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Abstract
Among five nucleobases, adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U), uracil is a key distinctive constituent existing only in ribonucleic acid (RNA). RNA shares the common A, G, and C with deoxyribonucleic acid (DNA) made of A-T, G-C hydrogen bonding. We explored a new attempt to combine uracil (U) with DNA, successfully realizing U-doped DNA thin solid films for the first time. Impacts of uracil on optical properties of the films were thoroughly investigated. The method was based on optimal spin-coating of an aqueous solution of DNA and uracil over silicon or silica substrates. Optical absorption of both aqueous solution and U-doped DNA thin solid films was characterized in a wide spectral range covering UV-visible-IR. Immobilization of uracil within DNA thin solid films was experimentally confirmed by FTIR spectroscopy studies. By using an ellipsometer, we measured the refractive indices of the films and discovered that U-doping was a very effective means to control optical dispersion DNA thin solid film. We further investigated thermo-optic behavior to find impacts of U-doping in DNA films. Detailed thin film processes and optical characterizations are discussed.
© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
1. Introduction
Bio-photonics materials are being incessantly investigated for their high potential not only in biomedical detection, monitoring, and therapeutics but also in new applications in physical sciences [1–4]. Among these materials, deoxyribose nucleic acid (DNA) thin films have recently received intense attention in optoelectronics applications including optical gain media in the visible [5,6], electron-blocking layers in organic light-emitting diodes (OLED) [7,8], nonlinear saturable absorbers for femtosecond pulse generation [9], cladding layers for polymeric electro-optic waveguide modulators [10], functional layers in thin-film transistors [11], and optical-radiation sensors [12,13], to name a few. As a host material, DNA thin solid films also provide a stable structure which is highly amenable to the binding of small organic molecules by a combination of three processes: intercalation, groove binding, and ionic bonding to allow functionalizing dopants embedded in DNA solids [14,15]. Most of the previous reports in DNA thin solid films have focused on chemical complexes consisting of DNA and a surfactant, most frequently cetyltrimethylammonium (CTMA), which are soluble in organic solvents facilitating conventional spin-coating processes [16–18]. However, the amounts of both CTMA and hydroxyl bound in the DNA-CTMA complexes have not been precisely controlled and additional refinement process had to follow to secure stable and reliable optical properties [19,20]. The authors’ group recently has succeeded in developing a surfactant-free DNA thin film process based on aqueous solutions [21,22] by optimizing the substrate surface preparation and the spin coating process. Despite high potentials in precise optical properties control of DNA films, these prior reports have required additional chemicals such as organic fluorescent substance [21] and NaOH [22]. These chemicals were very different from DNA constituents and therefore the long-term stability of the structure might be limited. In order to further pursue all-DNA photonic devices fully utilizing the inherently biocompatible nature of DNA, development of systematic, precise, and repeatable control of the optical dispersion in DNA thin solid film is still imperative.
In this study, we attempted a very different avenue that has not been explored by focusing on the nucleobases that constitute ribonucleic acid (RNA). Among five nucleobases, adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U), A, G, and C constitute both RNA and DNA, while U exists only in RNA [23,24] and T only in DNA [25,26]. See Fig. 1(a). It is a generally accepted postulate that replacement of U in RNA by T was developed as an evolutionary process in the molecular level, which initiated a successful transition from RNA to DNA to further improve the stability and efficiency of replication process [27,28].
Fig. 1. Schematic diagram of controlling the optical dispersion of pristine DNA thin film by uracil doping. (a) Four nucleobases consisting of DNA (Adenine, Cytosine, Guanine, Thymine) and four nucleobases consisting of RNA (Adenine, Cytosine, Guanine, Uracil). (b) A mixture of DNA and uracil in aqueous solution and thin film deposition by spin coating process. (c) Optical dispersion controlling of DNA thin film and solution by varying uracil concentration.
