Allele-specific PCR with fluorescently labeled probes: criteria for selecting primers for genotyping by V. A. Devyatkin, A. A. Shklyar, A. Zh. Fursova, Yu. V. Rumyantseva, O. S. Kozhevnikova

“…The method consists of real-time PCR with a pair of primers and two oligonucleotide probes that are complementary to a sequence near a given locus in such a way that one probe is complementary to the wild-type allele, and the other to a mutant one. …”
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Assessment of genetic diversity of some Siberian and Far Eastern species of the genus Spiraea (Rosaceae) by newly developed multiplex panels of nuclear SSR loci by T. A. Poliakova, A. V. Shatokhina, G. N. Bondarenko, D. V. Politov

“…We screened 37 previously published heterologous oligonucleotide primer pairs for nuclear microsatellite loci and selected eight polymorphic and most reproducible of them for PCR multiplexing which substantially increases performance of routine mass genotyping. …”
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Differential Expression of -Associated Genes in Autosomal Dominant Polycystic Kidney Disease by Yeon Joo Yook, Yu Mi Woo, Moon Hee Yang, Je Yeong Ko, Bo Hye Kim, Eun Ji Lee, Eun Sun Chang, Min Joo Lee, Sunyoung Lee, Jong Hoon Park

“…To address this question, we presently created Pkd2 knockout and PKD2 transgenic mouse embryo fibroblasts. We used a mouse oligonucleotide microarray to identify messenger RNAs whose expression was altered by the overexpression of the PKD2 or knockout of the Pkd2. …”
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Mutation Analysis of Synthetic DNA Barcodes in a Fission Yeast Gene Deletion Library by Sanger Sequencing by Minho Lee, Shin-Jung Choi, Sangjo Han, Miyoung Nam, Dongsup Kim, Dong-Uk Kim, Kwang-Lae Hoe

“…Peculiarly, the frequency of substitutions (67.6%) was unexpectedly higher than in budding yeast (~28%) and well above the predicted error of Sanger sequencing (~2%), which might have arisen during the solid-phase oligonucleotide synthesis and PCR amplification of the barcodes during strain construction. …”
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The Construction of a Standard Karyotype of Intermediate Wheatgrass and Its Potential Progenitor Species by Lin Wang, Shuang Liang, Fei Qi, Yinguang Bao, Richard R.-C. Wang, Xingfeng Li

“…FISH karyotype was established using pSc119.2-1, (GAA)₁₀, AFA-3, AFA-4, pAs1-1, pAs1-3, pAs1-4, and pAs1-6 as a combined multiplex oligonucleotide probe. MATO software was used to analyze chromosome length, arm ratio, and karyotype structure. …”
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Massively parallel homogeneous amplification of chip-scale DNA for DNA information storage (MPHAC-DIS) by Zhi Weng, Jiangxue Li, Yi Wu, Xuehao Xiu, Fei Wang, Xiaolei Zuo, Ping Song, Chunhai Fan

“…The MPHAC-DIS system using 35,406 encoded oligonucleotide allows simultaneous access of multimedia files including text, images, and videos with high decoding accuracy at very low sequencing depths. …”
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Structural Characterization of B-DNA d(CGTGAATTCACG)₂ in Complex with the Specific Minor Groove Binding Fluorescent Marker Hoechst 33342 by Hristina Sbirkova-Dimitrova, Rusi Rusew, Hristo Gerginov, Annie Heroux, Boris L. Shivachev

“…The structure is nearly isomorphous with that of previously reported crystal structures of the oligonucleotide d(CGTGAATTCACG)₂ alone (PDB ID: 5JU4) and with that in complexes with DAPI (5T4W). …”
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Prediction and verification of the influence of the rs367781716 SN P on the interaction of ТАТА -binding protein with the promoter of the human АВСА9 gene by O. V. Arkova, I. A. Drachkova, T. V. Arshinova, D. A. Rasskazov, V. V. Suslov, P. M. Ponomarenko, M. P. Ponomarenko, N. A. Kolchanov, L. K. Savinkova

“…For preclinical empirical verification of rs367781716, we used an electrophoretic mobility shift assay (EMSA) to measure the rates of formation (ka) and decay (kd) of the complexes of TBP with an oligonucleotide matching either allele –37C or –37T of the АВСА9 gene. …”
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Exploring the Mechanism of Skeletal Muscle in a Tacrolimus-Induced Posttransplantation Diabetes Mellitus Model on Gene Expression Profiles by Chenlei Zheng, Cheng Wang, Tan Zhang, Ding Li, Xiao-feng Ni, Jian-Hu Lin, Linxiao Sun, Bicheng Chen

“…Gene expression profiles in quadriceps muscle from this rat model were characterized by oligonucleotide microarrays. Then, differences in gene expression profiles in muscle from PTDM rats that received tacrolimus and control subjects were analyzed by using GeneSpring GX 11.0 software (Agilent). …”
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Epidemiology of bacterial biofilms on polyps and normal tissues in a screening colonoscopy cohort by Julia L. Drewes, Samara B. Rifkin, Madison McMann, Sara Glass, Emma Spence, Caroline R. Wensel, Abby L. Geis, Courtney Stevens, Joell J. Gills, Hao Wang, Linda M. Hylind, Gerard Mullin, David Kafonek, David Cromwell, Louis La Luna, Francis M. Giardiello, Cynthia L. Sears

