Optical decomposition of DNA gel and modification of object mobility on micrometre scale

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Abstract

DNA gels can be engineered to exhibit specific properties through the choice of DNA sequences and modification with dye molecules, and can therefore be useful in biomedical applications such as the detection of biomolecules. State transitions of DNA gels on the micrometre scale can generate a viscosity gradient, which can be used to modify the mobility of micrometre-sized objects. In this paper, we propose a method for changing the viscosity of DNA gels using optical decomposition. The use of light allows for decomposition on the micrometre scale, which can be used to achieve patterned viscosity changes within DNA gels. Decomposition was induced by thermal energy released through non-radiative relaxation of excited quenchers. We demonstrated the decomposition of DNA gels in response to irradiation patterns on the micrometre scale. In addition, as a result of changes in DNA gel viscosity due to decomposition, the mobility of polystyrene beads was shown to increase. This technique could provide a new optical approach for controlling the mobility of micrometre-sized objects.

Introduction

The use of purpose designed DNA sequences can allow for the self-assembly of various structures from the nanometre to millimetre scale1,2,3,4,5. DNA gels, which are formed by crosslinking numerous DNA motifs6,7,8, can transition to the sol state in response to temperature9, pH10 or the presence of specific molecules11, and are biocompatible and useful in bioesensing. For example, the state change of DNA gels can be applied to the detection of biomolecules such as cocaine12 and thrombin13. In addition, live cells can be trapped selectively by cloaking circulating tumour cells with DNA gels in response to the presence of epithelial cell adhesion molecules14. This suggests that DNA gels have significant potential to regulate the mobility of micrometre-scale objects, including cells. However, these functions are based on a passive reaction, and the mobility cannot be modulated dynamically. The control of an object’s motion by changing the viscosity of DNA gels would provide a method for the sorting and arrangement of cells, which are necessary steps in the creation of cellular tissues15. To realise this, patterning by spatially controlling the state transition of DNA gels is required. Previous research in DNA gel patterning includes an ink-jet method using different DNA solutions16 and a patterning method using a substrate coated with DNA initiators17. However, scanning nozzles containing DNA solutions or coating DNA strands on a substrate can result in slow and complicated DNA gel production.

Optical methods provide a promising solution to this problem owing to their features, which include spatial parallelism and controllability. Light irradiation can remotely induce a gel-sol transition18,19,20, swelling, and shrinking21. Moreover, light patterns can be generated and dynamically changed using a spatial light modulator (SLM), which makes rapid processing at the micrometre scale possible. We have already demonstrated optical fabrication of DNA gels in a few seconds by using a photothermal conversion effect of dark quenchers22. This method enables us to control the amount of DNA gel produced and any gel patterning on the basis of the light power distribution on the micrometre scale, which initiates a viscosity increase and leads to reduced mobility. The reverse method of DNA gel decomposition provides a different mode of mobility modulation. The decomposition of DNA gels leads to a reduction of their viscosity and an increase in the mobility of associated objects. For flexible control of object mobility, it is important to realise the spatial decomposition of DNA gels.

In this paper, we propose a method for controlling the mobility of micrometre-sized objects through optical decomposition of DNA gels. The use of light enables the decomposition of the DNA gels on a micrometre scale. Moreover, the local reduction of DNA gel viscosity through irradiation enhances the motion of associated objects. To demonstrate the spatial and temporal shaping of DNA gels, we acquired fluorescence images of DNA gels stained with fluorescent dyes with various irradiation patterns. In addition, the degree of motion of micrometre-sized beads in response to irradiation was measured to verify the modulation of object mobility as a result of decomposition.

Results

Optical decomposition of DNA gels

A schematic diagram of mobility modification as a result of optical decomposition of DNA gels is shown in Fig. 1. The sequences of the individual DNA components are noted in the Materials and Methods section. For optical decomposition, the sticky ends of the L-DNA were modified with quenchers. In the initial state, the DNA gels encapsulate micrometre-sized objects and regulate their mobility. Optical excitation causes quenchers to generate thermal energy through a non-radiative relaxation process23. The energy dissipated from excited quenchers is sufficient to denature 10-bp double-stranded DNA (dsDNA) to two single DNA strands (ssDNAs)24. Thus, the bonds between the Y-DNA and the L-DNA in the DNA gel are cleaved by light excitation, and the DNA gels within the irradiation area are decomposed. The viscosity then decreases owing to the state change of the DNA gel, and the mobility of the micrometre-sized objects is enhanced. After the irradiation, the cleaved sticky ends of Y-DNA bind to ssDNA (Cap-DNA) that prevents rebinding with L-DNA due to the presence of a large amount of Cap-DNA. As a result, the DNA solution maintains its state and viscosity even after the irradiation is stopped. The decomposition ratio depends on the light intensity; therefore the mobility of each object can be modulated according to a light pattern.

