A Supramolecular Counter Circuit Based on Cyanine Dye Assembly

Article abstract of DOI:10.1002/chem.202001240

Molecular computation, a rapidly developing multidisciplinary research field, has attracted increasing attention. A series of combinational logic circuits at the molecular level have been constructed, however, the development of sequential logic circuits is still in its infancy due to the lack of ideal design tools. Taking advantage of unique assembly behaviors of cyanine dyes, we constructed a two-bit molecular counter circuit that can implement fundamental sequential logic functions, including number cumulating and descending. Further introducing a guanine-rich DNA strand as the cycle index, the counter can be reused several times and eventually be scaled up to count up to 16 numbers. The supramolecular circuit shows high programmability, flexibility, and reversibility, and it is prospected that the strategy would be applied in designing other advanced molecular circuits.

Full text of DOI:10.1002/chem.202001240

Accepted Article
Accepted Article
Title: A supramolecular counter circuit based on cyanine dye assembly
Authors: Die Chen, Shu Yang, Zhiming Wu, and Xiaoping Xu
This manuscript has been accepted after peer review and appears as an
Accepted Article online prior to editing, proofing, and formal publication
of the final Version of Record (VoR). This work is currently citable by
using the Digital Object Identifier (DOI) given below. The VoR will be
published online in Early View as soon as possible and may be different
to this Accepted Article as a result of editing. Readers should obtain
the VoR from the journal website shown below when it is published
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content of this Accepted Article.
To be cited as: Chem. Eur. J. 10.1002/chem.202001240
Link to VoR: https://doi.org/10.1002/chem.202001240
01/2020

10.1002/chem.202001240
Chemistry - A European Journal
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A supramolecular counter circuit based on cyanine dye assembly
a
b
a
Die Chen,[ ] Zhiming Wu, [ ] Xiaoping Xu,[ ] Shu Yang*[a]
[a]
D Chen, Dr X Xu, Dr S Yang
Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan
Research Center for Drug Precision Industrial Technology, West China School of Pharmacy
Sichuan University
Chengdu, 610041, PR China
E-mail: yangshu1106@scu.edu.cn
[b]
Dr Z Wu
College of Computer Science
Sichuan University
Chengdu, 610065, China
Supporting information for this article is given via a link at the end of the document.
Abstract:
Molecular
computation,
a
rapidly
developing
calculation of stimuli pulses, timing, and arithmetic operations[11]
.
multidisciplinary research field, has attracted increasing attention. A
series of combinational logic circuits at molecular level have been
constructed, however, the development of sequential logic circuits is
still in its infancy due to the lack of ideal design tools. Taking
advantage of unique assembly behaviors of a cyanine dye, we
constructed a two-bit molecular counter circuit that can implement
fundamental sequential logic functions, including number cumulating
and descending. Further introducing a guanine-rich DNA strand as
the cycle index, the counter can be reused several times and
eventually be scaled-up to count up to 16 numbers. The
supramolecular circuit shows high programmability, flexibility and
reversibility, and it is prospected that the strategy would be applied in
designing other advanced molecular circuits.
To construct an analogue of electronic counter at molecular level,
we believed three issues should be considered: (1) multi-channel
compatibility; (2) transformations among different output channels
triggered by the same stimulus but different amounts; and (3)
availability of chemical or biochemical pairs with opposite effects
to realize both the cumulating and descending functions.
Satisfactorily meeting all the criteria is so laborious that there are
few reports on the construction of molecular counters.
Introduction
Molecular computation has emerged as a promising alternative to
traditional silicon-based circuits for information processing and its
practical applications have been explored in various fields,
including chemical/biological sensing[1], smart diagnosis[2],
controllable drug delivery[3], artificial intelligence[4] and so forth. Up
to now, a mass of molecular systems mimicking electronic
devices, from basic Boolean logic gates[5] to advanced functional
circuits[6], have been developed. However, most of them are
combinational ones, where the state of output is only determined
by the present input combination. Although combinational circuits
can cascade to large scale and implement numerous arithmetic
and nonarithmetic functions[7], it is hard for them to accomplish
synergetic successive work flows. Sequential logics are another
kind of electronic devices, whose outputs depend on both present
and previous inputs. The memory function endows the sequential
logic circuits huge possibilities in practice, but poses a great
challenge for designing their molecular analogues. During the last
two decades, there were only a few molecular sequential circuits
have been reported, and their functions were primarily limited in
Scheme 1. A) The molecule structure of MTC and its various assembly states.
B) The absorption spectra of 6 µM MTC in 10 mM Tris-HCl buffer solution with
various cations: a) without cation; b) with 0.4 mM Pb2+, c) with 0.4 mM Ca2+, d)
with 0.1 mM Co2+. Inserts demonstrate the assembly states assigned to the
featured absorption peaks.
