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Abstract

  1. Top of page
  2. Abstract
  3. Introduction
  4. FRET and fluorescence quenching
  5. Structure and conformational dynamics of i-motif
  6. Visualization of reversible conformational switching of i-motif DNA and its application
  7. Conclusion and outlook
  8. Acknowledgements
  9. References
  10. Biographies

Non-B DNAs, which can form unique structures other than double helix of B-DNA, have attracted considerable attention from scientists in various fields including biology, chemistry and physics etc. Among them, i-motif DNA, which is formed from cytosine (C)-rich sequences found in telomeric DNA and the promoter region of oncogenes, has been extensively investigated as a signpost and controller for the oncogene expression at the transcription level and as a promising material in nanotechnology. Fluorescence techniques such as fluorescence resonance energy transfer (FRET) and the fluorescence quenching are important for studying DNA and in particular for the visualization of reversible conformational switching of i-motif DNA that is triggered by the protonation. Here, we review the latest studies on the conformational dynamics of i-motif DNA as well as the application of FRET and fluorescence quenching techniques to the visualization of reversible conformational switching of i-motif DNA in nano-biotechnology.


Introduction

  1. Top of page
  2. Abstract
  3. Introduction
  4. FRET and fluorescence quenching
  5. Structure and conformational dynamics of i-motif
  6. Visualization of reversible conformational switching of i-motif DNA and its application
  7. Conclusion and outlook
  8. Acknowledgements
  9. References
  10. Biographies

In science, especially chemistry and biology, the visualization of the reaction mechanism and structures of biomolecules is useful to easily and exactly understand their functional and structural features in vitro and in vivo. Indeed, the visualization of the real structure and conformational change of biomolecules has been a major objective since the DNA structure was proven by Watson and Crick using X-ray diffraction in 1953 [1]. From this perspective, X-ray crystallography and nuclear magnetic resonance (NMR) are valuable techniques for determining a molecular structure [2-7]. Especially, X-ray crystallography is most precise method to determine structures of biomolecules, which have a very complicated structure [3]. Recently, using superb time resolution of ultrashort X-ray and laser pulses, time-resolved X-ray Laue crystallography [8, 9] and time-resolved X-ray liquidography (TRXL) [10, 11] have been developed and extensively used to capture the real-time conformational changes of various biomolecules occurring in the solid and solution phase, respectively. However, X-ray crystallography and time-resolved X-ray Laue crystallography requires certainly crystals to determine the molecular structures, whereas in case of TRXL, the high concentration of solutes is necessary to determine the molecular structures. Furthermore, it is still challenging to crystalize various biomolecules including intrinsic membrane proteins. In contrast with time-resolved X-ray Laue crystallography and TRXL, fluorescence techniques such as the fluorescence resonance energy transfer (FRET) and the fluorescence quenching have been intensively used to study and visualize the conformational dynamics of various biomolecules [12]. Especially, in the absence of crystal structure, FRET, which is a mechanism describing energy transfer between two fluorescent dye molecules, has been accepted as a powerful technique to provide information on the distance between two fluorescent dye molecules. The basic principle of FRET and fluorescence quenching will be further explained in the following section.

Practically, using FRET and fluorescence quenching technique, the inter- or intramolecular interaction as well as the intramolecular conformational change in biomolecules including protein, DNA, etc., have been extensively investigated in vivo as well as in vitro [12-18]. Especially, the enzymatic activity and the conformation of DNA, which exists in all known living organisms as a carrier of the genetic information, has greatly investigated using FRET and fluorescence quenching technique because the DNA sequence can be easily modified with commercially available fluorescent tags and quencher using DNA synthesizer. In addition, DNA (or B-DNA) is also an excellent material for building artificial nanostructures in nanotechnology, material science, molecular computing and bio-analysis because of the Watson-Crick base pairing to easily make hybridization between DNA strands, the highly predictable and well-defined double-helix structure, its excellent biocompatibility and its structural stiffness and flexibility [19-24]. Thus, fluorescence techniques such as FRET and the fluorescence quenching are important for detecting and evaluating the nanoscale motion and function of a DNA-based nanodevice.