Schematic diagram to explain the principle of this study is summarized in Figs. 1(b) and 1(c). Nucleobases share the common Benzen ring structures and their optical properties in the aqueous solutions are known to be very similar [29–31]. Against commonsense that U belongs to only RNA, we explored a new attempt to combine U with DNA in the aqueous solution and successfully realized U-doped DNA thin solid film, for the first time to the best knowledge of the authors. We developed an optimal spin-coating process of an aqueous solution of DNA and U directly over silicon or silica substrate to immobilize U inside DNA solid film as schematically shown in Fig. 1(b). By doping U into DNA thin solid film, we observed significant changes in optical absorption especially in the UV region, which resulted in an efficient and linear refractive increase in the film as schematically shown in Fig. 1(c). Thermo-optic coefficient dn/dT was also found to be systematically controlled by doping U in the DNA film. Detailed experimental observations are discussed in the following sections.
2. Optimization of spin-coating for U-doped DNA film fabrication
We used salmon testis DNA powder purchased from Ogata Research Laboratories Ltd in Japan, which has been widely used in DNA thin solid film fabrication [20,32]. And we used uracil powder from sigma Aldrich, which has been also used in prior studies [33,34]. Uracil powder was mixed with deionized water in vial, and the solution was heated at 43 °C in an oven to fully dissolve the uracil [35,36]. In order to prepare DNA-uracil aqueous solution, we further mix DNA aqueous solution with uracil aqueous solution with various concentrations. The DNA concentration was fixed at 0.37 wt% and the uracil concentration was varied from 0.1 to 2.4 mM, which was fully dissolved in the water [37,38]. We used these DNA-uracil solutions as the precursor of DNA thin sold films in order to immobilize uracil molecule within DNA thin solid films. The DNA-uracil aqueous solution precursors were then spin-coated on Si and silica substrates at 20 °C in a similar manner to the previous DNA thin film fabrication processes [21,22,32]. The processes are schematically illustrated in Fig. 2. Key issues in optimal spin-coating were; 1) oxygen plasma treatment of substrate surface for efficient wetting of precursors, 2) viscosity control of the precursor solution for uniform thin-film formation, 3) spinning rate and post-drying conditions for solidifying thin films.
Fig. 2. DNA-uracil thin solid film fabrication processes. A. spin coating process: (a) DNA aqueous solution and uracil aqueous solution preparation. (b) mixing DNA with uracil aqueous solutions to make a homogeneous solution. (c) O2 plasma treatment on Si and silica substrates to make hydrophilic surfaces. (d) Dispensing aqueous solution precursor on the substrate. (e) spinning and solidification by water evaporation. (f) ∼50 nm film on Si and ∼110 nm film on silica substrates. B. drop-casting process: (g) dropping aqueous solution on a petri dish. (h) drying and solidification by water evaporation. (i) peeling off a freestanding film with the thickness of a few µm.
Oxygen plasma treated Si substrate (2cm × 2 cm) and silica substrate (2 cm × 2 cm) were used after the following preparation steps: ultrasonic cleaning in deionized water, 5 minutes in acetone, 5 minutes in isopropyl alcohol. The intensity and duration of the oxygen plasma were optimized to make hydrophilic surfaces for spin-coating of DNA-uracil solutions. The DNA-uracil solution was then dispensed over the prepared substrate, which was then spun at 850 ∼ 900 rpm using a commercial spin-coater (ACE-200) for 5 minutes for water evaporation. For additional residual water evaporation, these DNA-uracil thin films were vacuum dried at 20 °C in a vacuum oven for 24 hours to obtain uniform thin solid films. We controlled the film thickness of ∼50 nm on Si substrates for ellipsometric measurements of refractive indices and of ∼110 nm on silica substrates for UV-visible-IR absorbance measurements. For thicker films in the µm range, we applied the drop-casting method by dispensing a certain volume of the DNA-uracil aqueous solution onto a petri dish. The sample was then dried at 30 °C in an oven for 24 hours to slowly evaporate water contents avoiding bubbles. The freestanding film was then peeled off from the petri dish and used in FTIR measurements to investigate molecular structural change of solid DNA due to uracil doping.
