Sequence specific recognition of ssDNA by fluorophore 3-hydroxyflavone

Article abstract of DOI:10.1016/j.jphotobiol.2015.10.019

A fully water soluble 3-hydroxyflavone (3HF) derivative, N-(3-hydroxy-4′-flavonyl)-N,N,N-trimethylammonium sulfate (3HFNMe3) was synthesized. Investigation of its emissions at varying wavelengths revealed that it had three emission bands of normal (N), an

Full text of DOI:10.1016/j.jphotobiol.2015.10.019

Sequence specific recognition of ssDNA by fluorophore 3-hydroxyflavone
Asli Capan, Muge S. Bostan, Erkan Mozioglu, Muslum Akoz, Ahmet
C. Goren, Mehmet S. Eroglu, Turan Ozturk
PII:
DOI:
Reference:
S1011-1344(15)00348-6
doi: 10.1016/j.jphotobiol.2015.10.019
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29 March 2015
1 October 2015
23 October 2015
Please cite this article as: Asli Capan, Muge S. Bostan, Erkan Mozioglu, Muslum Akoz,
Ahmet C. Goren, Mehmet S. Eroglu, Turan Ozturk, Sequence specific recognition of
ssDNA by fluorophore 3-hydroxyflavone, (2015), doi: 10.1016/j.jphotobiol.2015.10.019
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ACCEPTED MANUSCRIPT
Sequence specific recognition of ssDNA by fluorophore 3-
hydroxyflavone
1
2
3
3
3
Asli Capan, Muge S. Bostan, Erkan Mozioglu, Muslum Akoz, Ahmet C. Goren, Mehmet S.
2
,3,*
1,3,*
Eroglu,
and Turan Ozturk
1
Department of Chemistry, Faculty of Science, Istanbul Technical University, Maslak, Istanbul 34469,
Turkey
2
Marmara University, Department of Chemical Engineering, 34722, Kadikoy, Istanbul, Turkey
3
TUBITAK UME, Chemistry Group Laboratories, PBox 54, 41470, Gebze-Kocaeli, Turkey
ABSTRACT
A fully water soluble 3-hydroxyflavone (3HF) derivative, N-(3-hydroxy-4’-flavonyl)-N,N,N-
trimethylammonium sulfate (3HFNMe3) was synthesized. Invesitgation of its emissions at
*
*
varying wavelengths revealed that it had three emission bands of normal (N ), anionic (A ) and
*
tautomeric (T ), in ultrapure water. Recognition of single-stranded ten ssDNA chains, having
different nucleotide sequences was studied, using the ratiometric change of the intensities of the
*
*
two bands (A /T ), depending upon the varying environment of the 3HFNMe3 with different
ssDNA chains. Addition of the ssDNA chains to the 3HFNMe3 solution caused gradual
*
*
quenching of the A band and had almost no effect on the T band. As the ratios of the two bands
*
*
(
A /T ) vs increasing amount of the ssDNAs generated characteristic curves for each ssDNA
chain, it became possible to identify the chains with their characteristic curves.
Keywords : fluorophore, 3-hydroxyflavone, DNA, specific recognition, spectroscopic methods
1
. Introduction
Designing DNA probes for detecting DNA chains, having varying sequences is a great
challenge [1]. The motivation for DNA detection is due to its widespread applications in various
1

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fields such as DNA diagnostics, gene analysis and detection of genetic mutations, which may
lead to the gene analysis before symptom(s) of a disease appears.
Majority of the probes synthesized so far depends on designing complementary probes for
targeted DNA sequences to allow them to hybridize with the probe. Such a process could be
performed in solution or probe could be presented on a solid support. Their detection could be
electrochemical [2, 3] or optical [4-8]. However, in majority of the cases, nucleic acid is
covalently labeled by a fluorescent probe and the detection is studied by fluorescence resonance
energy transfer (FRET) or fluorescence quenching. On the other hand, detection of DNA through
the interactions of positively charged fluorophore with negative charges of DNA is rare [9].
Scheme1.
3
-Hydroxyflavones (3HF) 1 (Scheme 1) have unique photophysical properties, which exhibit
well-resolved and intense two fluorescence bands in the visible region, resulting from excited-
state intramolecular proton transfer (ESIPT) (Scheme 2), i.e. the initially excited normal form
*
*
(
N ) and the tautomeric form (T ) [10-13]. Their ratios are highly sensitive to the environment
such as polarity and hydrogen bonding perturbations of the solvents. As the ratio between two
bands depends on the microenvironment of 3HF, not on its concentration or the instrument
settings, this property provides 3HF with an important advantage over conventional single-band
dyes[14-16]. Information could be obtained about the microenvironment of 3HF with the change
of the ratios of its two emission bands (IN* / I ) and this ratio could be specific for each
T*
environment. Examples have already been reported for sensing lipid bilayers, cell membranes,
proteins and peptides using 3HF as a sensor [17-19]. Concerning the use of 3HF as a two-band
switchable fuorescence sensor for the interactions of DNA, 3HF as a nucleobase mimic has been
demonstrated [4]. Double- and single-stranded DNAs were sensed through their characteristic
effects on binding to 3HF, possesing polycationic spermine [20]. It was disclosed that while on
binding to a double-stranded DNA, emission bands of the 3HF changed up to 16-fold, only
moderate changes in the dual emission on binding to a single-stranded DNA was observed. In a
separate study, ratiometric change in two emission bands of 3HF was used as a tool to distinguish
2