In contrast with DNA that has a right-handed double-helical structure with Watson-Crick base pairing under the physiological conditions, however, repetitive DNA sequences under certain conditions have the potential to fold into non-B DNA structures such as hairpin, triplex, cruciform, left-handed Z-form, tetraplex such as G-quadruplex and i-motif, A-motif, etc [25-31]. As it is also known that non-B DNA-forming sequences induce the genetic instability and consequently can cause human diseases [26], the mechanism on the structural change of non-B DNAs has been widely studied in biomedical fields. Furthermore, they are also considered fascinating materials for the nanotechnology because they have a unique structure that do not produce any toxic by-products and are robust enough for the repetitive working cycle. Especially, tetraplex DNAs such as G-quadruplex and i-motif have been an important target for the DNA-based nanomachine application as well as biomedical application. However, most studies performed on non-B DNA sequences have focused on the G-quadruplex due to its inherent structural stability even at neutral pH [29, 31-34], whereas relatively few studies have been done on i-motif DNA. Recently, the importance of i-motif DNA as a signpost for the oncogene expression at the transcription level and as fascinating materials for the nanotechnology has received great attention from many researchers.

In this review, we briefly outline the basic concept on the FRET and fluorescence quenching and then describe the latest studies on the conformational dynamics of i-motif DNA using fluorescence techniques. In addition, we introduce the application of FRET and the fluorescence quenching technique to the visualization of reversible conformational switching of i-motif DNA in nano-biotechnology. As nucleic acids including DNA and non-B DNA perform their biological functions through the conformational changes in living cells, an understanding on the mechanism and dynamics of their structural changes is important in terms of biological and bioengineering sciences.

FRET and fluorescence quenching

  1. Top of page
  2. Abstract
  3. Introduction
  4. FRET and fluorescence quenching
  5. Structure and conformational dynamics of i-motif
  6. Visualization of reversible conformational switching of i-motif DNA and its application
  7. Conclusion and outlook
  8. Acknowledgements
  9. References
  10. Biographies

FRET occurs between energy donor (D) molecule in the excited state and an energy acceptor (A) molecule in the ground state. The donor molecule emits at shorter wavelengths that overlap with the absorption spectrum of the acceptor. It is known that the energy transfer occurs through long-range nonradiative dipole–dipole interactions between the donor and acceptor. Thus, FRET is more efficient when they are in close proximity, usually in a distance range of 3–8 nm, and its probability of energy transfer depends on the donor-acceptor distance. Practically, FRET with a high sensitivity has been frequently used to measure the distance between domains a single biomolecule and consequently to provide information about the conformation of a biomolecule.

In general, the FRET efficiency (EFRET) can be simply calculated using the relative intensity of the donor in the absence and presence of the acceptor, and is used to measure the D–A distance (rD-A) as follows.

  • display math(1)

where R0 is the Förster radius at which E = 0.5 (see Fig. 1a). Furthermore, the FRET efficiency (E) can be also calculated from the D's fluorescence lifetime:

  • display math(2)

where τDA and τD are the D's fluorescence lifetimes in the presence and absence of an acceptor, respectively.

image

Figure 1. (a) Principle of the fluorescence resonance energy transfer (FRET). Dependence of the energy transfer efficiency (EFRET) on distance. R0 and r is the Förster distance and the distance between an energy donor (D) and an energy acceptor (A), respectively. τD and τA are the fluorescence lifetime of D in the absence and presence of A, respectively. ID and IDA are the fluorescence intensity of D in the absence and presence of A, respectively. (b) Fluorescence quenching (S and Q are a photosensitizer and quencher, respectively).

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Meanwhile, fluorescence quenching refers to any process that decreases the fluorescence intensity of a fluorophore; for instance, the photoinduced electron transfer (PET), molecular rearrangements, energy transfer, ground-state complex formation, collisional quenching, etc. Thus, fluorescence quenching has been extensively utilized both as a fundamental reaction and as a source of information on various biological phenomena occurring over wide time scale (femtosecond ~second) in vivo and in vitro. Among them, PET is extensively used to observe fast dynamics and short-range events occurring in biochemical and biological systems because PET occurs in the femtosecond to picoseconds time regime and requires a contact formation for efficient fluorescence quenching with a separation between the electron donor and the electron acceptor on the subnanometer length scale. In addition, like FRET technique, fluorescence quenching upon interaction with a specific molecular biological target is the basis for valuable optical contrast agents for molecular imaging. From this point of view, the inter- or intramolecular interaction as well as the intramolecular conformational change in various biomolecules occurring in vitro and in vivo can be easily detected by the color change in emission due to FRET and fluorescence quenching. The detailed principles and applications of FRET and fluorescence quenching in various chemical and biochemical systems in vivo and in vitro were excellently summarized by Lakowicz [12].

