71, 126.65, 126.03, 125.69, 119.65, 117.09, 112.49, 48.39, 48.13,
46.23, 45.90, 37.84, 35.71, 27.60, 26.41, 26.10, 22.76; IR (cm-1) 1680;
ESI-HRMS (m/z) Calcd. for 563.3129 ([M+H]+), Found 563.3162. The
concentration of a stock solution of the ligand was determined by an
NMR integration value using maleic acid as the internal standard.
2,13-Dimethoxy[5]helicene-Spermine ligand (8b)
Five M aqueous KOH (124 mL) was added to a solution of 7b (125 mg,
0.252 mmol) in THF (125 mL) stirred at 60 °C for 17 h, then the mixture
was acidified to pH 1 with 6 M aqueous HCl. After 1.5 h, Et2O was added
to the reaction mixture and extracted with Et2O. The organic layers were
washed with water, brine and dried over Na2SO4, then evaporated to give
the corresponding anhydrous material as orange amorphous form. This
material was used for the next reaction without further purification. A
mixture of this anhydrous material and tri-Boc spermine (152 mg, 0.302
mmol) in toluene-DMF was heated at 110 °C for 13 h. The reaction
mixture was diluted with AcOEt and extracted with AcOEt. The organic
layers were washed with brine and dried over Na2SO4, then evaporated.
The residue was chromatographed (silica gel, n-hexane:AcOEt
=
gradient 10:1 to 3:1) to give the Tri-Boc-spermine-2,13-dimethoxy
[5]helicene conjugate (199 mg, 88% in 2 steps) as a yellow amorphous
form. 1H-NMR (400 MHz, CDCl3)  ppm, 8.97 (2H, d, J=8.9 Hz), 8.01
(2H, d, J=8.9 Hz), 7.88 (2H, d, J=8.5 Hz), 7.68 (2H, s), 7.22-7.20 (2H, m),
3.49 (6H, s), 3.78 (2H, t, J=7.0 Hz), 3.26-3.04 (10H, m), 2.61 (1H, s),
2.08-1.96 (2H, m), 1.24 (27H, s), 0.99-0.78 (6H, m); IR (cm-1) 2932, 1695,
1368, 1171; ESI-MS (m/z) 893.42 ([M+H]+). This material (25 mg, 0.0280
mmol) was treated with 25 % TFA in CH2Cl2 (4 mL) at room temperature
for 30 min. The crude material was purified by HPLC (Nacalai Tesque
COSMOSIL
5C18-AR-II)
(Figure
S3)
to
give
the
2,13-
dimethoxy[5]helicene-spermine ligand 8b (22.3 mg as tri-trifluoroacetate,
85 %) as a yellow solids. 1H-NMR (400 MHz, CD3OD)  ppm, 8.91 (2H, d,
J=8.9 Hz), 8.08 (2H, d, J=8.2 Hz), 7.99 (2H, d, J=8.9 Hz), 7.65 (2H, s),
7.29 (2H, d, J=9.5 Hz), 3.96-3.90 (2H, m), 3.50 (6H, s), 3.15-2.98 (10H,
m), 2.21-2.12 (2H, m), 2.11-2.02 (2H, m), 1.87-1.74 (4H, m); 13C-NMR
(500 MHz, (CD3)2SO)  ppm, 169.32, 158.16, 156.68, 130.45, 130.26,
129.83, 129.71, 127.87, 126.23, 119.27, 118.43, 110.11, 54.68, 46.14,
44.63, 43.90, 36.21, 34.87, 25.09, 23.79, 22.74, 22.67; IR (cm-1) 1679,
1207, 1136; ESI-HRMS (m/z) Calcd. for 593.3122 ([M+H]+), Found
593.3131. The concentration of a stock solution of the ligand was
determined by an NMR integration value using maleic acid as the internal
standard.
Bismethoxynaphthalene-benzylmaleimide intermediate (6b)
1-Benzyl-3,4-dibromopyrrole-2,5-dione 4 (511 mg, 1.48 mmol), 5b (1.05
g, 3.69 mmol) and [1,1′-bis(diphenylphosphino)ferrocene]dichloro-
palladium(II) (400 mg, 0.490 mmol) and K3PO4 (1.57 g, 7.40 mmol) were
dissolved in degassed 1,4-dioxane (12.9 mL) and H2O (2.1 mL). The
mixture was stirred at 90 °C for 12 h. The reaction mixture was diluted
with AcOEt and filtered using celite, then saturated aqueous NH4Cl was
added to the filtrate and extracted with AcOEt. The organic layers were
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10.1002/chem.201605276
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The 2,13-dimethoxy[5]helicene-
spermine ligand 8b possesses an
axial chirality. The racemic 8b was
bound to the B-DNA with
Kensuke Kawara, Genichiro Tsuji, and
Shigeki Sasaki＊
Page No. – Page No.
accompanying induction of its (P)-
chirality together with the B-to-Z
helicity change of the duplex DNA,
[(dC-dG)3]2. The (P)-chirality of the
bound 8b, in turn, transitioned to the
(M)-chirality according to the Z-helicity
of DNA. These results have illustrated
the chirality synchronization between
the DNA and ligand.
Synchronized Chiral Induction
Between [5]Helicene-Ligand and B-Z
DNA Transition
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