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DNA enzymes (DNAzymes), which cleave target RNA with high specificity, have been widely investigated as potential oligonucleotide-based therapeutics. Recently, xeno-nucleic acid (XNA)-modified DNAzymes (XNAzymes), exhibiting cleavage activity in cultured cells, have been developed. However, a versatile approach to modify XNAzymes that function in cells has not yet been established. Here, we report an X-ray crystal structure-based approach to modify 8–17 DNAzymes; this approach enables us to effectively locate suitable XNAs to modify. Our approach, combined with a modification strategy used in designing antisense oligonucleotides (ASOs), rationally modified 8–17 DNAzyme (X8–17) that achieved high potency in terms of RNA cleavage and biostability against nucleases. In cells, X8–17, modified with 2′-OMe RNA, locked nucleic acid, and phosphorothioate, successfully induced endogenous MALAT-1and SRB1 RNA knockdown. This approach may help in developing XNAzyme-based novel therapeutic agents.

Naturally occurring 5-hydroxycytosine (

The artificial nucleobase 1,3-diaza-2-oxophenoxazine (tC

Therapeutic oligonucleotides have molecular weights of more than 6000 Da. They typically contain chemically modified structures such as phosphorothioate (PS) and a locked nucleic acid (LNA). To determine the effect of the length and chemical modification on the physicochemical properties, various nucleic acids with different lengths and modified structures were analyzed using traveling-wave ion mobility mass spectrometry (TWIMS).The physicochemical characteristics of the modified oligonucleotides were determined using IM-MS. Each oligonucleotide was evaluated by confirming the multivalent charge state drift times, collision cross-section (CCS) values, and CCS widths.By plotting the m/z for oligonucleotides of different lengths and the CCS values at each charge state, a bottoming-out shape plot at one charge per 4.0-3.5 bases was confirmed. Moreover, significant differences were observed in the CCS values between the PS-modified and unmodified oligonucleotides. The PS-modified oligonucleotide showed a wider CCS range that was proportional to the PS modification ratio of the oligonucleotide sequence.The TWIMS results showed a correlation between the length and modification of oligonucleotides and the CCS values. In addition, it suggested that each charge state of the oligonucleotide ion has different physicochemical properties.

Fat mass obesity-associated protein (FTO) is a DNA/RNA demethylase involved in the epigenetic regulation of various genes and is considered a therapeutic target for obesity, cancer, and neurological disorders. Here, we aimed to design novel FTO-selective inhibitors by merging fragments of previously reported FTO inhibitors. Among the synthesized analogues, compound 11b, which merges key fragments of Hz (3) and MA (4), inhibited FTO selectively over alkylation repair homologue 5 (ALKBH5), another DNA/RNA demethylase. Treatment of acute monocytic leukemia NOMO-1 cells with a prodrug of 11b decreased the viability of acute monocytic leukemia cells, increased the level of the FTO substrate N6-methyladenosine in mRNA, and induced upregulation of MYC and downregulation of RARA, which are FTO target genes. Thus, Hz (3)/MA (4) hybrid analogues represent an entry into a new class of FTO-selective inhibitors.

We recently designed guanidine-bridged nucleic acids (GuNA), and GuNA bearing a thymine (T) nucleobase was synthesized and successfully incorporated into oligonucleotides. The GuNA-T-modified oligonucleotides possessed high duplex-forming ability towards their complementary single-stranded RNAs and were highly stable against 3'-exonuclease. Therefore, GuNA is a promissing artificial nucleic acid for therapeutic antisense oligonucleotides. We herein report the facile synthesis of GuNA phosphoramidites bearing adenine (A), guanine (G), and 5-methylcytosine (mC) nucleobases and a robust method for the preparation of GuNA-modified oligonucleotides, even with sequences having acid-sensitive purine nucleobases. Oligonucleotides modified with GuNA-A, -G, or -mC possessed high duplex-forming ability, similar to those modified with GuNA-T. Moreover, some of the GuNA-modified oligonucleotides were revealed to have high base discriminating ability compared with that of their natural counterparts. GuNA nucleosides exhibited no genotoxicity in bacterial reverse mutation assays. Thus, all GuNAs (GuNA-T, -A, -G, and -mC) are now available to be examined in therapeutic applications.