Moreover, recent advances in optical imaging and biomechanical techniques using FRET and fluorescence quenching offer opportunities to observe the dynamics of a single biomolecule, to determine reaction mechanisms at the level of an individual molecule and to explore heterogeneity in the reaction mechanisms observed between in the single-molecule level and in the bulk phase.

Structure and conformational dynamics of i-motif

  1. Top of page
  2. Abstract
  3. Introduction
  4. FRET and fluorescence quenching
  5. Structure and conformational dynamics of i-motif
  6. Visualization of reversible conformational switching of i-motif DNA and its application
  7. Conclusion and outlook
  8. Acknowledgements
  9. References
  10. Biographies

Structure

The i-motif DNA is formed from cytosine (C)-rich sequences at slightly acidic pH or even neutral pH. As C-rich sequences are frequently found in the promoter region of oncogene and human telomeric DNA and the formed i-motif can act as a signpost and controller for the oncogene expression at the transcription level, i-motif DNA has been an emerging topic in nucleic acids research [4, 35-37]. As shown in Fig. 2, the i-motif structure is formed by the antiparallel intercalation of two parallel hemiprotonated C:C+ base-paired duplexes. Using time-resolved NMR spectroscopy, Lieblein et al. reported that in the i-motif folding process, the kinetically favored minor conformation (3′E) is initially stabilized by stacking interactions and then refolds into a major conformation (5′E) that is stabilized by an extra T–T base pair [38]. However, i-motif DNA has been shown a high degree of structural polymorphism depending on the number of cytosine bases [39], loop length [40], environmental condition [41, 42] and attached or interacting material with the DNA strands [43-45]. The structural polymorphism of i-motif was excellently summarized in reviews [29, 46].

image

Figure 2. The i-motif structure (PDB id: 1EL2) and hemiprotonated C:C base pair. (i-motif sequence: 5′-CCCTAACCCTAACCCTAACCC-3′).

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As mentioned above, some sequences showed stable i-motif structures even at neutral pH. For example, the sequence 5′-CTTTCCTACCCTCCCTACCCTAA-3′, which is a mutant c-MTC P1 promoter sequence, formed multiple “i-motif-like”, classical i-motif and single-stranded structures as a function of pH [47]. The classical i-motif structures are predominant in the pH range 4.2–5.2, whereas “i-motif-like” and single-stranded structures are major species in solution at pH higher and lower than that range, respectively. Meanwhile, using small-angle X-ray techniques, Jin et al. showed that the conformation of i-motif DNA at mild acidic conditions is similar to that of the partially unfolded i-motif DNA rather than the fully folded i-motif DNA [48]. In addition, Dhakal et al. suggested the coexistence of the partially folded form and i-motif in the C-rich human ILPR oligonucleotides using laser-tweezers technique and found that the unfolding of i-motif DNA takes place through the partially folded structure [49]. They also showed that the formation of i-motif is decreased by increasing pH, while the partially folded structure with a small fraction is pH-independent. Using MCR-ALS (multivariate curve resolution–alternating least-squares) analysis of FRET spectra measured at different temperature, pH and salt concentrations, Kumar et al. showed that multiple-folded pyrimidine tetraplexes within the c-MYC promoter are in equilibrium at neutral pH [18]. Zhou et al. suggested the possibility that i-motif structure can be formed not only under acidic condition but also at physiological pH condition [42]. Our group also reported that the partially folded species, which could not be observed by the CD spectra, coexist with the single-stranded structure at neutral pH using the FRET technique in the bulk phases and at the single-molecule level [50]. These previous results indicate that i-motif DNA, which shows a high degree of structural polymorphism, may exist in vivo and probably participate in a biological process such as replication, regulation and transcription.

