1、Small Circular DNA Nanotechnology
Design rules for DNA nanotechnology have been mostly learnt from using linear single stranded (ss) DNAs as the source materials. How about using circular ss-DNA molecules as scaffolds for assembling DNA nanostructures? Over the past decade, we have been working on it and have found out that small circular ss-DNA molecules as scaffolds do have their own assembly rules to build DNA nanostructures. For example, we fabricated two kinds of coupled DAO (cDAO) tiles of cDAO-c64nt and cDAO-c84nt, and assembled their 2D lattices. (1) cDAO-c64nt, shaped as a solid parallelogram, is constructed with a Holliday junction (HJ) at the center and two HJs at both poles of a circular 64 nucleotides (c64nt); similarly, cDAO-c84nt, shaped as a crossed quadrilateral composed of two congruent hollow triangles, is formed with a HJ at the center and four three-way junctions at the triangle corners of a c84nt. Perfect 2D lattices were assembled from cDAO tiles: infinite nanostructures of nanoribbons, nanotubes, and nanospirals, and finite nanostructures. The structural relationship between the visible lattices imaged by AFM and their corresponding invisible secondary and tertiary molecular structures of HJs, inclination angle of hydrogen bonds against the double helical axis, and the tile chirality can be interpreted very well. The topological constraint should be the main parameter to be concerned in construction of DNA motifs and lattices using circular DNA tiles instead of linear ones.
Figure 1. The upper flow diagram represents the evolution from an individual cDAO-64nt motif to its assembly of cDAO-64nt–O, and to the assembly’s AFM image; the lower flow diagram represents the evolution from an individual cDAO-84nt to its assembly of cDAO-84nt–O, and to the assembly’s AFM image.
1. Y. Ma, H. Zheng, C. Wang, Q. Yan, J. Chao, C. Fan, and S.-J. Xiao*, RCA strands as scaffolds to create nanoscale shapes by a few staple strands, J. Am. Chem. Soc., 2013, 135, 8, 2959-2962.
2. H. Zheng, M.-Y. Xiao, Q. Yan, Y.-Z. Ma, S.-J. Xiao, Small circular DNA molecules act as rigid motifs to build DNA nanotubes, J. Am. Chem. Soc. 2014, 136(29), 10194–10197.
3. M. Wang, H. Huang, Z. Zhang, S.-J. Xiao*, 2D DNA lattices constructed from two-tile DAE-O systems possessing circular central strands, Nanoscale, 2016, 8(45), 18870-18875.
4. N. Afshan，M. Ali，M. Wang，M. M. F. A. Baig，S.-J. Xiao*， DNA nanotubes assembled from tensegrity triangle tiles with circular DNA scaffolds, Nanoscale, 2017,18(44), 17181-17185.
5. X. Guo, X.-M. Wang, S. Wei, S.-J. Xiao*，Construction of a holliday junction in small circular DNA molecules for stable motifs and two-dimensional lattices, ChemBioChem, 2018, 19, 1379-1382.
6. M. Ali， N. Afshan， C. Jiang，H. Zheng，S.-J. Xiao*, 2D DNA lattice arrays assembled from DNA dumbbell tiles using poly(A-T)-rich stems, Nanoscale, 2019,11(46), 22216-22221.
2. Soft Materials Functionalization and Patterning of Silicon by Surface Hydrosilylation Chemistry: A New Silicon Revolution?
Silicon, the second most abundant element in the earth's crust, has played and continues to play an important role in our human being's life:
1) Silicon-based semiconductor industry, as a miracle in our human being's history, has revolutionized our life in every aspect. We cannot imagine how we live if we have no computer, mobile phone, washing machine, intelligent transportation system such as airplane, high speed train, automobile, and so on, that are all based on the core technology of silicon chips. The number of the transistors in a CPU chip has been increased by following Moore's law from ~20 in 1960 to ~3 billion in 2013. Every day, most people interact with around tens of devices equipped with silicon chips. Silicon is always around us and works for you and me.
2) Due to the increased awareness of the global energy crisis, solar energy has been recognized in common as an alternative sustainable energy source. Silicon solar cells have become the most important photovoltaic products owing to the sophisticated manufacturing technology and the reliable cell quality.
It seems that the microelectronic silicon technology is mature. However a new technology of covalent grafting soft materials onto silicon surface intrigues the great interest of scientists. Functionalization and patterning of silicon by surface hydrosilylation chemistry are arising. This technology can be utilized for diverse applications such as nanoelectronics, solar cells, and bio-detection.
