6,436 results match your criteria novel single-stranded

DNAzyme based three-way junction assay for antibody-free detection of locus-specific N-methyladenosine modifications.

Biosens Bioelectron 2021 Sep 11;194:113625. Epub 2021 Sep 11.

Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, PR China. Electronic address:

N-methyladenosine (m6A) is the most abundant post-transcriptional modification in RNA and has important implications in physiological processes and tumor development. However, sensitive and specific quantification of locus-specific m6A modification levels remains a challenging task. In the present work, a novel m6A-sensitive DNAzyme was utilized to directly detect m6A by coupling with a three-way junction-mediated isothermal exponential CRISPR amplification reaction for the first time. Read More

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September 2021

Influence of viral transport media and freeze-thaw cycling on the sensitivity of qRT-PCR detection of SARS-CoV-2 nucleic acids.

Nanoscale 2021 Sep 17. Epub 2021 Sep 17.

School of Chemistry and Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Republic of Ireland.

: The events of the last year have highlighted the complexity of implementing large-scale molecular diagnostic testing for novel pathogens. The purpose of this study was to determine the chemical influences of sample collection media and storage on the stability and detection of viral nucleic acids by qRT-PCR. We studied the mechanism(s) through which viral transport media (VTM) and number of freeze-thaw cycles influenced the analytical sensitivity of qRT-PCR detection of SARS-CoV-2. Read More

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September 2021

Extracellular Vesicle-Shuttling MicroRNAs Regulate the Development of Inflammatory Lung Responses.

Ann Pulm Crit Care Med 2018 Oct 23;1(2):1-4. Epub 2018 Dec 23.

Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, MA 02118, USA.

MicroRNAs are small single-stranded, non-coding RNAs which have a known role in post-transcriptional regulation of gene expression. Recent studies have reported that extracellular vesicles are capable of specific delivery of miRNAs to a target cell or tissue from a host cell. MiRNAs are generated by host cells, selectively packaged into EVs, and then delivered to nearby target cells with full functionality. Read More

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October 2018

Symbiotic Interactions Between Mosquitoes and Mosquito Viruses.

Front Cell Infect Microbiol 2021 30;11:694020. Epub 2021 Aug 30.

ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.

Mosquitoes not only transmit human and veterinary pathogens called arboviruses (arthropod-borne viruses) but also harbor mosquito-associated insect-specific viruses (mosquito viruses) that cannot infect vertebrates. In the past, studies investigating mosquito viruses mainly focused on highly pathogenic interactions that were easier to detect than those without visible symptoms. However, the recent advances in viral metagenomics have highlighted the abundance and diversity of viruses which do not generate mass mortality in host populations. Read More

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Unveiling the Microscopic Mechanism of Current Variation in the Sensing Region of the MspA Nanopore for DNA Sequencing.

J Phys Chem Lett 2021 Sep 15:9132-9141. Epub 2021 Sep 15.

BGI-ShenZhen, Shenzhen 518103, China.

Different nucleotides generate specific ionic currents that discriminate between the nucleotides while they are passing through the nanopore constriction. MspA is a commonly used nanopore for DNA sequencing. However, the reasons of the current variation remain ambiguous. Read More

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September 2021

Complete genome sequence of a novel varicosavirus infecting tall morning glory (Ipomoea purpurea).

Arch Virol 2021 Sep 14. Epub 2021 Sep 14.

Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.

A novel varicosa-like virus was identified in a tall morning glory (Ipomoea purpurea) plant by high-throughput sequencing and tentatively named "morning glory varicosavirus" (MGVV). The complete genome of MGVV contains two segments of negative-sense single-stranded RNA of 6409 (RNA1) and 5288 (RNA2) nucleotides. RNA1 encodes a 224. Read More

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September 2021

DNA functionalized double quantum dots-based fluorescence biosensor for one-step simultaneous detection of multiple microRNAs.

Talanta 2021 Dec 30;235:122763. Epub 2021 Jul 30.