In contrast with results observed in vitro, the structure of i-motif in vivo has not been directly observed. This implies that the conformation of i-motif in vivo is greatly different with that observed in vitro or is not formed in vivo. In practice, biomolecules such as DNA, RNA and proteins evolve and function within the crowded intracellular environments that are including a number of other biomolecules, ions, etc. [51]. In addition, the intracellular environments are very heterogeneous compared with in vitro experimental conditions in terms of temperature, pH, viscosity, etc. Practically, this difference may result in the significant change in the structure and stability of i-motif DNA. In this regard, the conformational dynamics of various biomolecules in the molecular crowding condition or living organisms has been actively investigated [51-54]. In general, the effect induced by the crowded intracellular environment is defined by the excluded volume effect and dehydration effect. Rajendran et al. reported that triplet repeat DNA oligomers, 5′-CGG(CCT)nCGG-3′ (= 4, 6, 8 and 10), form i-motif structure at neutral pH and molecular crowding environments made by PEG 200 and PEG 8000 [55]. However, this is in contrast with the result reported by Zhao et al [56]. They showed that although single-walled carbon nanotubes (SWNTs) cause the formation of intramolecular i-motif structure in the mimic intracellular crowding conditions, the molecular crowding made by PEG did not induce the structural change from the single-stranded DNA to i-motif at physiological pH. Our group also found that the molecular crowding effect, especially excluded volume effect, does not induce the compactness or folding of the single-stranded DNA, whereas structures of i-motif and the partially folded form may be affected by dehydration effect of CH3CN and the complex interaction of PEG 200 (J. Choi & T. Majima, unpublished data). This means that the structure and stability of biomolecules in vivo, which is more complicated systems compared with in vitro, cannot be regulated by a single specific factor such as the excluded volume or dehydration effect, but result from a combination of various factors.

Conformational dynamics

In 1999, Mergny revealed that using a dye-labeled C-rich sequences and FRET technique, the intramolecular folding of i-motif DNA is independent on the concentration of the fluorescent oligonucleotide up to 50 pM, demonstrating that FRET is a very valuable tool for investigating the secondary structure of an oligonucleotide in vitro and in vivo [57].

Zhou et al. investigated the folding kinetics of four C-rich sequences at neutral and slightly alkaline pH using CD and FRET technique [42]. As a result, the formation time constants of i-motif obtained by CD and fluorescence experiments are 214 and 493 s, respectively, indicating that human telomeric sequences can slowly form i-motif structure at pH 7 and 4°C. Liu and Balasubramanian also revealed that the folding and unfolding processes of i-motif are both completed in about 5 s in a proton-fueled DNA nanomachine using the fluorescence spectroscopy [58] (see Fig. 3). On the other hand, the i-motif immobilized on gold surface showed the folding and unfolding times from several tens of seconds to several hours, depending on the degree of the surface coverage of i-motif [59]. Consequently, these results indicate that although the folding dynamics of i-motif DNA depends strongly on the sequences, its folding and unfolding kinetics is very slow. Recently, our group investigated an early stage interaction in the folding process of i-motif DNA using the combination of FRET and the fluorescence correlation spectroscopy [50]. FCS is a very useful technique to observe the translational diffusion of a biomolecule as well as the submicrosecond relaxation corresponding to the intrachain contact formation [12, 60, 61]. As a consequence, we observed the gradual decrease in the diffusion coefficient (D) of i-motif with increasing pH. The quantitative analysis of FCS curves supports that the gradual decrease of D associated with the conformational change in i-motif DNA is not only due to the change in the intermolecular interaction between i-motif and solvent accompanied by the increase of pH but also due to the change of the shape of DNA. Furthermore, we reported that the intrachain contact formation (k+) corresponding to an early stage dynamics in the folding process of i-motif DNA (open form) takes place with a rate constant of (5.5 ± 4.1) × 103 s−1 at neutral pH (see Fig. 4).

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Figure 3. (a) pH-driven DNA machine. The underlined DNA bases indicate the mismatched nucleotide positions in the duplex. The green circle represents rhodamine green dye, and the black circle the dabcyl group. (b) Oligonucleotide sequences and working cycling of the machine (X*/Y), as observed by fluorescence spectroscopy. (λEx = 503 nm and λEm = 534 nm). These figures are reproduced with permission from Ref. [59]. Copyright 2012 Wiley-VCH Verlag GmbH & Co.

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image

Figure 4. Rates of the intrachain contact formation (k+, filled circle) and dissociation (k-, open circle) of i-motif DNA determined from the FCS experiments as a function of pH. Inset: Illustration of the folding cycle of i-motif DNA and the structural fluctuation. This figure is reproduced with permission from Ref. [50]. Copyright 2012 American Chemical Society.