To record our work on molecular engineering on silicon surface, we first developed the Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR). Using this technology, we easily monitor the quality and performance of molecular monolayers and polymer brushes grown on the silicon surface, the in-situ multiple surface transformations of end functional groups such as hydroxyl and carboxyl groups to target species such as proteins and DNAs. We are working with both surface chemistry and micro- and nano-patterning techniques to develop biochips, molo- and nano-electronics, further solar cells and silicon photonics.
References:
1. DNA microarray fabricated on poly(acrylic acid) brushes-coated porous silicon by in situ rolling circle amplification, Analyst, Cuie Wang, Xue-Mei Jia, Chuan Jiang, Guang-Nan Zhuang, Qin Yan and Shou-Jun Xiao* 2012, 137, 4539
2. Different EDC/NHS Activation Mechanisms between PAA and PMAA Brushes and the Following Amidation Reactions, Langmuir, Cuie Wang, Qin Yan, Hong-Bo Liu, Xiao-Hui Zhou, and Shou-Jun Xiao* 2011, 27 (19), pp 12058–68
3. Fluorescence Enhancement by Surface Plasmon Polaritons on Metallic Nanohole Arrays,Peng-Feng Guo, Shan Wu, Qin-Jun Ren, Jian Lu, Zhanghai Chen, Shou-Jun Xiao*, Yong-Yuan Zhu*, J. Phys. Chem. Lett.2010, 1, 315–318.
4. Gel-pad microarrays templated by patterned porous silicon for dual-mode detection of proteins, Ling Chen, Zeng-Tai Chen, Jing Wang, Shou-Jun Xiao*, Zu-Hong Lu, Zhong-Ze Gu, Lin Kang, Jian Chen, Pei-Heng Wu, Yan-Chun Tang, and Jian-Ning Liu*, Lab on a Chip, 2009, 9, 756–760
3. Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR):A Powerful Tool for Self-Assembled Surface Chemistry on Infrared Transparent Substrates
Infrared spectral characterization of organic nano-films on silicon surfaces provides much information such as molecular structures and orientations, chemical conversions, surface components and densities. Over years, the mostly recognized infrared method for sensitive detection of silicon-supported organic nano-films is the multiple internal reflection (MIR)1, in which the nano-film is fabricated on an attenuated total reflection (ATR) silicon crystal with 45 degree bevel cuts at both ends, and the sensitivity is increased by multiple internal reflections. However, a qualified MIR-IR spectrum is limited to delicate fabrications of thick silicon chips over a thickness of several millimeters. The configuration of the infrared multiple reflections had been suggested by R.G. Greenler2 to enhance the signal of untrathin organic films coated on gold. However until we re-examined the multiple transmission-reflection infrared spectroscopy (MTR-IR) (Figure 1) and found its power in characterization of covalently bound organic monolayers, polymer brushes, and of the following in-situ surface chemistries on thin silicon chips (0.2 ~ 2.0 mm thick silicon chips), it has not yet been developed and used widely. With MTR-IR, we illustrated many delicate details of surface functionalities which have rarely been reported hitherto, such as the triazole ring υ(H-C=) at 3139 cm-1 produced by click reactions, υ(C-Cl) at 660 cm-1, υ(H-C≡C) at 3283 cm-1, υ(C≡C) at 2115 cm-1, and asymmetric and symmetric stretching bands of amide υ(NH) at 3441 and 3345 cm-1 from molecular monolayers or polymer brushes. These delicate details clarify some unresolved chemical reaction mechanisms. Further the molecular orientation organized on the substrate surface can be demonstrated by measuring the dichroic ratios3,4 of both p- and s-polarized spectra quantitatively.
Figure 1. Scheme of IR measurements for detection and orientation analysis of monolayers on silicon surface. GMBR5 is a combination of external reflection and transmission by placing a gold mirror on one side of a silicon chip. To increase the sensitivity, MTR was established by inserting a silicon chip between two parallel gold mirrors. Three types of surface modifications were performed as examples: hydrosilylation on Si(111)-H; silane SAMs on SiO2/Si and phosphate SAMs on TiO2/Si. The tilt angle of alkyl chains against the surface normal can be obtained with the dichroic ratio of s- against p-polarized absorbance from MTR-IR spectra.
References:
1. N. J. Harrick, Internal Reflection Spectroscopy; Wiley: New York, 1967;
2. R.G. Greenler, J. Chem. Phys.1969, 50, 1963;
3. H.-B. Liu, N.V. Venkataraman, T.E. Bauert, M. Textor, S.-J. Xiao*, J. Phy. Chem. A2008, 112, 12372;
4. H.-B. Liu, N.V. Venkataraman, N.D. Spencer, M. Textor, S.-J. Xiao*, ChemPhyChem, 2008, 9, 1979;
5. H.-B. Liu, S.-J. Xiao*, Y.-Q. Chen, J. Chao, J. Wang, Y. Wang, Y. Pan, X.-Z. You, Z.-Z. Gu, J. Phy. Chem. B, 2006, 110, 17702.