Supramolecules, especially cyanine dye assembly, have
been increasingly recognized as powerful candidates to construct
multi-output molecular logic circuits[12] due to their ability to
present multiple metastable states. Cyanine dyes have the ability
to self-assemble to various aggregates with distinguished
keyboard lock[8], flip-flop[9] and register[10]
. Thus, designing
versatile sequential devices at molecular level are attractive, and
urgently needed concerning the blossom of molecular
computation.
Counter is one of the fundamental sequential logic circuits,
which has been widely employed in frequency division,
photochemical properties[13]
, which could be employed as
compatible multiplex output channels of complicated logic circuits
(1st requirement). More importantly, the assembly behaviors of
1
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cyanine dyes are regulable. Numerous external stimuli, including
temperature[14], cations[15] and biomolecule[16] are able to tune
their assembly processes and states finely. It is reported that the
assembly behaviors of cyanine dyes are not only sensitive to
metal cation species, but also to the ion strength[6c] (2nd
requirement). In addition, the supramolecular aggregating
process of cyanine dyes are reversible[13a], which meets the 3rd
requirement. All these features make cyanine dye an ideal
candidate to achieve counter function at molecular level.
states by accumulated Ca2+, i.e. from dimer to Jb-aggregates and
finally to H-ones. Moreover, the assembly process of MTC is
reversible. As shown in Figure 1C and 1D, introducing ethylene
diamine tetra acetic acid (EDTA) in succession can effectively
complex Ca2+ and consequently regulate MTC assembly state
backward step-by-step, i.e. from H-aggregates to Jb-ones and
finally to dimer. It is indicated that EDTA's influence on the
solvent's dielectric constant perturbation by ionic strength is
inapparent. One of the reasons is that EDTA acid is dissociated
incompletely in Tris-HCl buffer and its effect on ionic strength
probably not be equal to metal ions. Moreover, the net anionic
nature of MTC probably also makes it more sensitive to metal
cations.
Herein, we designed a cyanine dye 3,3'-di(3-sulfopropyl)-
4,5,4',5'-dibenzo-9-methyl-thiacarbo-cyanine triethylammonium
salt (MTC, the molecular formula was shown in Scheme 1A) as
the building block to construct a supramolecular counter.
The results show that the distinct assembly behavior of MTC
can be programmed by certain chemical pairs and provide
compatible multi-channel output signals. The feature endows
MTC serving as an ideal building block for molecular counters.
Results and Discussion
Self-assembly behavior of MTC
Construction of the two-bit counter
As a typical cyanine dye, the assembly state of MTC can be
regulated by different external stimuli. In 10 mM Tris-HCl buffer
solution, it is primarily in the form of dimer, whose typical
absorption peak is approximately at 530 nm[7b] (termed D-band).
It is reported that some metal cations can regulate the self-
assembly of MTC due to metal-specific interactions plus solvent's
dielectric constant perturbation by ionic strength[17].As shown in
Scheme 1B, MTC can be induced to various assembly states by
different cations, such as Ja-aggregates (typical absorption peak
The counter is a fundamental element in sequential logic systems
which can implement the accumulating, descending, resetting
and recycle operations. To demonstrate the feasibility of
engineering molecular counter with MTC, we firstly designed a
two-bit counter by choosing Ca2+-EDTA as the impulse pair
(Figure 2). To translate the MTC spectral signal to binary readout,
the normalized Jb- and H-band signals that above or under the
threshold (set as 0.2) were defined as “1” or “0”, respectively.
at 660 nm[6d]
,
termed Ja-band) by Co2+, Jb-aggregates
(representative absorption peak at 640 nm[13c], termed Jb-band)
by Ca2+, and H-aggregates (absorption band in the range of 440-
480 nm[18], termed H-band) by Pb2+.
Figure 1. The absorption spectra of 6 μM MTC in Tris-HCl buffer with different
impulses: A) with 0 to 0.2 mM Ca2+, B) with 0.3 to 0.6 mM Ca2+, C) with 0.6 mM
Ca2+ and 0 to 0.3 mM EDTA and D) with 0.6 mM Ca2+ and 0.4 to 0.6 mM EDTA.
Figure 2. The schematic diagram A) and the truth table B) of the two-bit
molecular counter based on the MTC platform. The corresponding normalized
histogram of 6 μM MTC with different impulses: C) with successive 0.2 mM Ca2+
and D) with 0.6 mM Ca2+ and successive 0.2 mM EDTA.
The dot lines in B) and C) represent MTC without Ca2+
.