First, we created DNA gels in a DNA solution containing all of the DNA components and observed it using a fluorescence microscope. To identify the DNA gel, the DNA solution was stained with a fluorescent dye, DAPI (Dojindo Molecular Technologies, Inc., absorption wavelength: 360 nm, fluorescence wavelength: 460 nm), which selectively binds to dsDNAs. Since DNA gels are constructed from many DNA motifs, their DNA density and the fluorescence that indicates the existence of Y-DNAs and L-DNAs are higher than those in the DNA solution. Figure 2(a) shows a fluorescence image of the DNA solution. A high fluorescence-intensity area was observed in the DNA solution, which shows that DNA gels were formed as anticipated. Next, we investigated the decomposition of DNA gels by light irradiation. Two test tubes of DNA solution containing the same components as in the first experiment were prepared. One test tube was not irradiated, and the other was exposed to excitation light (wavelength: 660 nm, intensity: $$3.0\times {10}^{-1}\,{\rm{W}}/{{\rm{cm}}}^{2}$$) emitted from a laser diode (ML101J27, Mitsubishi Electric) for 1 h. Figure 2(b,c) show fluorescence images of the non-irradiated and irradiated samples, which were dropped onto glass slides, respectively. The variation of fluorescence intensity in the irradiated sample is much less than that in the non-irradiated sample. These results indicate that the DNA gels were decomposed by light irradiation.

Conclusion

We have presented a method for modifying the mobility of a micrometre-sized object by optical decomposition of a DNA gel. Thermal energy from optically excited quenchers in the irradiation area induced the decomposition of DNA gels. We demonstrated the pattering of DNA gels on a micrometre scale using light pattern irradiation. Furthermore, the viscosity decrease due to the optical decomposition of the DNA gels increased the mobility of the PSBs. Spatial viscosity control of DNA gels will enable remote modulation of the motion of micrometre-sized objects using suitable irradiation patterns. Our method provides a new approach for controlling the motion of micrometre-sized objects. It is expected that combining methods for fabricating DNA gels with those for controlling their viscosity will allow the construction of complex cell tissue and analysis of cell motion.

Materials and Methods

DNA sequences used to construct the DNA gels and the sample preparation procedure

The designed DNA components are listed in Table 1. All DNA strands were purchased from TsukubaOligo Service Co. Ltd. The Y-DNA and the L-DNA consisted of three (Y1, Y2, Y3) and two (L1, L2) kinds of DNA strands, respectively. The 5′- end of L1 and of L2 was modified with BlackBerry Quencher 650 (BBQ-650), which is a quencher absorbing light in the wavelength range 550–750 nm. DNA gels were created with these DNA components (with concentrations Y-DNA: 28.6 μM, L-DNA: 28.6 μM, and Cap-DNA: 228.8 μM) in buffer (NaCl: 7.1 mM, H3PO4: 2.2 mM). To create sufficient DNA gels, Y-DNAs and L-DNAs were mixed in two test tubes and the temperature was maintained at 6 °C. After 3 h, Cap-DNAs were added to both samples. Each sample was dropped onto a glass slide and was observed using a fluorescence microscope (BX51WI, Olympus Corp.). To capture the images in Fig. 2, we used a complementary metal-oxide-semiconductor (CMOS) image sensor (C13440-20CU, Hamamatsu Photonics K.K., pixel pitch: 6.5 × 6.5 μm2), an objective lens (UMPlan FI, Olympus Corp., ×10), a dichroic mirror (transmission wavelength: 400 nm-), and two band-pass filters (transmission wavelengths: 330–385 nm for excitation, and 414–452 nm for detection). The fluorescence excitation light source was a halogen lamp.