3. Results and discussion
3.1 UV-visible-IR absorption spectra of DNA-uracil aqueous solution
In order to investigate absorption properties, we used a commercial UV-visible-IR spectrometer (V-650, JASCO Corporation) and the uracil aqueous solution without DNA was investigated as a reference. The solution was contained in a 1 mm path length quartz cuvette. Uracil concentration was varied from 0.1 to 2.4 mM and the corresponding UV-visible-near IR absorbance spectra are summarized in Fig. 3. Nucleobases have been known to strongly absorb the UV light due to the π-π*transition of the pyrimidine and purine ring system [39,40] and the characteristic absorption peak of uracil in the aqueous solution occurs at the wavelength of λ = 258 ∼259 nm [31,41]. We observed that absorbance of the peak at λ = 258 nm was directly proportional to the concentration uracil in aqueous solution. The molar extinction coefficient of uracil at λ = 258 nm of the prepared solutions was obtained by using Beer-Lambert law and the value was 8334 M−1cm−1, which is consistent with prior reports [42,43].
Fig. 3. (a) UV-visible-near IR absorption spectra of uracil aqueous solution without DNA for various uracil concentrations. (b) absorbance in the UV region.
As a next step, we prepared DNA-uracil solution with the DNA concentration of 0.02 wt % keeping the uracil concentration the same from 0.1 to 2.4 mM. The absorption spectra of the solutions are summarized in Fig. 4. Here the DNA concentration was intentionally reduced to keep the solution clear from scattering loss. Consistent with prior reports, the characteristic absorption peaks of salmon testis DNA was observed in the UV near λ = 258 nm [44,45], which overlapped with the absorption peak of uracil. As we increased the uracil concentration, the absorbance of the DNA-uracil solution increased in a linear manner without any spectral shifts. We also calculated the molar extinction coefficient of the DNA-uracil solution at λ = 258 nm and found the value of the DNA-uracil solution was almost identical to that of the uracil solution without DNA as shown in the linear plot in Fig. 5. Considering the nearly invariant molar extinction coefficient and almost zero spectral shift in the DNA-uracil solution in comparison to the uracil solution, it is believed that the DNA and the uracil were nearly non-interacting in the aqueous solutions. In the following section, we discussed the absorption spectra of thin solid films, which showed quite a different behavior compared with the solution cases.
Fig. 4. (a) UV-visible-near IR absorption spectra of DNA-uracil aqueous solutions with various uracil concentrations. (b) absorbance in the UV region.
Fig. 5. The absorbance of DNA-uracil aqueous solution and uracil aqueous solution without DNA at λ=258 nm as a function of the uracil concentration. The slope corresponds to the molar extinction coefficient of each solution.
3.2 UV-visible absorption spectra of U-doped DNA thin solid films
After confirming that DNA and uracil were non-interacting in the aqueous solutions as summarized in Figs. 3–5, we fabricated thin solid films using the DNA-uracil solutions as the precursors. We used a 0.8 wt % aqueous solution of DNA with various uracil concentrations 0 to 2.4 mM in the solution. The solution precursor was dispensed onto an O2-plasma-treated silica substrate and spun at 900 rpm for 5 minutes, which was followed by drying procedures as described in section 2. The final film had a uniform thickness of 110∼116 nm. We measured UV-visible-near IR absorption spectra of the DNA-uracil thin solid films using a spectrophotometer (Cary5000, Agilent) and the results are summarized in Fig. 6. We observed that the films were transparent in the visible-near IR region from 400 to 800 nm range for all of the uracil concentrations within the experimental measurement error. The UV absorption peaks in the spectral range of 200-300 nm grew with the uracil concentration, which was consistent with the observation in the precursor solutions shown in Fig. 4. It was noteworthy that the absorption peak position red-shifted to λ = 261 nm in the thin solid films in comparison to the peak at λ=258 nm in the aqueous precursors in Fig. 4. As the uracil concentration increased, the spectral position of this peak did not change within the experimental error but only the absorbance value increased as shown in Fig. 6(b).