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Visualization of reversible conformational switching of i-motif DNA and its application

  1. Top of page
  2. Abstract
  3. Introduction
  4. FRET and fluorescence quenching
  5. Structure and conformational dynamics of i-motif
  6. Visualization of reversible conformational switching of i-motif DNA and its application
  7. Conclusion and outlook
  8. Acknowledgements
  9. References
  10. Biographies

Fluorescence techniques such as FRET and the fluorescence quenching are very important for the visualization of the reversible conformational switching of i-motif DNA. Indeed, the visualization of the conformational change in i-motif DNA using fluorescence techniques has been extensively used for applying in the nano-biotechnology. For instance, Kim group developed novel systems for discriminating human i-motif structures based on the different stacking interaction between a nonpolar aromatic fluorophore (FlU) and a planar base pair (C∙CH+) at the terminal and mid-loop positions of human i-motif sequences [62]. They showed that the fluorophore moiety was sensitive to the presence of cytosine base in either C∙CH+ or C–G base pairs, resulting in a significantly different emission intensity, and suggested that this system allows probing the human i-motif structure and sensing G-quadruplex sequences. Furthermore, they also showed that pairs of pyrene-modified deoxyadenosine (PyA) units induce a stable i-motif structure with an exciplex emission that was not observable in its single-strand structure [63]. This system, which uses simple fluorophore (PyA) without any additional quencher, is useful and simple for proving the conformational change in i-motif because its fluorescence emission at various pHs reveals unique color to detect by the naked eye.

Tørring et al. reported a new approach to reversibly control photosensitized 1O2 production using i-motif DNA as a pH-sensitive regulator [64]. This reversible pH-controlled on-and-off switching of a singlet oxygen sensitizer is achieved when i-motif DNA sequence is employed to control the proximity of a singlet oxygen sensitizer and a quencher. In other words, at pH values less than 5, the i-motif DNA is stable and the singlet oxygen sensitizer quenched, whereas at pH values above 8, the i-motif DNA is denatured and singlet oxygen production is increased by a factor of 35. They also suggested that this new approach leads to a promising outlook for the development of a plethora of molecule-based 1O2-releasing system. On the other hand, the pH-responsive carrier and release system based on i-motif DNA nanoswitch-controlled organization of Au nanoparticles attached to mesoporous silica was developed by Chen et al. and its successful performance was confirmed by monitoring the fluorescence intensity of a cargo molecule followed by sequential adjustment of the pH of the solution [65]. Recently, Willner et al. reported on the construction of two DNA machines activated by H+/OH or Hg2+/cysteine triggers [66]. The assembly of a “bipedal walker” and of a “bipedal stepper” using DNA constructs is described. These DNA machines perform a reversible bipedal walking function or a clockwise/anticlockwise stepper function on a DNA wheel. The forward “walking” of the DNA on the template track is activated by Hg2+ ions and H+ ions, respectively, using the thymine–Hg2+–thymine complex or the i-motif structure as the DNA translocation driving forces. The backward “walking” is activated by OH ions and cysteine, triggers that destroy i-motif or thymine–Hg2+–thymine complexes. The operation of the DNA machines is followed optically by the appropriate labeling of the walker-foothold components with the respective fluorophores/quenchers units.