School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China. Electronic address:

The disease diagnosis by detecting single microRNAs (miRNAs) can produce high false positive rate. Herein, a novel fluorescence biosensor method for one-step simultaneous detection of multiple miRNAs was proposed by using single-stranded DNA (ssDNA) functionalized double quantum dots (QDs) and black hole quencher (BHQ)-decorated magnetic nanobeads (MNs). MNs were linked with two black hole quenchers (BHQ1 and BHQ3) via a complementary DNA (cDNA). Read More

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December 2021

An artificial enzyme cascade amplification strategy for highly sensitive and specific detection of breast cancer-derived exosomes.

Analyst 2021 Sep 13;146(18):5542-5549. Epub 2021 Sep 13.

Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.

Tumor-related exosomes, which are heterogeneous membrane-enclosed nanovesicles shed from cancer cells, have been widely recognized as potential noninvasive biomarkers for early cancer diagnosis. Herein, an artificial enzyme cascade amplification strategy based on a switchable DNA tetrahedral (SDT) scaffold was proposed for quantification of breast cancer-derived exosomes. The SDT scaffold is composed of G-quadruplex mimicking DNAzyme sequences on its two single-stranded edges and glucose oxidase (GOx) on the four termini of the complementary strands. Read More

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September 2021

SAR of novel benzothiazoles targeting an allosteric pocket of DENV and ZIKV NS2B/NS3 proteases.

Bioorg Med Chem 2021 Sep 4;47:116392. Epub 2021 Sep 4.

Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany. Electronic address:

In recent years, dengue virus (DENV) and Zika virus (ZIKV), both mosquito-borne members of the Flaviviridae family, have emerged as intercontinental health issues since their vectors have spread from their tropical origins to temperate climate zones due to climate change and increasing globalization. DENV and ZIKV are positive-sense, single-stranded RNA viruses, whose genomes consist of three structural (capsid, membrane precursor, envelope) and seven non-structural (NS) proteins, all of which are initially expressed as a single precursor polyprotein. For virus maturation, the polyprotein processing is accomplished by host proteases and the viral NS2B/NS3 protease complex, whose inhibitors have been shown to be effective antiviral agents with loss of viral pathogenicity. Read More

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September 2021

Truly ubiquitous CRESS DNA viruses scattered across the eukaryotic tree of life.

J Evol Biol 2021 Sep 9. Epub 2021 Sep 9.

Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey.

Until recently, most viruses detected and characterized were of economic significance, associated with agricultural and medical diseases. This was certainly true for the eukaryote-infecting circular Rep (replication-associated protein)-encoding single-stranded DNA (CRESS DNA) viruses, which were thought to be a relatively small group of viruses. With the explosion of metagenomic sequencing over the past decade and increasing use of rolling-circle replication for sequence amplification, scientists have identified and annotated copious numbers of novel CRESS DNA viruses - many without known hosts but which have been found in association with eukaryotes. Read More

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September 2021

A Bayesian model based computational analysis of the relationship between bisulfite accessible single-stranded DNA in chromatin and somatic hypermutation of immunoglobulin genes.

PLoS Comput Biol 2021 Sep 7;17(9):e1009323. Epub 2021 Sep 7.

Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America.

The B cells in our body generate protective antibodies by introducing somatic hypermutations (SHM) into the variable region of immunoglobulin genes (IgVs). The mutations are generated by activation induced deaminase (AID) that converts cytosine to uracil in single stranded DNA (ssDNA) generated during transcription. Attempts have been made to correlate SHM with ssDNA using bisulfite to chemically convert cytosines that are accessible in the intact chromatin of mutating B cells. Read More

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September 2021

Isothermal Self-Primer EXPonential Amplification Reaction (SPEXPAR) for Highly Sensitive Detection of Single-Stranded Nucleic Acids and Proteins.

Anal Chem 2021 Sep 7. Epub 2021 Sep 7.

School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China.