Fig. 6. (a) UV-visible-near IR absorption spectra of DNA-uracil thin solid films with various uracil concentrations. (b) UV absorption spectra near the peak at λ=261 nm.
From the absorbance measurements, we plotted the absorbance of the UV peak at λ=261 nm as a function of the uracil concentration in the precursor solution similar to Fig. 5 in the aqueous solution. The change of absorbance by the uracil in the precursor was linear within the experimental errors and the slope was 0.0394/mM, which was significantly decreased by a factor of ∼20 in comparison to aqueous precursors in Fig. 5. However, this value might not fully represent the concentration of uracil in thin solid films. The exact amount of uracil in the DNA thin solid film was not easy to detect because the characteristic absorption peaks of uracil significantly overlap with those of DNA, which was not resolved in commercial spectrometers and the authors are investigating methods to identify the uracil concentration in the solid films. Nonetheless, it is a good qualitative comparison to recognize the difference between thin solid films in Fig. 7 and their aqueous precursors in Fig. 5. It is likely that the concentration of uracil relative to DNA was lower in the solid films than in the aqueous precursors.
Fig. 7. Absorbance at the peak λ=261 nm in the U-doped DNA thin solid films as a function of the uracil concentration in the precursor solution.
3.3 FTIR analyses of U-doped DNA free-standing films
We further investigated the molecular structure of U-doped DNA thin solid film using Fourier transform infrared (FTIR) spectroscopy in the spectral range from 700 to 4000 cm−1 and the results are summarized in Fig. 8. Here, we used a 0.37 wt % DNA aqueous solution with various uracil concentrations as a solution precursor. The solution was dropped onto a petri dish and dried in an oven at 30 °C to fully evaporate water in the film. Freestanding DNA films with a thickness of 1∼5 µm were obtained as described in section 2 and Fig. 2.
Fig. 8. (a) FTIR absorption spectra of U-doped DNA freestanding solid films for various uracil concentrations in the aqueous precursor. (b) Spectra shift of the thymine vibration peak as a function of uracil concentration in the aqueous precursor.
Figure 8(a) shows FTIR absorption spectra of the U-doped DNA freestanding solid films for various uracil concentrations in the solution precursors. The FTIR absorption spectra of DNA can be categorized into three regions: 3600-3000 cm−1 for the OH stretching, 1800-1300 cm−1 for nucleobase vibrations, and 1250-700 cm−1 for the sugar and phosphate backbone groups [46]. In a pristine DNA film without U-doping, the thymine peak was identified near 1656 cm−1 [47,48] as shown in the top graph of Fig. 8(a). We observed that the thymine peak significantly shifted to a higher wavenumber from 1656 to 1670 cm−1 as the uracil in the aqueous precursor increased. Some of the spectra are shown in Fig. 8(a) and the spectral position thymine peak was plotted as a function of the uracil concentration in the aqueous solution in Fig. 8(b). In contrast, the peak corresponding to deoxyribose phosphate in the DNA backbone shifted to a lower wavenumber from 833 to 831 cm−1. In previous studies in doping small molecules to DNA thin films [21,46], some of dopants have shown spectral shifts in the vibrational modes of nucleobases, which have been attributed to the intercalation of the dopant within the corresponding base-pair in DNA [49,50]. In other reports, spectral shifts in the deoxyribose phosphate have been attributed to the interaction between the dopant and the DNA backbone by electrostatic attractions [51,52]. Judging from our observations that showed a significant spectral shift in the thymine peak caused by U-doping, it is highly likely that uracil could be bound by the intercalation to A-T base pairs. While a discernible shift in deoxyribose phosphate would indicate some of the uracil molecules did interact with the phosphate backbone of DNA in thin solid film. It has been reported that the absorption peak of uracil in RNA was located near ∼ 1657 cm−1 [53,54] which is very similar to that of thymine in DNA thin solid films.
