Photochemical Regulation of Gene Expression Using Caged siRNAs with Single Terminal Vitamin E Modification

Caged siRNAs with a single photolabile linker and/or vitamin E (vitE) modification at the 5′ terminal were rationally designed and synthesized. These virtually inactive caged siRNAs were successfully used to photoregulate both firefly luciferase and GFP gene expression in cells with up to an 18.6‐fold enhancement of gene silencing activity, which represents one of the best reported photomodulation of gene silencing efficiencies to date. siRNA tracking and vitE competition experiments indicated that the inactivity of vitE‐modified siRNAs was not due to the bulky moiety of vitE; rather, the involvement of vitE‐binding proteins has a large contribution to caged siRNA inactivation by preventing the dissociation of siRNA/lipo complexes and/or siRNA release. Further patterning experiments revealed the ability to spatially regulate gene expression through simple light irradiation.     

Cubic Siloxanes with Both Si−H and Si−OtBu Groups for Site‐Selective Siloxane Bond Formation

Cage‐type siloxanes have attracted increasing attention as building blocks for silica‐based nanomaterials as their corners can be modified with various functional groups. Cubic octasiloxanes incorporating both Si?H and Si?OtBu groups [(tBuO)_nH_8?nSi₈O₁₂; n=1, 2 or 7] have been synthesized by the reaction of octa(hydridosilsesquioxane) (H₈Si₈O₁₂) and tert‐butyl alcohol in the presence of a Et₂NOH catalyst. The Si?H and Si?OtBu groups are useful for site‐selective formation of Si?O?Si linkages without cage structure deterioration. The Si?H group can be selectively hydrolyzed to form a Si?OH group in the presence of Et₂NOH, enabling the formation of the monosilanol compound (tBuO)₇(HO)Si₈O₁₂. The Si?OH group can be used for either intermolecular condensation to form a dimeric cage compound or silylation to introduce new reaction sites. Additionally, the alkoxy groups of (tBuO)₇HSi₈O₁₂ can be treated with organochlorosilanes in the presence of a BiCl₃ catalyst to form Si?O?Si linkages, while the Si?H group remains intact. These results indicate that such bifunctional cage siloxanes allow for stepwise Si?O?Si bond formation to design new siloxane‐based nanomaterials.     

Synthesis and Properties of Isobicyclo‐DNA

We present the synthesis of the isobicyclo‐DNA building blocks with the nucleobases A, C, G and T, as well as biophysical and biological properties of oligonucleotides derived thereof. The synthesis of the sugar part was achieved in 5 steps starting from a known intermediate of the tricyclo‐DNA synthesis. Dodecamers containing single isobicyclo‐thymidine incorporations, fully modified A‐ and T‐containing sequences, and fully modified oligonucleotides containing all four bases were synthesized and characterized. Isobicyclo‐DNA forms stable duplexes with natural nucleic acids with a pronounced preference for DNA over RNA as complements. The most stable duplexes, however, arise by self‐pairing. Isobicyclo‐DNA forms preferentially B‐DNA‐like duplexes with DNA and A‐like duplexes with complementary RNA as determined by circular dichroism (CD) spectroscopy. Self‐paired duplexes show a yet unknown structure, as judged from CD spectroscopy. Biochemical tests revealed that isobicyclo‐DNA is stable in fetal bovine serum and does not elicit RNaseH activity.     

Synthesis and Antimicrobial Activity of New 2,5‐Disubstituted 1,3,4‐Oxadiazoles and 1,2,4‐Triazoles and Their Sugar Derivatives

A series of new 2,5‐disubstituted‐1,3,4‐oxadiazole and 1,2,4‐triazole derivatives were synthesized by heterocyclization of acid hydrazide 1 and thiosemicarbazide derivative 2 . Furthermore, the acyclic C‐nucleoside analogs were prepared by cyclization of their corresponding sugar hydrazones by reaction with acetic anhydride. The antimicrobial activity of the prepared compounds was evaluated and some of the synthesized compounds revealed good activities against fungi.     

Near‐IR‐Triggered,Remote‐Controlled Release of Metal Ions: A Novel Strategy for Caged Ions

A ligand incorporating a dithioethenyl moiety is cleaved into fragments which have a lower metal‐ion affinity upon irradiation with low‐energy red/near‐IR light. The cleavage is a result of singlet oxygen generation which occurs on excitation of the photosensitizer modules. The method has many tunable factors that could make it a satisfactory caging strategy for metal ions.     

双环笼状四配位硅的合成及其结构表征

研究了以SiO₂为原料低温合成高反应活性的五配位硅酸酯, 并与1-氧代-1-磷杂-2,6,7-三氧杂双环[2.2.2]-4-氯甲基辛烷反应合成出具有对称结构的双环笼状四配位硅, 通过红外光谱、¹³C和²⁹Si固体核磁共振、质谱等测试手段确定了其结构. 热分析结果表明, 双环笼状四配位硅在700 ℃的失重仅为19.98%, 且炭层呈密实片层状, 说明目标产物具有优异的热稳定性和成炭性质.     