Target identification (target-ID) is an important step in elucidating the mechanisms of action of bioactive small molecules. In the past few decades, a number of target-ID methods have been developed. Among these, affinity labeling has been reliably used for specific modifications, as well as for the identification of weakly interacting protein targets, membrane-associated protein targets, and target-interacting proteins under native cellular conditions, which are generally difficult to achieve by conventional pull-down methods. In general, affinity labeling utilizes chemical probes composed of a bioactive small molecule, a reactive group, and a detection unit. However, the design and synthesis of highly functionalized chemical probes is often time-consuming. To address this issue, we have recently developed some simple affinity labeling methods using small fluorogenic tags, such as 4-alkoxy-7-nitro-2,1,3-benzoxadiazole (O-NBD), 2,3-dichloromaleimide (diCMI), and 4-azidophthalimide (AzPI), and successfully achieved the specific fluorescent labeling of target proteins, even in living cells. These methods should be useful for target-ID in phenotypic drug discovery.

In the present paper, we define a notion of good coverings of Alexandrov spaces with curvature bounded below, and prove that every Alexandrov space admits such a good covering and that it has the same homotopy type as the nerve of the good covering. We also prove the stability of the isomorphism classes of the nerves of good coverings in the non-collapsing case. In the proof, we need a version of Perelman's fibration theorem, which is also proved in this paper., Minor change basically on the proof of Theorem 1.2 in Section 5

We designed a conjugated molecule bearing an O-nitrobenzoxadiazole (O-NBD) unit and an acetylated trimethyl lock as a chromogenic and fluorogenic probe for the detection of esterase activity. The designed molecule was briefly synthesized from a commercially available compound in two steps. Several experiments revealed that the conjugated molecule serves as a sensitive chromogenic and fluorogenic probe for the detection of porcine liver esterase activity. Mechanistic studies indicated that an intramolecular O- to N-NBD migration is involved in the chromogenic/fluorogenic phenomena. The results here would be helpful for designing other O-NBD-based chromogenic/fluorogenic probes in future.

To enable positron emission tomography (PET) imaging of the in vivo kinetics of ubiquinone and ubiquinol, which is referred to as coenzyme Q10 , their 11 C-radiolabeled counterparts were synthesized herein. 11 C-Labeled ubiquinone [11 C]-1 was realized by Pd-mediated rapid C-[11 C]methylation of [11 C]CH3 I with 39-demethyl-39-(pinacolboryl)ubiquinone, prepared by Ru-catalyzed olefin metathesis of unradiolabeled ubiquinone with 2-(pinacolboryl)propene. Subsequent reduction of [11 C]-1 using Na2 S2 O4 yielded 11 C-labeled ubiquinol [11 C]-2. The synthesis time and [11 C]CH3 I-based radiochemical yield of [11 C]-1 were within 36 minutes and up to 53%, while those of [11 C]-2 were within 38 minutes and up to 39%, respectively. After radiopharmaceutical formulation, the qualities of [11 C]-1 and [11 C]-2 were confirmed to be applicable for animal PET studies. The analytical values of [11 C]-1 and [11 C]-2 are as follows: radioactivity of up to 3.5 and 1.4 GBq, molar activity of 21 to 78 and 48 to 76 GBq/μmol, radiochemical purity of greater than 99% and greater than 95%, and chemical purity of greater than 99% and 77%, respectively. The concept behind this radiolabeling procedure is that unradiolabeled natural ubiquinone can be converted to 11 C-radiolabeled ubiquinone and ubiquinol via a pinacolborane-substituted ubiquinone derivative. Each PET probe was used for molecular imaging using rats to investigate the in vivo kinetics and biodistribution of the coenzyme Q10 .

We describe herein the design and synthesis of 4′-C,5′-C-methylene-bridged nucleic acid (4′,5′-BNA), a novel artificial nucleic acid with the torsion angle γ in a non-canonical +ac range. The 4′,5′-BNA phosphoramidite bearing a thymine nucleobase was synthesized from a commercially available thymidine analog in 11 steps and successfully incorporated into oligonucleotides. The resulting oligonucleotides were evaluated for their duplex-forming ability toward single-stranded DNA and RNA.