Development of versatile sensing methods for sensitive and specific detection of clinically relevant nucleic acids and proteins is of great value for disease monitoring and diagnosis. In this work, we propose a novel isothermal Self-primer EXPonential Amplification Reaction (SPEXPAR) strategy based on a rationally engineered structure-switchable Metastable Hairpin template (MH-template). The MH-template initially keeps inactive with its self-primer overhanging a part of target recognition region to inhibit polymerization. Read More

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September 2021

Circoviruses and cycloviruses identified in Weddell seal fecal samples from McMurdo Sound, Antarctica.

Infect Genet Evol 2021 Sep 3;95:105070. Epub 2021 Sep 3.

The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925 Cape Town, South Africa. Electronic address:

Circoviridae is a family of circular single-stranded DNA viruses whose members infect a wide variety of hosts. While well characterized in avian and mammalian hosts, little is known about circoviruses associated with Antarctic animals. From 48 Weddell seal (Leptonychotes weddellii) fecal samples collected on the sea ice in McMurdo between Nov 2014 and Dec 2014, we identified and determined the genomes of novel viruses that fall within two genera of the family Circoviridae, i. Read More

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September 2021

Production of therapeutic iduronate-2-sulfatase enzyme with a novel single-stranded RNA virus vector.

Genes Cells 2021 Sep 4. Epub 2021 Sep 4.

Department of Clinical Laboratory Medicine, National Center for Child Health and Development, Tokyo, Japan.

The Sendai virus vector has received a lot of attention due to its broad tropism for mammalian cells. As a result of efforts for genetic studies based on a mutant virus, we can now express more than 10 genes of up to 13.5 kilo nucleotides in a single vector with high protein expression efficiency. Read More

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September 2021

Evaluation of a new viral vaccine vector in mice and rhesus macaques: J paramyxovirus (JPV)-expressing HA of influenza A virus H5N1.

J Virol 2021 Sep 1:JVI0132121. Epub 2021 Sep 1.

Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, USA.

H5N1, an avian influenza virus, is known to circulate in many Asian countries like Bangladesh, China, Cambodia, Indonesia, and Vietnam. The current FDA-approved H5N1 vaccine has a moderate level of efficacy. A safe and effective vaccine is needed to prevent the outbreaks of highly pathogenic avian influenza (HPAI) H5N1 in humans. Read More

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September 2021

Acute Limb Ischemia: A Catastrophic COVID-19 Sequel Leading to Amputation.

Cureus 2021 Jul 18;13(7):e16456. Epub 2021 Jul 18.

Surgery, Srirama Chandra Bhanja Medical College and Hospital, Cuttack, IND.

A positive-sense single-stranded ribonucleic acid (RNA) virus causes the novel coronavirus illness 2019 (COVID-19). COVID-19 symptoms range from mild to moderate to severe and very severe. Fever, cough, headache, anosmia, ageusia, body ache, and diarrhoea are mild to moderate grade symptoms, whereas systemic involvements (pneumonia, myocarditis, stroke, and other coagulation abnormalities) are more serious. Read More

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Gimme shelter: three-dimensional architecture of the endoplasmic reticulum, the replication site of grapevine Pinot gris virus.

Funct Plant Biol 2021 Sep;48(10):1074-1085

Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine,via delle Scienze, 206, 33100 - Udine, Italy; and Corresponding author. Email:

Grapevine leaf mottling and deformation is a novel grapevine disease that has been associated with grapevine Pinot gris virus (GPGV). The virus was observed exclusively inside membrane-bound structures in the bundle sheath cells of the infected grapevines. As reported widely in the literature, many positive-sense single-stranded RNA viruses modify host-cell membranes to form a variety of deformed organelles, which shelter viral genome replication from host antiviral compounds. Read More

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September 2021

Photoactivation of Innate Immunity Receptor TLR8 in Live Mammalian Cells by Genetic Encoding of Photocaged Tyrosine.

Chembiochem 2021 Aug 30. Epub 2021 Aug 30.

Department of Chemistry, School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, P. R. China.

The effectiveness of innate immune responses relies on an intricate balance between activation and regulation. TLR8, a member of the Toll-like receptor (TLR) family, plays a fundamental role in host defense by sensing viral single-stranded RNAs (ssRNAs). However, the molecular recognition and regulatory mechanism of TLR8 is not fully understood, especially in a whole-cell environment. Read More

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Multiple targets identified with genome wide profiling of small RNA and mRNA expression are linked to fracture healing in mice.