4. Soft Materials Functionalization and Patterning of Silicon by Surface Hydrosilylation Chemistry:A New Silicon Revolution?
Silicon, the second most abundant element in the earth's crust, has played and continues to play an important role in our human being's life:
1) Silicon-based semiconductor industry, as a miracle in our human being's history, has revolutionized our life in every aspect. We cannot imagine how we live if we have no computer, mobile phone, washing machine, intelligent transportation system such as airplane, high speed train, automobile, and so on, that are all based on the core technology of silicon chips. The number of the transistors in a CPU chip has been increased by following Moore's law from ~20 in 1960 to ~3 billion in 2013. Every day, most people interact with around tens of devices equipped with silicon chips. Silicon is always around us and works for you and me.
2) Due to the increased awareness of the global energy crisis, solar energy has been recognized in common as an alternative sustainable energy source. Silicon solar cells have become the most important photovoltaic products owing to the sophisticated manufacturing technology and the reliable cell quality.
It seems that the microelectronic silicon technology is mature. However a new technology of covalent grafting soft materials onto silicon surface intrigues the great interest of scientists. Functionalization and patterning of silicon by surface hydrosilylation chemistry are arising. This technology can be utilized for diverse applications such as nanoelectronics, solar cells, and bio-detection.
To record our work on molecular engineering on silicon surface, we first developed the Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR). Using this technology, we easily monitor the quality and performance of molecular monolayers and polymer brushes grown on the silicon surface, the in-situ multiple surface transformations of end functional groups such as hydroxyl and carboxyl groups to target species such as proteins and DNAs. We are working with both surface chemistry and micro- and nano-patterning techniques to develop biochips, molo- and nano-electronics, further solar cells and silicon photonics.
1. DNA microarray fabricated on poly(acrylic acid) brushes-coated porous silicon by in situ rolling circle amplification, Analyst, Cuie Wang, Xue-Mei Jia, Chuan Jiang, Guang-Nan Zhuang, Qin Yan and Shou-Jun Xiao* 2012, 137, 4539
2.Different EDC/NHS Activation Mechanisms between PAA and PMAA Brushes and the Following Amidation Reactions, Langmuir, Cuie Wang, Qin Yan, Hong-Bo Liu, Xiao-Hui Zhou, and Shou-Jun Xiao* 2011, 27 (19), pp 12058–68
3. Fluorescence Enhancement by Surface Plasmon Polaritons on Metallic Nanohole Arrays,Peng-Feng Guo, Shan Wu, Qin-Jun Ren, Jian Lu, Zhanghai Chen, Shou-Jun Xiao*, Yong-Yuan Zhu*, J. Phys. Chem. Lett.2010, 1, 315–318.
4.Gel-pad microarrays templated by patterned porous silicon for dual-mode detection of proteins, Ling Chen, Zeng-Tai Chen, Jing Wang, Shou-Jun Xiao*, Zu-Hong Lu , Zhong-Ze Gu, Lin Kang, Jian Chen, Pei-Heng Wu, Yan-Chun Tang, and Jian-Ning Liu*, Lab on a Chip, 2009, 9, 756–760
Infrared spectral characterization of organic nano-films on silicon surfaces provides much information such as molecular structures and orientations, chemical conversions, surface components and densities. Over years, the mostly recognized infrared method for sensitive detection of silicon-supported organic nano-films is the multiple internal reflection (MIR)1, in which the nano-film is fabricated on an attenuated total reflection (ATR) silicon crystal with 45 degree bevel cuts at both ends, and the sensitivity is increased by multiple internal reflections. However, a qualified MIR-IR spectrum is limited to delicate fabrications of thick silicon chips over a thickness of several millimeters. The configuration of the infrared multiple reflections had been suggested by R.G. Greenler2 to enhance the signal of untrathin organic films coated on gold. However until we re-examined the multiple transmission-reflection infrared spectroscopy (MTR-IR) (Figure 1) and found its power in characterization of covalently bound organic monolayers, polymer brushes, and of the following in-situ surface chemistries on thin silicon chips (0.2 ~ 2.0 mm thick silicon chips), it has not yet been developed and used widely. With MTR-IR, we illustrated many delicate details of surface functionalities which have rarely been reported hitherto, such as the triazole ring υ(H-C=) at 3139 cm-1 produced by click reactions, υ(C-Cl) at 660 cm-1, υ(H-C≡C) at 3283 cm-1, υ(C≡C) at 2115 cm-1, and asymmetric and symmetric stretching bands of amide υ(NH) at 3441 and 3345 cm-1 from molecular monolayers or polymer brushes. These delicate details clarify some unresolved chemical reaction mechanisms. Further the molecular orientation organized on the substrate surface can be demonstrated by measuring the dichroic ratios3,4 of both p- and s-polarized spectra quantitatively.