The 176 Lu– 176 Hf radioactive decay system has been widely used to study planetary crust–mantle differentiation. Of considerable utility in this regard is zircon, a resistant mineral that can be precisely dated by the U–Pb chronometer and record its initial Hf isotope composition due to having low Lu/Hf. Here we review zircon U–Pb age and Hf isotopic data mainly obtained over the last two decades and discuss their contributions to our current understanding of crust–mantle evolution, with emphasis on the Lu–Hf isotope composition of the bulk silicate Earth (BSE), early differentiation of the silicate Earth, and the evolution of the continental crust over geologic history. Meteorite zircon encapsulates the most primitive Hf isotope composition of our solar system, which was used to identify chondritic meteorites best representative of the BSE ( 176 Hf/ 177 Hf = 0.282793 ± 0.000011; 176 Lu/ 177 Hf = 0.0338 ± 0.0001). Hadean–Eoarchean detrital zircons yield highly unradiogenic Hf isotope compositions relative to the BSE, providing evidence for the development of a geochemically enriched silicate reservoir as early as 4.5 Ga. By combining the Hf and O isotope systematics, we propose that the early enriched silicate reservoir has resided at depth within the Earth rather than near the surface and may represent a fractionated residuum of a magma ocean underlying the proto-crust, like urKREEP beneath the anorthositic crust on the Moon. Detrital zircons from world major rivers potentially provide the most robust Hf isotope record of the preserved granitoid crust on a continental scale, whereas mafic rocks with various emplacement ages offer an opportunity to trace the Hf isotope evolution of juvenile continental crust (from eHf [4.5 Ga] = 0 to eHf [present] = + 13). The river zircon data as compared to the juvenile crust composition highlight that the supercontinent cycle has controlled the evolution of the continental crust by regulating the rates of crustal generation and intra-crustal reworking processes and the preservation potential of granitoid crust. We use the data to explore the timing of generation of the preserved continental crust. Taking into account the crustal residence times of continental crust recycled back into the mantle, we further propose a model of net continental growth that stable continental crust was firstly established in the Paleo- and Mesoarchean and significantly grew in the Paleoproterozoic.

Ethynylphosphonate (EP)-linked thymidine dimers were synthesized via a palladium-catalyzed cross-coupling reaction and successfully incorporated into oligonucleotides. The oligonucleotides containing EP linkages appropriately formed a duplex with their complementary single-stranded RNA (ssRNA) and single-stranded DNA. The oligonucleotides containing both the EP linkages and 2'

We introduce a new geometric invariant called the obtuse constant of spaces with curvature bounded below. We first find relations between this invariant and the normalized volume. We also discuss the case of maximal obtuse constant equal to $\pi/2$, where we prove some rigidity for spaces. Although we consider Alexandrov spaces with curvature bounded below, the results are new even in the Riemannian case., Comment: We have changed the definition of obtuse constants in the first vertion "Comaparison angles and volume" because of an error in the first verson

The presence of a stereoisomeric center at the phosphorus atom in phosphorothioate-modified oligonucleotides (PS-ONs) has been recognized as an important feature since the early stages of their development. Therefore, several studies have been conducted on the chirality of PS-ONs. In this study, we evaluated the stereo-biased chemistry of PS-ON duplexes. Depending on their absolute configurations, PS-ON duplexes were found to have significantly different and stereospecific reactivities towards simple alkylating reagent.

A structure-activity relationship (SAR) for the oxadiazole class of antibacterials was evaluated by syntheses of 72 analogs and determination of the minimal-inhibitory concentrations (MICs) against the ESKAPE panel of bacteria. Selected compounds were further evaluated for in vitro toxicity, plasma protein binding, pharmacokinetics (PK), and a mouse model of methicillin-resistant Staphylococcus aureus (MRSA) infection. Oxadiazole 72c shows potent in vitro antibacterial activity, exhibits low clearance, a high volume of distribution, and 41% oral bioavailability, and shows efficacy in mouse models of MRSA infection. Fil: Boudreau, Marc A.. University of Notre Dame; Estados Unidos Fil: Ding, Derong. University of Notre Dame; Estados Unidos Fil: Meisel, Jayda E.. University of Notre Dame; Estados Unidos Fil: Janardhanan, Jeshina. University of Notre Dame; Estados Unidos Fil: Spink, Edward. University of Notre Dame; Estados Unidos Fil: Peng, Zhihong. University of Notre Dame; Estados Unidos Fil: Qian, Yuanyuan. University of Notre Dame; Estados Unidos Fil: Yamaguchi, Takao. University of Notre Dame; Estados Unidos Fil: Testero, Sebastian Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Química Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Química Rosario; Argentina. University of Notre Dame; Estados Unidos Fil: O'Daniel, Peter I.. University of Notre Dame; Estados Unidos Fil: Leemans, Erika. University of Notre Dame; Estados Unidos Fil: Lastochkin, Elena. University of Notre Dame; Estados Unidos Fil: Song, Wei. University of Notre Dame; Estados Unidos Fil: Schroeder, Valerie A.. University of Notre Dame; Estados Unidos Fil: Wolter, William R.. University of Notre Dame; Estados Unidos Fil: Suckow, Mark A.. University of Notre Dame; Estados Unidos Fil: Mobashery, Shahriar. University of Notre Dame; Estados Unidos Fil: Chang, Mayland. University of Notre Dame; Estados Unidos