Bone Rep 2021 Dec 5;15:101115. Epub 2021 Aug 5.

Institute of Biomedicine, University of Turku, Finland.

Long-bone fracture is a common injury and its healing process at the fracture site involves several overlapping phases, including inflammation, migration of mesenchymal progenitors into the fracture site, endochondral ossification, angiogenesis and finally bone remodelling. Increasing evidence shows that small noncoding RNAs are important regulators of chondrogenesis, osteogenesis and fracture healing. MicroRNAs are small single-stranded, non-coding RNA-molecules intervening in most physiological and biological processes, including fracture healing. Read More

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December 2021

CRISPR/Cas12a collateral cleavage activity for simple and rapid detection of protein/small molecule interaction.

Biosens Bioelectron 2021 Aug 25;194:113587. Epub 2021 Aug 25.

Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea. Electronic address:

To realize the full potential of the CRISPR/Cas system and expand its applicability up to the detection of molecular interactions, we herein describe a novel method to identify protein/small molecule interactions by utilizing the CRISPR/Cas12a collateral cleavage activity. This technique employs a single-stranded activator DNA modified with a specific small molecule, which would switch on the CRISPR/Cas12a collateral cleavage activity upon binding to crRNA within the CRISPR/Cas12a system. When the target protein binds to the small molecule on the activator DNA, the bound protein sterically hinders the access of the activator DNA to crRNA, thereby promoting less collateral cleavage activity of CRISPR/Cas12a. Read More

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Interfacial Engineering of Hybrid Polydopamine/Polypyrrole Nanosheets with Narrow Band Gaps for Fluorescence Sensing of MicroRNA.

ACS Appl Mater Interfaces 2021 Sep 26;13(35):42183-42194. Epub 2021 Aug 26.

Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No. 174 Shazheng Road, Chongqing 400044, China.

Nanoquencher-based biosensors have emerged as powerful tools for the detection of tumor markers, where challenges in efficiently docking the π-electron interaction interface toward nucleic acid probes containing π-electron-rich units of bases and fluorescent dyes still remain. Herein, we present hybrid polydopamine/polypyrrole nanosheets (PDA-PPy-NS) with π electron coupling and ultranarrow band gap (0.29 eV) by interfacial engineering of polymer hybrids at the nanoscale. Read More

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September 2021

Predicting base editing outcomes with an attention-based deep learning algorithm trained on high-throughput target library screens.

Nat Commun 2021 08 25;12(1):5114. Epub 2021 Aug 25.

Department of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.

Base editors are chimeric ribonucleoprotein complexes consisting of a DNA-targeting CRISPR-Cas module and a single-stranded DNA deaminase. They enable transition of C•G into T•A base pairs and vice versa on genomic DNA. While base editors have great potential as genome editing tools for basic research and gene therapy, their application has been hampered by a broad variation in editing efficiencies on different genomic loci. Read More

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Strategic analyses to identify key structural features of antiviral/antimalarial compounds for their binding interactions with 3CLpro, PLpro and RdRp of SARS-CoV-2: molecular docking and dynamic simulation studies.

J Biomol Struct Dyn 2021 Aug 25:1-18. Epub 2021 Aug 25.

Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, India.

Severe acute respiratory syndrome coronavirus (SARS-CoV-2), a novel member of the betacoronavirus family is a single-stranded RNA virus that has spread worldwide prompting the World Health Organization to declare a global pandemic. This creates an alarming situation and generates an urgent need to develop innovative therapeutic agents. In this context, an molecular docking and molecular dynamics (MD) simulation study on the existing 58 antiviral and antimalarial compounds was performed on 3CLpro, PLpro and RdRp SARS-CoV-2 proteins. Read More

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A CRISPR/Cas9-based single-stranded DNA recombineering system for genome editing of PD630.

Synth Syst Biotechnol 2021 Sep 10;6(3):200-208. Epub 2021 Aug 10.

Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.

Genome engineering of PD630, an important microorganism used for the bioconversion of lignin, is currently dependent on inefficient homologous recombination. Although a CRISPR interference procedure for gene repression has previously been developed for PD630, a CRISPR/Cas9 system for gene knockout has yet to be reported for the strain. In this study, we found that the cytotoxicity of Cas9 and the deficiency in pathways for repairing DNA double-strand breaks (DSBs) were the major causes of the failure of conventional CRISPR/Cas9 technologies in , even when augmented with the recombinases Che9c60 and Che9c61. Read More

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September 2021

Involvement of miR-214-3p/FOXM1 Axis During the Progression of Psoriasis.

Inflammation 2021 Aug 24. Epub 2021 Aug 24.

Department of Dermatology, Wuhan No 1 Hospital, Wuhan, China.

Psoriasis is a common, chronic, and relapsing skin disease characterized by hyperproliferation of keratinocytes and apoptosis delay. However, the molecular mechanisms underlying the progression of psoriasis remain elusive. MicroRNAs (miRNAs) are single-stranded, small non-coding RNAs that play a crucial role in the development of psoriasis by promoting targeted mRNA degradation or translational inhibition. Read More

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A New Type of Satellite associated with Cassava Mosaic Begomoviruses.

J Virol 2021 Aug 18:JVI0043221. Epub 2021 Aug 18.

Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695 USA.

Cassava mosaic disease (CMD), which is caused by single-stranded DNA begomoviruses, severely limits cassava production across Africa. A previous study showed that CMD symptom severity and viral DNA accumulation increase in cassava in the presence of a DNA sequence designated as SEGS-2 (equence nhancing eminivirus ymptoms). We report here that when SEGS-2 is co-inoculated with (ACMV) onto , viral symptoms increase. Read More

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Detection of bat-associated circoviruses in Korean bats.

Arch Virol 2021 Aug 17. Epub 2021 Aug 17.

Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea.

In recent years, several novel circular single-stranded DNA viruses have been detected in various mammals, birds, insects, and environmental samples using metagenomic and high-throughput sequencing approaches. In this study, we tested for the presence of circoviruses in 243 bat fecal samples collected between 2018 and 2019 from 48 sampling sites across Korea. To detect circoviruses, nested PCR was performed with degenerate primers targeting a conserved replication-associated protein (rep) gene of circovirus/cyclovirus. Read More

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Control of Liquid Crystal Microarray Optical Signals Using a Microspectral Mode Based on Photonic Crystal Structures.

Anal Chem 2021 08 16;93(34):11887-11895. Epub 2021 Aug 16.

State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China.

Herein, a novel liquid crystal microarray (LCM) film with optical regulation ability is first constructed by combining liquid crystals (LC) and the highly ordered microporous structure of inverse opal photonic crystals (IOPhCs). The LCM films are fabricated by infiltrating LC molecules into the LC polymer with the structure of IOPhCs, and their properties are very different from those without the LC. Interestingly, the optical property of LCM films can be controlled by changing the orientation of LC molecules, which varies with the interfacial force. Read More

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SARS-CoV-2 spike protein and RNA dependent RNA polymerase as targets for drug and vaccine development: A review.

Biosaf Health 2021 Jul 21. Epub 2021 Jul 21.

Department of Biochemistry, Abubakar Tafawa Balewa University Bauchi, Nigeria.

The present pandemic has posed a crisis to the economy of the world and the health sector. Therefore, the race to expand research to understand some good molecular targets for vaccine and therapeutic development for SARS-CoV-2 is inevitable. The newly discovered coronavirus 2019 (COVID-19) is a positive sense, single-stranded RNA, and enveloped virus, assigned to the beta CoV genus. Read More

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Synthesis and duplex-forming ability of oligonucleotides modified with 4'-C,5'-C-methylene-bridged nucleic acid (4',5'-BNA).

Bioorg Med Chem 2021 Aug 8;46:116359. Epub 2021 Aug 8.

Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan. Electronic address:

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. Read More

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