It is generally accepted that an absorption peak shift in the FITR spectra is correlated with a structural modification in the corresponding molecule [55,56]. Therefore, the blue-shift of thymine peak induced by uracil doping strongly indicates that the immobilized uracil in the thin solid film was selectively interacting with thymine in DNA to alter its IR vibrational modes and molecular structure. This is consistent with the postulate that replacement of uracil in RNA by thymine was developed as an evolutionary process in the molecular level, which initiated a successful transition from RNA to DNA to further improve the stability and efficiency of replication process [27].
When the uracil concentration increased further beyond 2.55 mM in the precursor solution, the thymine absorption peak did not blue-shift any more but slightly red-shifted. This could be due to saturation of the uracil concentration within DNA thin solid film. The spectra shifts of thymine in FTIR absorption due to the uracil doping might be an informative tool to quantify the actual concentration of the immobilized uracil within DNA thin solid film, which is being pursued by the authors.
3.4 Ellipsometry to measure optical properties
Before we investigated the refractive index of U-doped DNA films, we analyzed their thickness variation for various uracil concentrations in the precursor solutions. If the film thickness significantly varies with the uracil concentration, it could affect the refractive index calculations [21,57]. A SiO2 layer with the thickness of 2 nm was prepared on Si substrate on which U-doped DNA films were deposited using the spin-coating process as described in section 2. The thickness of the films was measured by spectroscopic Ellipsometer [Woollam, alpha-SE]. For the uracil concentration range from 0 to 2.4 mM, the average thickness of U-doped DNA varied less than 2.4 nm for the same DNA concentration of 0.37 wt%, as summarized in Table 1. We further optimized the spinning speed in the range from 850 to 900 rpm to compensate the thickness variation due to the uracil concentration and we successfully obtained a nearly same film thickness of 48 ± 1nm in the U-doped DNA thin solid films to ensure accurate refractive index measurements. For U-doped DNA thin solid films, the refractive indices were measured using a Woollam ellipsometry system and the results are summarized in Fig. 9 in the spectral range from 380 to 800 nm. Here, DNA concentration was fixed at 0.37 wt % and we varied the uracil concentration up to 2.4 mM in the aqueous solution. In the optical dispersion calculation we used the isotropic Cauchy model [4,9] because there were no resonant absorption bands in the spectral range of interests as shown in Fig. 6. Firstly, we confirmed our measurements for pristine DNA films without uracil, n = 1.534 at λ = 633 nm, were consistent with prior reports [9,22,32], which ensures the validity of our experiments. In Fig. 9(a), the refractive index as a function of the wavelength is plotted for U-doped DNA films with various uracil concentrations in the precursor solutions. The upward shift of the optical dispersion curve in the whole spectral range of 380-800 nm was observed as the uracil concentration increased from 0, 0.8, 1.6, and 2.4 mM in the precursor solutions. We plotted the refractive index change as a function of uracil concentration in Fig. 9(b), which showed a linear dependence in a wide spectral range. The refractive index difference between the pristine DNA film and the film doped with 2.4 mM uracil concentration was as large as Δn = 0.0118 at λ=633 nm and ∼ 0.0201 at λ=400 nm as summarized in Table 2. This wavelength-dependent Δn with a larger index difference in the shorter wavelength has not been observed in previous reports [20–22] and could be attributed to uracil doping. Higher refractive index by U-doping in DNA film was consistent with the increase in the UV absorption as in Fig. 6 since the refractive index would increase with a higher absorption by Kramers-Kronig relation [58]. Thin films made by sputtering of nucleobase powders have shown refractive indices that differed from that of DNA [59], and as we confirmed experimentally the role of uracil, other nucleobases (C,G,A and T) would serve as a dopant to efficiently control the optical dispersion of DNA films, which is being pursued by the authors.
Fig. 9. (a) The refractive indices of DNA thin solid film in the spectral range from 380 nm to 800 nm for various uracil concentration in the precursor solution. (b) The refractive indices of DNA thin solid film as a function of uracil concentration in the precursor solutions.
Table 1. The average thickness of DNA thin solid films made from precursor solutions before the optimization of spin-coating process. (DNA concentration = 0.37 wt%)
Table 2. Refractive index difference between a pristine DNA film and a film doped with uracil 2.4 mM in the precursor solution.