Based on the above results, 0.2 mM Ca2+ was selected as
the accumulating impulse while EDTA as the descending one. As
shown in Figure 1, in the absence of Ca2+, MTC was in the form
of dimer, thus the output Jb- and H-band signals were both “0”,
resulting in (0, 0) readout. When inputting 0.2 mM Ca2+, MTC was
induced to form Jb-aggregates completely, resulting in (1, 0). MTC
was induced to a mixture of Jb/H-aggregates by 0.4 mM Ca2+,
Moreover, it is found that the assembly behavior of MTC is
also regulated by the ionic concentration. Under our experimental
condition, inputting 0.2 mM CaCl2 caused a remarkable spectral
shift of MTC from D to Jb-band (Figure 1A). And further increasing
CaCl2 concentration resulted in sharply decrease of Jb-band and
gradually increase of H-band (centered at 455 nm) (Figure 1B).
Obviously, MTC can be programmed to form various assembly
2
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resulting in (1, 1); while to H-aggregates alone by 0.6 mM Ca2+,
resulting in (0, 1). The normalized MTC Jb-band (640 nm) and H-
band (455 nm) were plotted as bar charts in Figure 2C and 2D,
which satisfy the logic requirement of the counter (the truth table
was shown in Figure 2B). And the four different readouts can be
assigned as the four counting numbers (0 to 3) respectively. It has
to mention that the function of counter circuits is storing and
operating a series of numbers in any specific order. Therefore, the
binary codes of the counting numbers in this work are not exactly
equal to those for ascending natural numbers 0, 1, 2 and 3. With
regard to the descending operation, EDTA was gradually added
to complex Ca2+ (Figure 1) and resulted in the counting number
descended from 3 to 0 (Figure 2D).
Then, we tested the reconfiguration efficiency of the MTC
platform. It is shown that the conversion between MTC dimer and
H-aggregates can oscillate at least 4 rounds by alternately
inputting the same amounts of Ca2+ and EDTA impulses (Figure
3D), indicating the counter can be used several times and has the
potential to count more numbers.
In order to expand the counting capacity, a cycle index is
introduced to record the reusing round of the device. It is
previously reported that guanine (G)-rich oligonucleotides can
interact with MTC and enhance its monomer fluorescence
intensity[19]. Therefore, a G-rich DNA strand (termed CI) was
brought in the counter as the cycle index. It is shown that the
fluorescence intensity of MTC at 619 nm is positively correlated
with the added amount of CI (Figure 4A), and it is almost
independent with the absorption signals (Figure 4B), indicating
that CI could be used as the cycle index of the counter without
disturbing its function, and consequently expand its counting
scale. In this way, in each round of pulsing Ca2+, the counter can
accumulate 4 numbers, and the MTC system can at least run four
rounds reset by adding EDTA and CI together. As shown in Figure
5C and 5D, the results indicated that the MTC-based counter
circuit have the capacity to count maximum 16 numbers by using
the normalized Jb/H-band as the output signal and the enhanced
fluorescence intensity as the cycle index (the truth table was
shown in Figure 5B).
Thus, we have successfully realized both the accumulating
and descending operations of a two-bit counter by employing
Ca2+-EDTA as the impulse chemical pair and the normalized Jb/H-
band as the output signal.
Beside of Ca2+, K+ and Cu2+ can also regulate MTC
converting between D-Ja-H and D-Ja-Jb aggregates, respectively,
and their effects could be eliminated by 18-crown-6 (CE) and
EDTA, respectively. In the similar way, more counters can be
constructed by employing K+-CE (the normalized Ja-/H-band as
the output signal) or Cu2+-EDTA pairs (the normalized Ja- and Jb-
bands as the output signals) (Figure S5 and S6). It is shown that
the great potential application of the MTC platform in the
construction of molecular counter.
Expansion of the counting scale
It is of great significance to scale up the counting numbers which
determine the storage capacity and the level of complexity of the
circuit. Therefore, we further expanded the counting scale of the
MTC supramolecular counter by utilizing its reversible assembly
behavior.
Firstly, the recycle property of MTC supramolecular system
has been studied. As shown in Figure S7, MTC H-aggregates
induced by Ca2+ can be disassembled to dimer directly by adding
equivalent EDTA, providing a promising resetting operation of the
counter. The normalized histogram of the MTC spectral signals
were shown in Ficalgure 3C, which satisfies the truth table of the
resetting operation (Figure 3B).
Figure 4. A) The fluorescence spectra of 6 μM MTC with different amounts of
CI. B) The normalized histogram of 6 μM MTC without and with 0.3 μM CI. The
concentrations of Ca2+ were the same as those in Figure 2, which are 0 mM for
dimer, 0.2 mM for Jb- and 0.6 mM for H-aggregates.