In terms of bioengineering applications, it is growing the need for the development of the surface-immobilized DNA-based motors for nano-biotechnology exactly to explore their nanoscale motions and to demonstrate their functions. However, the operation (conformational switching) in most artificial DNA-based motors or machines has been carried out in buffer solutions without any immobilization and consequently produced only nondirected random nanoscale motions. In this respect, the surface-immobilized proton-fueled DNA nanomachines have been actively developed [58, 67-70]. Liedl et al. developed the chemical oscillations produced in a continuously stirred tank reactor to drive the conformational changes in i-motif DNA immobilized on a thin gold film [69]. This system allowed a firm covalent attachment of i-motif DNA to the gold surface and its autonomous conformational change can be characterized by the change of the fluorescence intensity due to the energy transfer between the fluorophores and gold substrate. Liu et al. showed that the i-motif DNA immobilized onto a microstructured thin gold surface can produce well-defined and highly reversible conformational changes when the pH is cycled between 4.5 and 9 [68]. This vertically lifts up and brings down the end-attached fluorophores from the gold surface and hence, transduces these mechanical motions into an optical nanoswitch driven by the pH. Furthermore, using the modified i-motif DNA with a hydrophobic fluorophore, Wang et al. demonstrated that a responsive surface can switch between stable superhydrophilic, metastable superhydrophobic and stable superhydrophobic states by an enthalpy-driven process [70] (see Fig. 5). That is, the reversible motion of i-motif DNA that lift up and lower the hydrophobic groups induces a conversion in surface wettability and switching between superhydrophilicity and superhydrophobicity. They explained that this macroscopic phenomenon of surface wettability is due to the coordinative effect of the collective nanoscale motion of DNA nanodevices and the surface microstructure. On the other hand, on the basis of the capability of SWNTs to specifically induce human telomeric i-motif formation [44, 56], Qu et al. showed that from the quantitative measurement of the Faradaic current and the fluorescence intensity, the i-motif-based electrochemical DNA (E-DNA) sensor immobilized on a gold electrode can selectively detect carboxyl-modified SWNTs with a detection limit of 0.2 ppm both in buffer and in cell extracts [71].

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Figure 5. (a) Reversibly switchable surface driven by DNA nanodevices. At low pH, the DNA adopts an i-motif conformation (state I). Raising the pH destabilizes i-motif DNA to produce a stretched single-stranded state (state II) or a duplex structure (state III, when a complementary strand is present). Lowering the pH induces a reverse conversion process from state II or III to state I. (b) Profiles of a water droplet at pH 4.5 and 8.5 on a smooth (i) and on a rough substrate (ii) showing the different wettability of states I and II. These figures are reproduced with permission from Ref. [70]. Copyright 2012 Wiley-VCH Verlag GmbH & Co.

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Meanwhile, Ren et al. and Wang et al. reported a label-free method using a water-soluble polymer (poly(3-alkoxy-4-methyl-thiophene), PMNT) for visualizing and sensing of the conformational change of i-motif DNA induced by the environmental pH change [72, 73] (see Fig. 6a). The pH-induced conformational change of i-motif DNA in a i-motif/PMNT complex system causes a corresponding conformational change of PMNT from a twist structure to relatively planar structure, resulting in a different observed color and dramatic change in its emission intensity. These methods are direct and simple because the conformational change of i-motif DNA cause a change in the color of the PMNT solution and the labeling of the DNA is not needed. Moreover, Ren et al. suggested that the i-motif DNA/PMNT complex could act as an environmentally friendly optical switch with a fast response, which could be reversibly cycled many times by adjusting the pH value. In a similar vein, Huang et al. reported a new supramolecular system based on cationic conjugated polymer/DNA/intercalating dyes assembly as a two-step FRET sequence to enable multiple logic gates [74] (see Fig. 6b). These multiple logic gates operating in parallel were simulated by the pH-induced conformational change of i-motif DNA and the two-step FRET process in this assembly. This logic system, which does not need any chemical modification or oligonucleotide labeling, offers the inherent advantages such as easy operation, multifunctionality, cost efficiency and reversibility. They suggested that this new strategy also gives rise to a new method for label-free detection of conformational conversion of DNA i-motif structure by working in a simple “mix-and-detect” manner. Ma et al. also developed a label-free oligonucleotide-based “OR” logic gate exploiting the target-induced structural transitions of i-motif or G-quadruplex [75]. The oligonucleotide-based label-free “OR” logic gate using i-motif and G-quadruplex showed a significant emission response in the presence of K+ and/or H+, due to the strong interaction of crystal violet to the G-quadruplex and i-motif DNAs, respectively. On the other hand, Sengupta et al. investigated whether the base arrangement in particular secondary structures of DNA or non-B DNA can affect fluorescent silver clusters [76, 77]. Their previous study showed that DNA directs and stabilizes particular types of silver clusters via base-specific interactions [76]. In addition, they showed that two i-motif forming oligonucleotides, (dTA2C4)4 and (dC4A2)3C4, coordinate red and green emissive species, and these fluorescent species are favored in slightly acidic and basic solutions, respectively. The red emissive species has a global structure and a pH sensitivity that is consistent with an i-motif matrix for the cluster. The green emissive species is favored at higher pH where the DNA template alone is unfolded, yet the cluster–DNA conjugate is structurally similar to the folded i-motif DNA. Consequently, they suggest that protons stabilize the DNA matrix for the red species while the clusters promote folding around the green species, indicating that polymorphic forms of DNA can serve as reaction templates for the synthesis of novel fluorescent nanomaterials.