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different peptide–ODN complexes, [21] and using the similar technology, a series of 3HFs were
synthesized and successfully applied to identify various peptide-ODN complexes [22]. Moreover,
fisetin, which is a 3HF derivative, was employed for recognition of DNA nucleotide based on
selective abasic site binding [23].
Scheme 2.
In this study, a novel fully water soluble 3-hydroxyflavone (3HF) derivative, N-(3-hydroxy-4’-
flavonyl)-N,N,N-trimethylammonium sulfate (3HFNMe3) 2 (Scheme 1), which had emission
*
*
*
bands of normal (N ), anionic (A ) and tautomeric (T ), in ultrapure water, was employed as a
fluorophore for recognition of single-stranded DNAs (ssDNA), having varying nucleotide chains.
The study discloses that gradual addition of ssDNA to the solution of the fluorophore,
3
HFNMe3, resulted in obtaining characteristic IA* / I curve, rather than conventional I / IT*
T* N*
ratio, for each single-stranded DNA chain.
2
. Experimental
All reagents were purchased from Aldrich, Acros and Merck, and were used without further
purification. All the solvents used in the syntheses were technical grade and freshly distilled prior
to use. The water used for the measurements had an ultrapure grade (distilled from Millipore
Milli-Q Academic). The single-stranded DNA chains were obtained from Metabion International
AG, Germany. UV-Vis and fluorescence measurements were studied on HITACHI U-0080D and
1
13
HITACHI F-4500, respectively. H and C NMR spectra were recorded on a Varian 600
spectrometer. Proton and carbon chemical shifts were reported in parts per million downfield
from tetramethylsilane, TMS. Mass spectra were recorded on ThermoLCQ-Deca ion trap mass
instruments.
Synthesis of N-(3-hydroxy-4’-flavonyl)-N,N,N-trimethylammonium sulfate 2 (3HFNMe3)
3

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Dimethylamine 3-hydroxyflavone (3HFNMe2) 3 was synthesized following the literature
procedure [24]. A solution of 3 (0.37 g, 1.3 mmol) and dimethylsulfate (6.55 mmol, 0.62 ml) in
THF was refluxed for 24 h. The precipitate was filtered after the mixture was reached room
temperature. The crude solid was purified by Soxhlet extraction, using dichloromethane as
solvent, which yielded N-(3-hydroxy-4’-flavonyl)-N,N,N-trimethylammonium sulfate
1
(
3HFNMe3) 2 as a white solid (0.122 g, 23%). H NMR (600 MHz, D O) δ (ppm) 8.11 (d, 2H,
2
J=8.4Hz), 7.82 (d, 2H, J=7.6Hz), 7.71 (d, 2H, J=8.4Hz), 7.61 (t, 1H, J=7.6Hz, J=7.5Hz), 7.44
1
3
(
d, 1H, J=7.6Hz), 7.25 (t, 1H, J=7.6Hz, J=7.5Hz), 5.32 (s, 9H), 3.61 (s, 1H), 3.55 (s, 3H); C
NMR (150 MHz, D O) δ (ppm) 157.2, 134.5, 132.1, 129.5, 129.4, 129.3, 125.1, 124.9, 124.4,
2
1
5
24.3, 119.8, 119.7, 118.3, 56.8, 53.8; Found C, 55.78, H, 5.35, N, 3.60, Calculated C, 56.03, H,
+
.22, N, 3.44; m/z 296 M
Fluorescence measurements
The single-stranded DNA chains comprising 25 Cytosines (d(C)25), 25 Guanines (d(G)25),
2
5 Adenines (d(A)25), 25 Thymines (d(T)25), 15 Cytosines and 5 Adenines (d(C)15-d(A)5), 10
Cytosines and 10 Adenines (d(C)10-d(A)10), 5 Cytosines and 15 Adenines (d(C)5-d(A)15), 15
Thymines and 5 Guanines (d(T)15-d(G)5), 10 Thymines and 10 Guanines (d(T)10-d(G)10) and 5
Thymines and 15 Guanines (d(T)5-d(G)15) were applied for the measurements.
-3
From a stock solution of 2 (3HFNMe3), dissolved in ultrapure water (2.1 mg, 2 ml, 2.5x10
M), was transferred 200 µl into a quartz cell (1x1x3 cm) and diluted to 2 ml with ultrapure water.
Fluorescence emission was then recorded after each addition the ssDNA solution (2 µl, 20
nmol/ml). The ratio of A* and T* bands was calculated and a graph, having A*/T* ratio vs DNA
concentration was plotted. Each experiment was repeated five times to understand the
repeatability of the results, which gave the same results.
3
. Results and Discussion
3
.1. Synthesis
The precursor, dimethylamino-3-hydroxyflavone (HFNMe2) 3, to the obtain its salt form N-
(3-hydroxy-4’-flavonyl)-N,N,N-trimethylammonium sulfate (3HFNMe3) 2, was synthesized
4