Figure 1. Scheme of IR measurements for detection and orientation analysis of monolayers on silicon surface. GMBR5 is a combination of external reflection and transmission by placing a gold mirror on one side of a silicon chip. To increase the sensitivity, MTR was established by inserting a silicon chip between two parallel gold mirrors. Three types of surface modifications were performed as examples: hydrosilylation on Si(111)-H; silane SAMs on SiO2/Si and phosphate SAMs on TiO2/Si. The tilt angle of alkyl chains against the surface normal can be obtained with the dichroic ratio of s- against p-polarized absorbance from MTR-IR spectra.
1.N. J. Harrick, Internal Reflection Spectroscopy; Wiley: New York, 1967;
2.R.G. Greenler, J. Chem. Phys.1969, 50, 1963;
3.H.-B. Liu, N.V. Venkataraman, T.E. Bauert, M. Textor, S.-J. Xiao*, J. Phy. Chem. A2008, 112, 12372;
4.H.-B. Liu, N.V. Venkataraman, N.D. Spencer, M. Textor, S.-J. Xiao*, ChemPhyChem, 2008, 9, 1979;
5.H.-B. Liu, S.-J. Xiao*, Y.-Q. Chen, J. Chao, J. Wang, Y. Wang, Y. Pan, X.-Z. You, Z.-Z. Gu, J. Phy. Chem. B, 2006, 110, 17702.
DNA nanotechnology, using the Watson–Crick base pairing of nucleic acids to construct 2- and 3-dimensional nanostructures, was established by Prof. Nadrian Seeman. In recent years, DNA origami has been developed greatly by controlled folding of a long single M13mp18 genomic DNA. Although DNA origami, in principle, could avoid the problems of stoichiometry and purification, it usually takes hundreds of different staple strands to fold a very few available sequence-identified native DNA scaffolds (until now only M13mp18 DNA) into a nanoscale shape. In order to simplify the assembly process of DNA origami, e.g., replacing hundreds of different staple strands with a few staple strands, we have developed the so-called RCA (rolling circle amplification) DNA origami, where the RCA products with tens and hundreds of tandemly repeated copies of a circularized template strand as the scaffold strand are folded by short staple strands at single-digit level to create nano-ribbons and lattices.
Scheme 1. Principle of Rolling Circle Amplification.
Figure 2. Folding strategies and the corresponding AFM images of RCA DNA origami from a 96nt circle template.
a, one type of nano-ribbons with only 3×32 staple strands (the double helix axis is perpendicular to the nano-ribbon longitudinal axis;
b, another type of nano-ribbons with 2×32 and 2×16 staple strands (the double helix axis is parallel to the nano-ribbon longitudinal axis);
c, over-crossing among a's nano-ribbons to generate 2-dimentional lattices.
Light is an ideal external trigger to switch, manipulate and control chemical and biological reactions. Photoregulation of the functions of nucleic acids has aroused much interest due to its wide applications in basic molecular biology, photo-therapeutics, as well as DNA nanotechnology. Modification of nucleic acids with photo-isomerizable molecules is a direct way to realize photo-responsiveness. Azobenzene is one of the popular photo-responsive molecules to modify nucleic acids due to its high photo-isomerization efficiency and high chemical stability. However a challenge remains in practical applications is the low trans-to-cis photoisomerization efficiency in the duplex form at room temperature. We introduced azobenzene to DNA by a glycerol linker, and greatly improved the trans-to-cis photoisomerization efficiency at room temperature.
Scheme 2. Schematic of the Forster energy transfer experiment between an artificial DNA (N9-DABCYL) and a native DNA (FAM-N'). Two sequences of FAM-N' and N9-DABCYL are associated under visible light irradiation with azobenzenes in trans-form and hence the fluorescence of FAM is quenched, while FAM-N' and N9-DABCYL are dissociated under UV light irradiation with azobenzenes in cis-form and hence the fluorescence of FAM is emitted.
1.RCA Strands as Scaffolds To Create Nanoscale Shapes by a Few Staple Strands，Yinzhou Ma, Hongning Zheng, Cuie Wang, Qin Yan, Jie Chao, Chunhai Fan, Shou-Jun Xiao*, J. Am. Chem. Soc.2013, 135, 2959-62
2.Room-temperature photoresponsive DNA tethering azobenzene through ether bond to improve trans-to-cis photoisomerization efficiency，Bo Kou, Xin Guo, Shou-Jun Xiao*, Xingguo Liang* Small, 2013, DOI: 10.1002/smll.201301134
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