Immobilized Native Bacteria as a Tool for Bioremediation of Soils and Waters: Implementation and Modeling by C. Lobo, M. Sanchez, C. Garbi, E. Ferrer, M.J. Martinez-Iñigo, J.L. Allende, C. Martinez, L. Casasas, R. Alonso, A. Gibello, M. Martin

“…Based on 3,4-dihydroxyphenylacetate (3,4-DHPA) dioxygenase amino acid sequence and DNA sequence data for homologous genes, two different oligonucleotides were designed. These were assayed to detect 3,4-DHPA related aromatic compound—degrading bacteria in soil samples by using the FISH method. …”
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Structural Properties of G,T-Parallel Duplexes by Anna Aviñó, Elena Cubero, Raimundo Gargallo, Carlos González, Modesto Orozco, Ramon Eritja

“…Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. …”
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Gene Therapy for HIV Infections: Intracellular Immunization by Alain Piché

“…These strategies include the use of single-chain antibodies, capsid-targeted viral inactivation, transdominant negative mutants, ribozymes, antisense oligonucleotides and RNA decoys. While a number of issues remain to be studied before intracellular immunization can be applied to the treatment of HIV infections, the significant progress already made in this field is likely to lead to clinical applications.…”
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Molecular Patterns of MEFV Gene Mutations in Egyptian Patients with Familial Mediterranean Fever: A Retrospective Cohort Study by Amal R. Mansour, Ayman El-Shayeb, Nihal El Habachi, Mohamad A. Khodair, Doaa Elwazzan, Nermeen Abdeen, Marwa Said, Riham Ebaid, Noha ElShahawy, Amr Seif, Nadia Zaki

“…This test is based on reverse hybridization of biotinylated PCR products on immobilized oligonucleotides for mutations and controls in a parallel array of allele-specific oligonucleotides. …”
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Diagnostic and Therapeutic Advances of RNAs in Precision Medicine of Gastrointestinal Tumors by Runhan Liu, Jiaxin Zhou, Xiaochen Chen, Jie Zhang, Qunzhi Chen, Xiaoming Liu, Kunhou Yao

“…Many RNA-based therapeutics, such as small interfering RNA (siRNA) and antisense oligonucleotides (ASO), have entered clinical trials or are available on the market. …”
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Research Progress in Small-Molecule Detection Using Aptamer-Based SERS Techniques by Li Zheng, Qingdan Ye, Mengmeng Wang, Fan Sun, Qiang Chen, Xiaoping Yu, Yufeng Wang, Pei Liang

“…Nucleic acid aptamers are single-stranded oligonucleotides that are selected through exponential enrichment (SELEX) technology from synthetic DNA/RNA libraries. …”
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Targeting RNA splicing modulation: new perspectives for anticancer strategy? by Xuemei Lv, Xiaoyu Sun, Yang Gao, Xinyue Song, Xiaoyun Hu, Lang Gong, Li Han, Miao He, Minjie Wei

“…Especially, we discuss current and emerging RNA splicing-targeted strategies for cancer therapy, including pharmacological approaches and splice-switching antisense oligonucleotides (ASOs). Finally, we address the challenges and opportunities in translating these findings into clinical practice.…”
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Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions by Shu-ichi Nakano, Masayuki Fujii, Naoki Sugimoto

“…Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. …”
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Design and structure of overlapping regions in PCA via deep learning by Yan Zheng, Xi-Chen Cui, Fei Guo, Ming-Liang Dou, Ze-Xiong Xie, Ying-Jin Yuan

“…Utilizing the model, we developed the SmartCut algorithm aimed at designing oligonucleotides and enhancing the success rate of PCA experiments. …”
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On-Chip DNA Assembly via Dielectrophoresis by Xichuan Rui, Lin-Sheng Wu, Xin Zhao

“…By applying an alternating current signal set at 2 MHz, we successfully achieve the desired directed movement of oligonucleotides. Additionally, chemical treatments combined with photoirradiation enabled the connection of complementary gene sequences and the subsequent release of single-stranded DNA products. …”
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SURFACE PLASMON RESONANCE STUDY OF THE INTERACTION BETWEEN THE HUMAN TATA-BOX BINDING PROTEIN AND THE TATA ELEMENT OF THE NOS2A GENE PROMOTER by I. A. Drachkova, S. V. Shekhovtsov, S. E. Peltek, P. M. Ponomarenko, T. V. Arshinova, M. P. Ponomarenko, T. I. Merkulova, L. K. Savinkova, N. A. Kolchanov