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applying the literature procedure (Scheme 3) [24]. Its methylation with dimethyldulfate and then
purification of the product with Soxhlet extraction successfully gave the product 2 in 23% yield.
Scheme 3.
3
.2. Spectroscopic Measurements
UV measurement of 3HFNMe3 2, methyl salt of 3HFNMe2 3, having maximum at 400 nm in
dichloromethane,[24] displayed two maxima at 305 and 345 nm in ultra-pure water (Fig 1).
While 3HFNMe2 had a broad peak between 330 – 450 nm, its methyl salt 3HFNMe3 had two
maxima covering a shorter area of 280 – 390 nm. Excitation of 3HFNMe3 at maximum 345 nm
*
*
produced two emissions at 405 (weak) and 520 nm (strong) as N and T bands (Fig. 1, A). As for
*
ratiometric study, such an emission was not suitable since the intensity of the N band was too
weak. Thus, an excitation screening was conducted, which displayed that the two best bands for a
ratiometric study were available with the excitation at 381 nm, as the excitations at various
*
wavelengths such as 385 and 405 nm caused the T band became weaker and then disappear (Fig.
1
, B). Although the intensities of the both emissions (ex. 381 nm) were not too strong, they were
found to be enough for a ratiometric study.
A close investigation of the emission bands of the excitations at 345 and 381 revealed that
their first emission bands appeared at different wavelengths of 405 and 460 nm, respectively, as
their second emissions were the same, 520 nm, which indicated that a different ESIPT
mechanism for 3HFNMe3 was taking place. As 3HFNMe3 had a positive charge on nitrogen
attached to the para of the phenyl group, proton of the hydroxyl group could be acidic enough to
be deprotonated to generate an anion. Indeed, pH measurement and computational study
*
indicated that 3HFNMe3 had pH of 5 and 5.77, respectively. Regarding the location of the T
*
band of 3HFNMe3, compare with the T band of 2-(4-(dialkylylamino)phenyl)-3-hydroxy-4H-
*
chromen-4-one 6 (Scheme 4), emissions of which studied in depth [18], while 3HFNMe3 had T
*
emission at shorter wavelength of 520 nm, dialkyl-3HF had T emission at longer wavelength of
around 580 nm. Such a difference arises from the participation of free electrons of amino group
5