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Figure 6. (a) Illustration of the detection strategy for the pH-induced conversion between i-motif and random coil of ssDNA using the PMNT. This figure is reproduced with permission from Ref. [73]. Copyright 2012 Elsevier B.V. (b) Schematic representation of the molecular basis of INH and NINH logic operations and the combinatorial logic scheme. This figure is reproduced with permission from Ref. [74]. Copyright 2012 the Royal Society of Chemistry.

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Heretofore, the performance of DNA-based devices has been mainly limited to in vitro applications as stated above. Recently, to map the spatial and temporal pH changes associated with endosome maturation in living cells using FRET technique, Krishnan group developed i-motif-based nanomachine (I-switch), consisting of two DNA duplexes connected to each other by a flexible hinge and bearing cytosine-rich single-stranded overhangs at the duplex termini [13] (see Fig. 7a). They showed that this FRET-based I-switch triggered by the protonation operate autonomously inside living cells and can be used as an intelligent pH sensor to track spatiotemporal pH changes associated with endosome maturation. Furthermore, this I-switch was applied to living organisms [14] (see Fig. 7b). As a result, Krishnan group found the existence of previously predicted cell-surface receptors and confirmed that their involvement in uptake of DNA nanostructures in the worm. As demonstrated by Krishnan group, I-switch as a FRET-based pH sensor has several advantages compared with many other pH sensors; that is, this system is nontoxic and can incorporate any appropriate FRET pair to cover wide wavelength, whereas many other pH sensors are limited by fixed wavelengths. These studies suggest that the great potential of DNA scaffolds responsive to complex triggers in sensing, diagnostics and targeted therapies in living cells. However, the time response of I-switch is relatively slow compared with that of the widely used pH sensors, although its response time of 1–2 min can well report the spatial and temporal pH changes associated with biological processes that occur on rather longer timescales.

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Figure 7. (a, Left) Schematic of the working principle of the I-switch in the ‘open’ state (low FRET) at high pH and in the ‘closed’ state (high FRET) at low pH. The I-switch consists of three oligonucleotides O1, O2 and O3, where O1 and O2 are hybridized onto sites adjacent to O3, leaving a one-base gap as shown in Fig. 1a. O1 and O2 have single-stranded cytosine-rich overhangs designed such that each overhang forms one-half of a bimolecular i-motif. (a, Right) Pseudocolor D/A map of hemocytes pulsed with I-switch (Alexa-488/647) at the indicated chase times. Scale bar: 5 μm. These figures are reproduced with permission from Ref. [13]. Copyright 2012 Nature publishing group. (b, Left) Probing the functionality of a DNA nanomachine in coelomocytes of C. elegans. (b, Right) Representative pseudocolor D/A images of IA488/A647 labeled coelomocytes in wild-type hermaphrodites at indicated times. Scale bar, 5 μm. These figures are reproduced with permission from Ref. [14]. Copyright 2012 Nature publishing group.

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To improve the operation speed of the DNA-based nanoswitch, Yang et al. reported the electrical actuation of i-motif DNA molecular device in a rapid and reliable manner with a microfabricated chip using water electrolysis and fluorescence quenching [78] (see Fig. 8). In this study, they used the three-electrode system containing Ir, IrO2 and Ag electrodes deposited in designed shapes and positions on the SiO2 surface to rapidly change and maintain the solution pH at arbitrary value by water electrolysis. As a result, they revealed that the conformation of the fluorescent-labeled i-motif DNA can be electrically switched within seconds, resulting in the significant change in the fluorescence intensity. Furthermore, this system can be switched without obvious decay of the fluorescence amplitudes for at least 30 cycles. These results indicate that this DNA switch is rapid in response and fairly robust. Therefore, this electrically driven method should lead to promote its application in the field of nano-biotechnology.

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Figure 8. (a) Principle for an electrically actuated i-motif-based DNA switch integrated in a microfabricated pH-stat electrochemical chip incorporating three electrodes. (b) Electrically driven DNA switch visualized by fluorescent intensity: Fluorescent images of the reaction region after applying different potentials between R.E. and W.E. for 5 min, each. These figures are reproduced with permission from Ref. [78]. Copyright 2012 American Chemical Society.