The optical setup shown in Fig. 3 was constructed by combining with the fluorescence microscope (BX51WI, Olympus Corp.). For observation of the fluorescence of DNA gels, the irradiation light was cut off by using two bandpass filters (transmission wavelength: 414–452 nm), and a shortpass filter (transmission wavelength: 500 nm). The intensity of each light pattern in Fig. 4(a–d) was (a) 570.0, (b) 558.9, (c) 553.0, and (d) 469.2 W/cm2 on the sample plane. These densities are values averaged over the pattern area. To generate the light patterns, a DMD (Discovery 1100, Texas Instruments, pixel pitch: 13.68 μm) was used. The images of the light patterns and the corresponding fluorescence images were captured using objective lenses with magnifications of 40× (156403, Olympus Corp.) and 20× (LWD MSPlan20, Olympus Corp.), respectively. The exposure time was 0.5 s, so that the frame rate for capturing the fluorescence images was 2.0 fps. In this experiment, a sample holder was made from a cover slip, a glass slide, and double-sided tape. The sample was placed in the region surrounded by the double-sided tape and sandwiched between the cover slip and the glass slide. The contrast of each image was adjusted so that the minimum and maximum pixel values of each image were 0 and 255, respectively. The line profiles shown in Fig. 4(i–l) show data sequences smoothed by using a five-point moving average filter, and these intensities were normalised so that the minimum and maximum intensities in each line were 0 and 1.

Fluorescence intensity of DNA solution depending on the binding state of DNA components

To investigate whether the intensity of DAPI increases when Y-DNAs are separated from L-DNAs and bind with Cap-DNAs, we measured the fluorescence intensity of two DNA solutions at different states using a fluorescence spectrophotometer (JASSO corp., FP-6200). We prepared two kinds of samples with different procedures shown in Fig. 6(a,b). The first sample contained Y-DNAs and L-DNAs, the other contained Y-DNAs and Cap-DNAs. After mixing DAPI dyes with each of the samples and keeping the temperature at 6 °C for 3 hours, Cap-DNAs and L-DNAs were added to the individual samples. While Y-DNAs bind with L-DNAs in the DNA solution shown in Fig. 6(a), they bind with Cap-DNAs in the DNA solution shown in Fig. 6(b) because Cap-DNAs prevent Y-DNAs from binding with L-DNAs. Figure 6(c) shows the fluorescence intensity of the DNA solutions measured immediately after the sample preparation. The irradiation wavelength for excitation of DAPI was 360 nm, and the detected fluorescence wavelength was 460 nm. We measured six samples prepared by each procedure, and the intensity values were normalised by the mean value for the DNA solution prepared shown in Fig. 6(a). The fluorescence intensity of the DNA solution containing Y-DNAs binding with L-DNAs was lower than that containing Y-DNAs binding with Cap-DNAs. These results show that fluorescence intensity increases when Y-DNAs in the DNA gels are cleaved from L-DNAs and bind with Cap-DNAs.

Motion analysis of SSD and PSB observation environment in DNA gels

To evaluate the degree of motion, SSD rt at observation time t is defined as

$${r}_{t}=\mathop{\sum }\limits_{i=1}^{t}\,{(x({t}_{i})-x({t}_{i-1}))}^{2},$$
(1)

where ti is the time for the i-th frame in a sequence of images, and $$x({t}_{i})$$ is the position at ti. To detect the position of a PSB from individual images, we used the imfindcircles function of MATLAB and obtained the center of the PSB detected by Hough transformation of the images. The individual images shown in Fig. 5 were captured by using the optical setup shown in Fig. 3. The DNA gels containing PSBs were created by mixing the Y-DNA solution with the PSBs and the L-DNA solution. After 3 h and whilst maintaining the temperature of the DNA solution at 6 °C, the samples were placed on the sample holder and observed at room temperature. Instead of the double-sided tape in the sample holder used in the patterning experiment, we used additional PSBs with a different size (Polysciences, Inc., 17136-5, diameter: 10.0 μm) to create the gap between the glass slide and the cover slip. This gap limited the movement of the PSBs within the observable depth, and thus the position could be measured. The diffusion coefficients in DNA gels under non-irradiated and irradiated conditions were measured from the mean square displacement of beads over 10.5 s. The dynamic viscosities before and after irradiation were obtained from the values of the diffusion coefficients at 10.5 s and 310.0 s. Each value was estimated using the Stokes-Einstein equation26. In the calculation, the temperature of the DNA solution was assumed to be room temperature, 23 °C.

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Acknowledgements

The authors thank the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan for the ‘Program for Leading Graduate School’. This work was supported by JSPS KAKENHI Grant Numbers JP18K19922 and JP16K16408.

Author information

S.S. implemented all of the experiments, analysed the data, and drafted the manuscript. T.N. designed the DNA sequences and coordinated the experiments. Y.O. designed the research and edited the manuscript. J.T. conducted the research. All authors reviewed the manuscript.

Correspondence to Suguru Shimomura.

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Shimomura, S., Nishimura, T., Ogura, Y. et al. Optical decomposition of DNA gel and modification of object mobility on micrometre scale. Sci Rep 9, 19858 (2019). https://doi.org/10.1038/s41598-019-56501-z