An approximation method for estimating the modal loss factors of a coupled structural-acoustical problem is proposed using the finite element method. This method provides a practical approach in terms of computational time and memory consumption. To validate our approach, we consider a coupled system in which the acoustical region is enclosed by a structural region, and both structural and acoustical regions are composed of various materials with individual damping characteristics. To obtain the modal loss factors, the modal strain and kinetic energy (MSKE) method is extended to the coupled problem by utilizing the sound pressure as a nodal unknown variable in the acoustical region. An air-filled PVC box was used as the test specimen. The measured and calculated frequency responses of the normalized sound pressure showed good agreement, verifying the reliability of the proposed method. Various damping parameters were tested for the sound-absorbing material inside the box to investigate the scope of the application of the proposed method. The discrepancy between the reference value and the proposed method is small considering fiberglass as a standard sound-absorbing material used in buildings. The proposed method also showed better management characteristics in terms of memory consumption and computational time.

We previously reported the synthesis and evaluation of 2′-O,4′-C-spirocyclopropylene-bridged nucleic acid (scpBNA) bearing a thymine (T) nucleobase. Oligonucleotides (ONs) modified with scpBNA-T exhibited strong binding affinity to complementary single-stranded RNA (ssRNA) and high enzymatic stability. These biophysical properties suggest that scpBNAs are well suited for use in antisense strategies. Herein, we describe the synthesis of scpBNA monomers bearing 5-methylcytosine (mC), adenine (A), and guanine (G) nucleobases for use in a variety of sequences. The prepared scpBNA monomers were incorporated into ONs at various positions. The scpBNA-modified ONs exhibited excellent duplex-forming ability with the complementary ssRNA comparable to ONs modified with 2′-O,4′-C-methylene-bridged nucleic acid (2′,4′-BNA/LNA). Moreover, ON modified with scpBNA-mC, -A, and -G showed higher enzymatic stability than the corresponding 2′,4′-BNA/LNA-modified ON. These results demonstrated a promising role for the incorpor...

Acetyl-CoA carboxylases (ACCs) catalyze a critical step in de novo lipogenesis, and are considered as promising targets for treatment of obesity, dyslipidemia and type 2 diabetes mellitus. On the other hand, peroxisome proliferator-activated receptors (PPARs) are well-established therapeutic targets for these metabolic syndrome-related diseases. Therefore, we considered that dual modulators of ACC and PPARs would be promising candidates as therapeutic agents. Here, we designed a series of acetamides based on the molecular similarity between ACC inhibitors and PPAR agonists. Screening of the synthesized compounds identified N-(1-(3-(4-phenoxyphenyl)-1,2,4-oxadiazol-5-yl)ethyl)acetamides as novel ACC2 inhibitors with PPARα/PPARδ dual agonistic activity. Structure–activity relationship studies and further structural elaboration afforded compounds with distinct activity profiles. Our findings should be helpful for the discovery of candidate agents with an appropriate balance of ACC-inhibitory and PPAR-activating activities for therapeutic lipid control.

At present, a method for evaluating dynamic characteristics of force sensors against small and short-duration impact forces has been developed. In this method, a small mass collides with a force sensor and the impact force is measured with high accuracy as the inertial force of the mass. A pneumatic linear bearing is used in order to realize linear motion with sufficiently small friction acting on the mass, i.e., the moving part of the bearing. Using this method, the dynamic characteristics of the force sensor are evaluated in detail: small and various-duration impact forces with maximum values of approximately 0.4-6.0 N and full width at half maximum (FWHM) of approximately 0.6-2.8 ms are applied to the force sensor and the impact responses of the force sensor are evaluated.