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Conclusion and outlook

  1. Top of page
  2. Abstract
  3. Introduction
  4. FRET and fluorescence quenching
  5. Structure and conformational dynamics of i-motif
  6. Visualization of reversible conformational switching of i-motif DNA and its application
  7. Conclusion and outlook
  8. Acknowledgements
  9. References
  10. Biographies

In the Orient, there is the adage: “A picture is worth a thousand words”. This means that large amounts of data can be replaced by just a single image. This adage can be applied to various fields including economy, science, etc. In science, thanks to recent advances in optical imaging and biomechanical techniques, fluorescence techniques such as FRET and fluorescence quenching have been greatly used to study and visualize the dynamic behavior of biomolecules in basic biological, biochemical and biomedical phenomena occurring in vitro and in vivo. Especially, single-molecule studies using fluorescence are providing a lot of information on the conformational dynamics of biomolecules at the level of an individual molecule as well as the heterogeneity in the conformational dynamics observed between at the single-molecule level and in the bulk phase. Furthermore, the visualization of the conformational change in biomolecules using FRET and fluorescence quenching method has been extensively performed for applying in the nano-biotechnology.

Recent trend in nano-biotechnology is moving from simple in vitro solution-based sensing to intracellular sensing for imaging in a living organism. Especially, the DNA-based nanodevice using fluorescence techniques has been intensively developed because of its excellent biocompatibility. Recently, non-B DNA as well as DNA (or B-DNA) has been received considerable attention from many scientists because of its genetic importance as well as its outstanding feature as an excellent material for building artificial nanostructures in nanotechnology. Thus, the detailed information on the conformational dynamics and the biological functions of non-B DNA and DNA in vitro and in vivo is necessary for applying in nano-biotechnology. Although the biological function and detailed conformational dynamics of non-B DNAs have not been clearly revealed yet, various spectroscopic techniques with a temporal and spatial resolution, especially single-molecule spectroscopy, should lead to significant advances in understanding the conformational dynamics and the biological functions of non-B DNAs in vitro and in vivo. With the improvement in sensitivity and specificity of fluorescent probes, the contribution of non-B DNA including i-motif in the nanotechnology as well as bioengineering field is like to increase.

Acknowledgements

  1. Top of page
  2. Abstract
  3. Introduction
  4. FRET and fluorescence quenching
  5. Structure and conformational dynamics of i-motif
  6. Visualization of reversible conformational switching of i-motif DNA and its application
  7. Conclusion and outlook
  8. Acknowledgements
  9. References
  10. Biographies

This work has been partly supported by a Grant-in-Aid for Scientific Research (projects 22245022, 24550188 and others) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japanese Government. T.M. thanks the World Class University program funded by the Ministry of Education, Science and Technology through the National Research Foundation of Korea (R31-2011-000-10035-0) for the support.

References

  1. Top of page
  2. Abstract
  3. Introduction
  4. FRET and fluorescence quenching
  5. Structure and conformational dynamics of i-motif
  6. Visualization of reversible conformational switching of i-motif DNA and its application
  7. Conclusion and outlook
  8. Acknowledgements
  9. References
  10. Biographies

Biographies

  1. Top of page
  2. Abstract
  3. Introduction
  4. FRET and fluorescence quenching
  5. Structure and conformational dynamics of i-motif
  6. Visualization of reversible conformational switching of i-motif DNA and its application
  7. Conclusion and outlook
  8. Acknowledgements
  9. References
  10. Biographies
  • Jungkweon Choi received his BS and MS in Chungnam National University in 1992 and 1998, respectively. He received PhD in Chemistry from Kyoto University in 2003. He worked as a research professor in KAIST, Korea until 2009 and then he is working as a special appointed assistant professor in the Institute of Scientific and Industrial Research (SANKEN), Osaka University, Japan.

  • Tetsuro Majima received his BS, MS, and PhD in 1975, 1977, and 1980, respectively. He worked as a research associate in the University of Texas at Dallas for 2 years (1980–1982), and worked as a scientist in the Institute of Physical and Chemical Research (RIKEN, Japan) for 12 years (1982–1994). In 1994 he became an associate professor in the Institute of Scientific and Industrial Research (SANKEN), Osaka University. He was promoted to a full professor in 1997.