Chemo‐Enzymatic Synthesis of Position‐Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy

The investigation of non‐coding RNAs requires RNAs containing modifications at every possible position within the oligonucleotide. Here, we present the chemo‐enzymatic RNA synthesis containing photoactivatable or ¹³C,¹⁵N‐labelled nucleosides. All four ribonucleotides containing ortho‐nitrophenylethyl (NPE) photocages, photoswitchable azobenzene C‐nucleotides and ¹³C,¹⁵N‐labelled nucleotides were incorporated position‐specifically in high yields. We applied this approach for the synthesis of light‐inducible 2′dG‐sensing riboswitch variants and detected ligand‐induced structural reorganization upon irradiation by NMR spectroscopy. This chemo‐enzymatic method opens the possibility to incorporate a wide range of modifications at any desired position of RNAs of any lengths beyond the limits of solid‐phase synthesis.     

Impaired Chaperone Activity of Human Heat Shock Protein Hsp27 Site‐Specifically Modified with Argpyrimidine

Non‐enzymatic posttranslational modifications (nPTMs) affect at least ～30 % of human proteins, but our understanding of their impact on protein structure and function is limited. Studies of nPTMs are difficult because many modifications are not included in common chemical libraries or protein expression systems and should be introduced site‐specifically. Herein, we probed the effect of the nPTM argpyrimidine on the structure and function of human protein Hsp27, which acquires argpyrimidine at residue 188 in vivo. We developed a synthetic approach to an argpyrimidine building block, which we then incorporated at position 188 of Hsp27 through protein semisynthesis. This modification did not affect the protein secondary structure, but perturbed the oligomeric assembly and impaired chaperone activity. Our work demonstrates that protein function can be altered by a single nPTM and opens up a new area of investigation only accessible by methods that allow site‐selective protein modification.     

Caged Phosphate and the Slips and Misses in Determination of Quantum Yields for Ultraviolet‐A‐Induced Photouncaging

The quantum yields for photouncaging reactions are mostly determined relative to other uncaging reactions, often using 1‐(2‐nitrophenyl)ethyl‐phosphate (“caged phosphate”). Herein, we demonstrate that the quantum yields acquired by using this method can be off by an order of magnitude at the typical irradiation wavelengths around 350 nm and describe an easy‐to‐use alternative procedure using inexpensive azobenzene.     

Electrophilic RNA for Peptidyl‐RNA Synthesis and Site‐Specific Cross‐Linking with tRNA‐Binding Enzymes

RNA functionalization is challenging due to the instability of RNA and the limited range of available enzymatic reactions. We developed a strategy based on solid phase synthesis and post‐functionalization to introduce an electrophilic site at the 3′ end of tRNA analogues. The squarate diester used as an electrophile enabled sequential amidation and provided asymmetric squaramides with high selectivity. The squaramate‐RNAs specifically reacted with the lysine of UDP‐MurNAc‐pentapeptide, a peptidoglycan precursor used by the aminoacyl‐transferase FemX_Wv for synthesis of the bacterial cell wall. The peptidyl‐RNA obtained with squaramate‐RNA and unprotected UDP‐MurNAc‐pentapeptide efficiently inhibited FemX_Wv. The squaramate unit also promoted specific cross‐linking of RNA to the catalytic Lys of FemX_Wv but not to related transferases recognizing different aminoacyl‐tRNAs. Thus, squaramate‐RNAs provide specificity for cross‐linking with defined groups in complex biomolecules due to its unique reactivity.     

Efficient Synthesis of 3‐Methyl‐Flavanones and Evaluation of Their Anti‐Bacterial Activity

A series of 2‐phenyl‐2,3‐dihydrochromon‐4‐one derivatives (flavanone derivatives) were synthesized by silica gel assisted isomerization of several α‐methyl‐2′‐hydroxy chalcones in 74%–88% yield. These flavanones were further oxidized to 3‐methyl flavones by using iodine in dimethyl sulphoxide at 60°C in presence of acid. The newly synthesized derivatives were evaluated for in vitro study against Staphylococcus aureus, Micrococcus luteus and Staphylococcus epidermis.     

Synthesis of a Far‐Red Photoactivatable Silicon‐Containing Rhodamine for Super‐Resolution Microscopy

The rhodamine system is a flexible framework for building small‐molecule fluorescent probes. Changing N‐substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si‐containing analogue of Q‐rhodamine. This probe is the first example of a “caged” Si‐rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red‐shifted to allow multicolor imaging. The dye is a useful label for super‐resolution imaging and constitutes a new scaffold for far‐red fluorogenic molecules.