“…Experiments utilizing the SPR method and classical EMSA have shown that ТВР immobilization on the microchip dextran surface does not alter its affinity to TATA-containing oligonucleotides.…”
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Selective Phenome Growth Adapted NK Model: A Novel Landscape to Represent Aptamer Ligand Binding by Andrew Brian Kinghorn, Julian Alexander Tanner

“…Aptamers are single-stranded oligonucleotides selected by evolutionary approaches from massive libraries with significant potential for specific molecular recognition in diagnostics and therapeutics. …”
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Aptamers: A Feasible Technology in Cancer Immunotherapy by M. M. Soldevilla, H. Villanueva, F. Pastor

“…Aptamers are single-chained RNA or DNA oligonucleotides (ODNs) with three-dimensional folding structures which allow them to bind to their targets with high specificity. …”
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Downregulation of an Evolutionary Young miR-1290 in an iPSC-Derived Neural Stem Cell Model of Autism Spectrum Disorder by Dalia Moore, Brittney M. Meays, Lepakshe S. V. Madduri, Farah Shahjin, Subhash Chand, Meng Niu, Abrar Albahrani, Chittibabu Guda, Gurudutt Pendyala, Howard S. Fox, Sowmya V. Yelamanchili

“…Supplementing ASD patient-derived neural stem cells (NSCs) with conditioned media from differentiated control-NSCs spiked with “artificial EVs” containing synthetic miR-1290 oligonucleotides significantly rescued differentiation deficits in ASD cell lines. …”
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Selection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencing by Delia J. Scoville, Tae Kyu Brian Uhm, Jamie A. Shallcross, Rebecca J. Whelan

“…Here, we report on our use of One-Pot SELEX to isolate single-stranded DNA aptamers with affinity for CA125, followed by high-throughput sequencing of the selected oligonucleotides. This data-rich approach, combined with bioinformatics tools, enabled the entire selection process to be characterized. …”
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Preclinical assessment of splicing modulation therapy for ABCA4 variant c.768G>T in Stargardt disease by Dyah W. Karjosukarso, Femke Bukkems, Lonneke Duijkers, Tomasz Z. Tomkiewicz, Julia Kiefmann, Andrei Sarlea, Sander Bervoets, Irene Vázquez-Domínguez, Laurie L. Molday, Robert S. Molday, Mihai G. Netea, Carel B. Hoyng, Alejandro Garanto, Rob W. J. Collin

“…Methods To correct this aberrant splicing, twenty-five 2′-O-methoxyethyl antisense oligonucleotides (AONs) were designed, spanning the entire exon elongation. …”
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Labeling tumor-associated extracellular vesicles with antibody-DNA conjugates for quantitative analysis by Xiao Du, Xiao Du, Xiao Du, Hongxiu Li, Hongxiu Li, Hongxiu Li, Shiyi Shen, Shiyi Shen, Shiyi Shen, Chao Tian, Chao Tian, Chao Tian, Xiaohuan Cao, Xiaohuan Cao, Xiaohuan Cao, Xingang Xu, Nan Xu, Shuling Wang, Shuling Wang, Shuling Wang, Qingchang Tian, Qingchang Tian, Qingchang Tian

“…The antibody-DNA conjugate contained one antibody associated with three oligonucleotides for signal amplification. The antibody in the conjugate can recognize the surface tumor antigens of TAEs. …”
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Natural Modulators of Endosomal Toll-Like Receptor-Mediated Psoriatic Skin Inflammation by Chao-Yang Lai, Yu-Wen Su, Kuo-I Lin, Li-Chung Hsu, Tsung-Hsien Chuang

“…Several immune modulatory oligonucleotides and small molecular weight compounds, including IMO-3100, IMO-8400, and CPG-52364, that block the interaction between endosomal TLRs and their ligands are under clinical investigation for their effectiveness in the treatment of psoriasis. …”
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Generation of barcoded plasmid libraries for massively parallel analysis of chromatin position effects by M. O. Lebedev, L. A. Yarinich, A. V. Ivankin, A. V. Pindyurin

“…First, we highlight the critical parameters that should be considered in the generation of barcoded plasmid libraries and introduce a simple method to assess the diversity of random sequences (barcodes) of synthetic oligonucleotides using PCR amplification followed by Sanger sequencing. …”
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Dynamics of REL, RELA and IRF1 transcription factor expression in U937 macrophages after dioxin exposure by E. V. Kashina, D. Y. Oshchepkov, E. V. Antontseva, M. Y. Shamanina, D. P. Furman, V. A. Mordvinov

“…The binding of the TCDD:AhR:ARNT transcription complex from the nuclear extract with double-stranded oligonucleotides containing the putative DREs was studied by the EMSA. …”
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