Conclusion
In summary, a two-bit molecular counter which can perform
cumulating, descending and reusing operations has been
successfully constructed based on the MTC supramolecular
platform. The uniqueness of the logic circuit lies in the conversion
among the different assembly aggregates of MTC induced by
distinct chemical pairs. By assigning Ca2+ and EDTA as the
impulses, the counter can record the cumulating and descending
Figure 3. The schematic diagram A) and the truth table B) of the two-bit
molecular counter. C) The normalized histogram of 6 μM MTC implementing
operation, reset and reoperation functions. D) The recycle oscillation between
MTC dimer and H-aggregates by adding Ca2+ and EDTA alternately.
3
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of four numbers according to MTC Jb- and H-band signals. Further
employing G-rich DNA CI as the cycle index, the counter can be
reused several times and eventually be scaled-up to count up to
16 numbers, which prove the powerful potential of the
supramolecular counter system. The construction strategy of the
molecular counter described here is straightforward in design and
facile in operation without any separation or washing steps, which
makes the smart prototype of ion-concentration-dependent
supramolecular assembly be a promising proof-of-principle in
sequential logic circuits.
Figure 5. The expanded counting operation via bringing in the cycle index. The schematic diagram A) and the truth table B) of the expanded counter. C) The
normalized histogram of Jb- and H-bands in four cycle rounds of counting. The fluorescence intensity at 619 nm D) of CI in four cycle rounds of counting. The
concentrations of CI in the four cycle rounds were 0 μM, 0.1 μM, 0.2 μM and 0.3 μM, respectively.
The fluorescence spectra were collected with
a
F-4600
Experimental Section
spectrophotometer (HITACHI, Japan) in a 10 mm quartz cell at 37℃ in the
range of 550 to 750 nm. Xenon arc lamp was used as the excitation light
source. Both the excitation and emission slits were 2 nm, the PMT voltage
was 400 V with a scan speed of 1200 nm min-1 and the excitation
wavelength was 530 nm. The absorption spectra were acquired with an
EVOLUTION 201 spectrophotometer (Thermo SCIENTIFIC, USA) in a 10
mm quartz cell at 37℃ in the range of 400 to 800 nm.
Chemicals and instruments
DNA oligonucleotides CI (5′-GTGGGTAGGGCGGGTGGT-3′) were
purchased from Sangon Biotechnology Co. Ltd. (Shanghai, China). The
cyanine dye MTC was synthesized according to the methods of Hame[20]
and Ficken[21], and the purity was determined by HRMS, NMR and
absorption spectroscopy (shown in Fig S1-4). Calcium chloride (CaCl2),
ethylenediaminetetraacetic acid (EDTA), trishydroxymethylaminomethane
(Tris), methanol and hydrochloric acid (HCl), lead chloride (PbCl2),
potassium chloride (KCl), copper chloride (CuCl2), and Cobalt sulfate
(CoSO4) were obtained from Sigma-Aldrich. All the chemicals are
analytical reagent grade and used as received without further purification.
Ultrapure water prepared by an ULUPURE (Chengdu China) ultrapure
water system and was used throughout the experiments.
Operation of the molecular counter
The stock solution of MTC was prepared by dissolving its powder in
methanol and was stored in darkness. The DNA stock solution was
prepared by dissolving certain amounts of oligonucleotides in 10 mM Tris-
HCl buffer solution (pH 5.0) and stored for more than 24 h at 4℃. Then the
DNA concentration was determined by measuring the absorbance at 260
nm. All samples were incubated in dark at 37℃ for 30 min before the
measurement. Under our experiment conditions, 6 μM MTC in 10 mM Tris-
HCl buffer solution (pH 5.0) was used as the initial state, 0.2 mM CaCl2
and0.2 mM EDTA were selected as the cumulating and descending pulses,
Absorption and fluorescent assays
4
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respectively. The time interval between the successive input of
accumulating/descending impulse was 30 min. Simultaneously, in each
recycle operation, 0.1 μM CI was introduced to the system and the
fluorescence intensity of MTC induced by CI served as the cycle indicator.
According to the desired function, the normalized absorbance signals An
was calculated according to the formula An=Ai/Amax, for which Amax was the
strongest absorbance intensity of MTC in all inputting situations and Ai was
that in each case.
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Keywords: molecular computing • sequential logic • counter •
cyanine dye • self-assembly
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Entry for the Table of Contents
A molecular counter which can effectively perform cumulating, descending and resetting operations based on the supramolecular
assembly was constructed. By inputting Ca2+ and EDTA as the chemical impulses and the cyanine dye assembly Jb and H aggregates
as the outputs, and further assigning the fluorescence intensity of a G-rich DNA strand as the cycle index, the counter can eventually
count up to 16 numbers.
6
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