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*
*
into conjugation, forming an H-N emission at shorter wavelength corresponding the T emission
of our quaternized 3HFNMe3. On the other hand, as the amino group of 3HFNMe3 did not have
*
any free electrons, the group is quaternized with methylation, such an emission (H-N ) could not
*
*
be expected. Thus, it was decided that while the N (405 nm) and T (520 nm) emission bands of
3
HFNMe3 are in good agreement with the emissions indicated by Kasha in his extensive study of
*
hydrated 3HF forms, [25] a new emission at 460 nm could belong to anionic form 11 (A ) of
*
3
HFNMe3. While the conventional ESIPT reaction of 3HFNMe3 2 was observed with N 7 and
*
T 8, excited forms of N 2 and T 9 ground states, respectively, a proton abstraction from
3
HFNMe3 2 generated the anionic form A 10 and its excitation at 381 nm produced the excited
*
anion A 11, emission of which gave the anionic emission peak at 460 nm (Scheme 5). As the
*
*
ratiometric study was performed with excitation at 381, the concerned emissions are A and T ,
*
*
which means that the ratiometric measurement in this study belongs to A /T ratio.
Fig. 1.
Scheme 4.
Scheme 5
Initially, phosphate buffer was planned to use in all measurements. Unfortunately, addition of
*
small amount of buffer to the solution resulted in quenching the A band of the sensor (See the
Supporting Information). Then, as the fluorophore was found to be so sensitive to the buffer, all
the measurements were decided to be conducted in solution without buffer. Indeed, it was noted
that pH of the solutions in all the measurements did not change. pH of the pure water was
measured to be 7.5, which became 5 with the addition of the probe 3HFNMe3 2 and remained at
5
in all measurements. The change of pH from 7.5 to 5 could be due to the presence of positive
charge on the nitrogen atom, which increases its electronegativity, causing the hydroxyl proton to
be more acidic. In order to clarify this, a computational study was decided to be conducted.
6

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3.3. Computational study
To shed more light on the relative acidity of dimethylamine, 3HFNMe2, 3 and its qaternized,
tetramethylamine 3HFNMe3, 2 forms, their pK values were predicted with the isodesmic
a
reaction, applying methodology reported in the literature [26]. The experimental pK value of
a
phenol (9.98) was taken as a reference. DFT calculations were carried out using the Gaussian 09
program [27] Becke’s three-parameter exchange functional (B3) [28,29] was employed with the
Lee-Yang-Parr correlation functional (LYP) [30] as implemented in Gaussian 09 together with
Pople’s split-valence 6-311++G(d,p) basis set. The minima of the calculated structures were
verified by analyzing the harmonic vibrational frequencies, using analytical second derivatives,
which have nimag=0. Solvent effect was included using water in the SMD solvation model [31].
Computational studies estimated the pK values of 3HFNMe2 and 3HFNMe3 as 8.94 and 5.77,
a
respectively, indicating the fact that aqueous 3HFNMe3 is substantially more acidic than
3
HFNMe2. Thus, the experimental pK of 3HFNMe3 is in good agreement with its calculated
a
value.
3.4. DNA Studies
Although some of the water soluble 3HF derivatives consisted of quaternized amine groups
*
[
32], they were not informative enough as the fluorophore had only one emission band (N ), and
could not be employed as sensor for ratiometric measurements of the band intensities (I / I ).
N*
T*
When we performed fluorescence measurements with the fluorophore 2 (3HFNMe3), having
quaternized amine group, in tap water and distilled water, same results, i.e. single emission band,
*
corresponding to anionic emission, A , was obtained (Figure 3A). Surprisingly, when the
*
*
experiment was repeated in ultrapure water, two emission bands of A and T appeared (Figure
3
B), and gradual addition of ssDNA to the fluorophore solution resulted in the quenching of the
*
A band.
7

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Fig.2.
*
*
Considering that the A /T ratio could change depending upon the nucleotide sequence of the
*
*
ssDNA, various ssDNA chains were employed to obtain characteristic A /T ratio for each
sequence. Then, gradual addition of ssDNA solutions into the 3HFNMe3 2 solution, both in ultra
*
*
pure water, resulted in varying A /T ratios with the nature of ssDNA chain (Figure 4). While
*
*
A /T curve of d(C)25 was calculated to be the highest, d(T)25 had the lowest curve. The curves
*
*
of A /T ratios of d(A)25 and d(G)25, which took place between the highest and the lowest
curves of d(C)25 and d(T)25, respectively, followed almost the same line. As it is known that
3
HFs are very sensitive to their environment, possible explanation could be that the ssDNA
chains had varying interactions with 3HFNMe3, due to their different chemical structures and
conformations, which affected the fluorescence intensities. Then, the ssDNA chains, possessing
two different nucleotides in different ratios were subjected to the recognition by 3HFNMe3. The
curves of d(C)15-d(A)5 (Figure 4), d(C)10-d(A)10, d(C)5-d(A)15 (Figure 5), d(T)15-d(G)5,
d(T)10-d(G)10 and d(T)5-d(G)15 (Figures 6 and 7) took part around the curve obtained from the
ssDNA chain d(C)25, which may imply that the mixture of single-stranded DNA chains have
closer conformation with d(C)25. Considering that the ssDNA chains have small structural
differences, such recognition is an important result.
Fig.3.
Fig.4.
8