3.5 Investigation of thermo-optic coefficients
Control of the refractive index by the external temperature, categorized as the thermo-optic effect, is a fundamental physical mechanism to add novel functionalities in photonic devices providing spectral tuning, switching, and sensing applications [13,60,61]. In this study we measured the changes in both the refractive index and the thickness of U-doped DNA films by installing a Peltier temperature control unit inside Woollam ellipsometry system. Here, we used aqueous solution precursors of 0.35 wt % DNA and various uracil concentrations up to 2.8 mM, which were dispensed onto Si substrates and spun at 900 rpm to prepare U-doped DNA thin films. In the room temperature, the thickness of pristine DNA film was ∼29 nm and it increased to 32 nm by doping uracil with the 2.8 mM in the precursor solution. The results are summarized in Fig. 10 and Table 3 for the temperature range from 40 to 80 °C and the heating/Cooling rate was about ± 10 °C/minute. We observed a linear and monotonic decrease of the refractive index of U-doped DNA films as the temperature increased, which is consistent to prior reports on a negative thermo-optic coefficient, dn/dT, of DNA thin films [21,22]. We also observed a monotonic decrease of the film thickness as the temperature increased and after the 1st cycle, the film thickness decreased slightly due to the water evaporation within U-doped DNA films, which is also consistent with prior reports [22,57]. We summarized the thermo-optic coefficient, dn/dT, of U-doped DNA thin films in Table 3. we found that |dn/dT| decreased by U-doping. See Table 3. The increase in the refractive index by uracil doping and subsequent decrease in the absolute magnitude of thermo-optics coefficient |dn/dT| could be attributed to net density increases by uracil immobilization in thin solid films and intrinsic thermo optical properties of uracil ingredients. Note that the magnitude of dn/dT of these U-doped DNA thin films is still significantly larger than those of conventional thermo-optic polymers [62] and a systematic control of dn/dT value by uracil doping could be a definite advantage in various device application.
Fig. 10. Thermally-induced changes in the refractive index and the film thickness of U-doped DNA thin solid films (a) the refractive index at λ = 633 nm in the 1st temperature cycle. (b) the refractive index at λ = 633 nm in the 2nd cycle. (c) the refractive index at λ = 533 nm in the 1st temperature cycle. (d) the refractive index at λ = 533 nm in the 2nd cycle. (e) the film thickness in the 1st cycle, and (f) the film thickness in the 2nd cycle.
Table 3. Thermo-optic coefficient (10−4 °C−1 ) of U-doped DNA thin solid film for various U-concentrations in the precursor solutions.
4. Conclusion
We developed a new method to control the optical dispersion and thermo-optics properties of surfactant-free DNA thin films by doping uracil (U) which is a distinctive constituent of RNA. In contrast to the common belief that uracil would not be compatible for DNA doping, we successfully immobilized uracil within DNA thin solid film by optimizing the spin-coating process and an aqueous solution precursor. In aqueous solution, uracil was found to be almost non-interacting with DNA, resulting in the nearly invariant molar extinction coefficient of uracil at λ = 258 nm. In the surfactant-free DNA thin solid films, uracil was successfully immobilized to effectively increase the refractive index in a very linear manner as large as Δn∼ 0.02 in the visible-near IR region. The FTIR spectra of uracil doped DNA films showed the thymine absorption peak shift and the deoxyribose phosphate vibrational mode, which strongly implicated that uracil was bound to A-T base-pairs by the intercalation as well as the electrostatic binding to phosphate backbone of DNA molecules. We also found that thermo-optic coefficients dn/dT of DNA thin solid films were systematically controlled in the temperature range 40 to 80 °C by the uracil doping, which can find various applications in biocompatible optical sensing and switching. We experimentally confirmed a new method to control the optical properties of DNA thin solid films by doping them with highly compatible nucleobases.
Funding
National Research Foundation of Korea (2019R1A2C2011293).
Disclosures
The authors declare no conflicts of interest.
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