Bamboo shinai is a practice sword for kendo which is the Japanese traditional fencing. The effectiveness of the shock absorption of the bamboo shinai has been shown in our previous study. Although shinai is usually made of bamboo, it is also made of carbon fiber reinforced plastic (CFRP). The impact response of bamboo shinai and CFRP shinai is compared. As a result, the difference of peak value of impact force between bamboo shinai and CFRP shinai against similar initial velocity is small. Impact response measurement of each shinai has been carried out using the Levitation Mass Method (LMM) which has been proposed by us. In this method, a mass, which is levitated with a pneumatic linear bearing and hence affected by negligible friction, is made to collide with a shinai under test. Because bamboo is natual product, resource of suitable bamboos for shinai is limited. On the other hand, carbon-fiber-reinforced-plastic (CFRP) can be designed to be suitable for a shinai, which has a fixed shock absorption characteristic for an application to the structure of robot arms. Therefore, if the shock absorption characteristic of CFRP shinai is the same as that of bamboo shinai, CFRP shinai is more suitable for the structure of robot arms.

Impact response of a bamboo sword “Shinai” which is a practice sword used in a Japanese traditional fencing and has an unique and simple structure of light-weight bamboo plates for moderating the impact force to the human body, is accurately measured by means of modifying the Levitation Mass Method (LMM). In the method, a mass, which is levitated with an aerostatic linear bearing and hence encounters negligible friction, is made to collide with a bamboo sword under test. During the collision, the Doppler shift frequency of a laser beam reflecting from the mass is accurately measured using an optical interferometer. The velocity, position, acceleration, and inertial force of the mass are calculated from the measured time-varying Doppler shift frequency. The measurement results show that “Shinai” considerably moderates the impact force and its unique structure might be effective for robotics and automobiles to moderate the impact force acting to the human body in the case of accidents.

Oligonucleotides modified with 2′-O,4′-C-spirocyclopropylene-bridged nucleic acid (scpBNA) exhibit excellent duplex-forming ability with their complementary single-stranded RNA (ssRNA). Here, we demonstrate that scpBNA bearing a 2-thiothymine (scpBNA-S2T) or 2-selenothymine (scpBNA-Se2T) nucleobase provides robust mismatch discrimination capabilities to oligonucleotides without compromising their high binding affinities toward the full complementary ssRNA. X-ray crystallographic analysis of a self-assembling oligonucleotide featuring 2′,4′-BNA/LNA-2-thiothymine (2′,4′-BNA/LNA-S2T, where 2′,4′-BNA and LNA stand for “2′-O,4′-C-methylene-bridged nucleic acid” and “locked nucleic acid”, respectively), a prototype of scpBNA-S2T, revealed that the 2-thiocarbonyl moiety plays a crucial role in the destabilization of thymine–guanine mismatched wobble base pairs.

Oligonucleotides containing bridged nucleic acids (BNAs) show high duplex-forming ability towards target single-stranded RNA, so many BNAs have been developed for antisense applications. Amide-bridged nucleic acids (AmNAs), which are BNA analogues bearing an amide bond at the bridge, exhibit high duplex-forming ability, enzymatic stability, and antisense activity; thus, the AmNA motif represents a promising BNA scaffold. The high enzymatic stability of the AmNA motif is presumably attributable to the bulky amide structure, because it inhibits the access of nucleases to the phosphodiester linkage. Here, to improve enzymatic stability further, we designed thioAmNAs: thioamide-bridged nucleotides that have a bulkier bridge structure than AmNA. The synthesis of thioAmNAs bearing either thymine (thioAmNA-T) or 2-thiothymine (thioAmNA-S2 T) bases was successful, and the obtained monomers were introduced into designed oligonucleotides without noticeable by-product generation. The thioAmNA-T- and thioAmNA-S2 T-modified oligonucleotides showed strong binding affinity toward complementary single-stranded RNA, with the thioAmNA-S2 T-modified oligonucleotide displaying excellent base-discrimination capability. Moreover, both thioAmNA-T and thioAmNA-S2 T endowed oligonucleotides with higher resistance to enzymatic degradation than AmNA-T. These results indicate that thioAmNAs are potentially useful chemical modifications for oligonucleotide-based therapeutics.