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Fig.5.
Fig.6.
4
. Conclusion
A water soluble fluorescent sensor has been developed to identify single-stranded DNAs having
*
different nucleotide sequences. This fluorophore had three emission bands of normal (N ),
*
*
anionic (A ) and tautomer (T ) at 405, 460 and 520 nm, respectively. The anionic emission arose
from the anionic form of 3HFNMe3, which had a slightly acidic hydroxyl proton having pH of 5.
*
*
The ratio of A /T was found to be suitable for a ratiometric study and the results presented
herein indicated that the flavone 3HFNMe3 is a potentially important sensor for identification of
various chemical conformations such as single-stranded DNAs. Although the results of this study
are moderate, they indicate that ratiometric technique of 3HF is an important tool to identify
various ssDNA chains. In this study, only single-stranded DNA chains were attempted to
identify, and the results have been reported. As a continuation of this study, identification of
various biological molecules, particularly water soluble onces, such as double-stranded DNA
chains will be conducted.
5
. Acknowledgement
We thank Dr Andrey Klymchenko of University of Strasbourg for his excellent successions on
anionic mechanism, Dr Mehmet Emin Cinar for useful discussions on computational calculations,
and the Scientific and Technological Research Council of Turkey (104T081), Istanbul Technical
University and Unsped Global Lojistik for financial supports. We also thank National Center for
High Performance Computing of Turkey (UYBHM) for computing resources.
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Figure captions
Scheme1. Structures of 3-hydroxyflavone and its derivatives 3HFNMe3 2 and 3HFNMe2 3.
Scheme 2. ESIPT reactions of 3HF
Scheme 3. Synthesis of 3HFNMe3 2.
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2

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Scheme 4. Resonance of N,N-dialkylamino-3HF
*
*
*
Scheme 5. Normal (N ), anionic (A ) and tautomeric (T ) emission mechanisms of 3HFNMe3.
Fig. 1. Absorption and fluorescence spectra of 3HFNMe3 2 in ultra-pure water.
Fig.2. Emissions of 3HFNMe3 2 A) in water; B) in ultra pure water (quenching of A* band with
the addition of ssDNA, Exct. 381 nm, pH = 5).
Fig.3. Emissions of 2 with the addition of d(C)25, d(G)25, d(A)25 and d(T)25 (Exct. 381 nm, pH
=
5).
Fig.4. Emissions of 2 after addition of d(C)25, d(G)25, d(A)25, d(T)25, d(C)15-d(A)5, d(C)10-
d(A)10 and d(C)5-d(A)15 (Exct. 381 nm, pH = 5).
Fig.5. Emissions of 2 after addition of d(C)25, d(G)25, d(A)25, d(T)25, d(T)15-d(G)5, d(T)10-
d(G)10 and d(T)5-d(G)15 (Exct. 381 nm, pH = 5).
Fig.6 . Emission of 2 with all the DNA chains (Exct. 381 nm, pH = 5)
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Fig. 1
A
B
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Fig 2
1
0
0
,0
,5
,0
A
4
50
500
550
600
650
2
1
1
00
50
00
B
5
0
0
4
00
450
500
550
600
650
wavelength (nm)
1
5

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Fig 3
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Fig 4
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Fig 5
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8

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Fig 6
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Graphical abstract
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Scheme 1
O
O
S
O
O
N
N
O
O
O
O
O
O
OH
OH
OH
1
(3HF)
2 (3HFNMe3)
3 (3HFNMe2)
2
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Scheme 2
N*
T*
O
O
ESIPT
O
O
O
H
OH
h
h
h
O
O
O
O
O
H
O
H
2
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Scheme 3
N
N
N
i) NaOH (solid)
O
OH
O
O
O
O
O
MeOH
(CH ) (SO )
3 2 4
S
+
O
O
ii) NaOH (0.5 N)
OH
OH
H O
2
2
O
O
4
5
3 (3HFNMe2)
2 (3HFNMe3)
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Scheme 4
R
N
R
O
OH
O
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2
4

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Scheme 5
A*
N
N*
N
T*
N
-H+
ESIPT
O
O
O
O
H+
OH
+
O
O
O
OH
11
7
8
~400 nm
460 nm
345 nm
405 nm
520 nm
A
N
N
N
T
N
-H+
O
O
O
O
O
H+
OH
O
+
O
OH
10
2
9
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Highlights
*
*
-
(
A new fully water soluble 3-hydroxyflavone derivative, having neutral (N ), anionic (A ) and tautomeric
T ) emissions.
*
*
*
-
-
A new sensing approach with anionic (A ) and tautomeric (T ) emissions.
*
*
Differentiating ssDNAs, having different nucleotide chains, using emission ratios of A /T .
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