“…Here we evaluated potential procedural and demographic risk factors associated with biofilm status using a cross-sectional observational cohort.Methods Histologically normal colonic biopsies from 2,051 individuals undergoing screening colonoscopy were evaluated for biofilm status using fluorescence in situ hybridization with oligonucleotide probes targeting bacterial 16S rRNA. Polyp tissues from 21 individuals were also examined. …”
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Trojan-horse silk fibroin nanocarriers loaded with a re-call antigen to redirect immunity against cancer by Luca Mastracci, Patrizio Castagnola, Elia Bari, Francesca Ferrera, Tiziana Altosole, Sara Perteghella, Pierluigi Mauri, Rossana Rossi, Giulia Passignani, Martina Galati, Giuseppina Iliana Astone, Maddalena Mastrogiacomo, Daniela Fenoglio, Dario Di Silvestre, Maria Luisa Torre, Gilberto Filaci

“…Since tumor immune escape mechanisms do not impact pre-existing and consolidated immune responses, we tested the hypothesis of redirecting a pregenerated immunity to cancer: to recall a non-tumor antigen response against the tumor, silk fibroin nanoparticles (SFNs) have been selected as ‘Trojan-horse’ carriers, promoting the antigen uptake by the tumor cells.Methods SFNs have been loaded with either ovalbumin (OVA) or CpG oligonucleotide (CpG) as antigen or adjuvant, respectively. …”
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The aptamer BC 007 for treatment of dilated cardiomyopathy: evaluation in Doberman  Pinschers of efficacy and outcomes by Sabine Werner, Gerd Wallukat, Niels‐Peter Becker, Katrin Wenzel, Johannes Müller, Ingolf Schimke, Gerhard Wess

“…Abstract Aims Aptamer BC 007, a 15‐mer single‐strand DNA oligonucleotide (5'‐GGTTGGTGTGGTTGG‐3'), was developed to neutralize functional autoantibodies that bind to the extracellular domains of G protein‐coupled receptors (GPCR‐AAB), leading to the modulation of receptor‐mediated signalling cascades that induce pathophysiological states. …”
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Recognition mechanism and sequence optimization of organophosphorus pesticides aptamers for better monitoring contaminations in food by Pengfei Chen, Chaoqiong Hu, Xuan Tao, Zheng Zhou, Lijun Wang, Xiao Yang, Zhenming Che, Xianggui Chen, Yukun Huang

“…The aim of the research was to develop a new strategy to design oligonucleotide sequences for binding OPPs by combination of experimental and molecular modeling methods. 3D models of aptamers binding OPPs were constructed, and binding energy and the most probable binding site for the OPPs were then determined by molecular docking, and the binding sites were further confirmed by the results of 2-AP replaced experiments. …”
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A concept of natural genome reconstruction. Part 2. Effect of extracellular double-stranded DNA fragments on hematopoietic stem cells by V. S. Ruzanova, S. G. Oshikhmina, A. S. Proskurina, G. S. Ritter, S. S. Kirikovich, E. V. Levites, Y. R. Efremov, T. V. Karamysheva, M. I. Meschaninova, A. L. Mamaev, O. S. Taranov, A. S. Bogachev, S. V. Sidorov, S. D. Nikonov, O. Y. Leplina, A. A. Ostanin, E. R. Chernykh, N. A. Kolchanov, E. V. Dolgova, S. S. Bogachev

“…In this case, up to five oligonucleotide monomers containing 9 telomeric TTAGGG repeats are stitched together into one structure. …”
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Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dsc... by Jacob M. Sadler, Alfred Simkin, Valery P. K. Tchuenkam, Isabela Gerdes Gyuricza, Isabela Gerdes Gyuricza, Abebe A. Fola, Kevin Wamae, Ashenafi Assefa, Ashenafi Assefa, Karamoko Niaré, Kyaw Thwai, Samuel J. White, William J. Moss, Rhoel R. Dinglasan, Sandrine Eveline Nsango, Christopher B. Tume, Jonathan B. Parr, Jonathan B. Parr, Jonathan B. Parr, Innocent Mbulli Ali, Jeffrey A. Bailey, Jeffrey A. Bailey, Jonathan J. Juliano, Jonathan J. Juliano, Jonathan J. Juliano, Jonathan J. Juliano

“…Moreover, genotyping of parasites and detection of molecular markers drug resistance in resource-limited regions requires open-source protocols for processing samples, using accessible reagents, and rapid methods for processing numerous samples including pooled sequencing.MethodsPlasmodium falciparum Streamlined Multiplex Antimalarial Resistance and Relatedness Testing (Pf-SMARRT) is a PCR-based amplicon panel consisting of 15 amplicons targeting antimalarial resistance mutations and 9 amplicons targeting hypervariable regions. This assay uses oligonucleotide primers in two pools and a non-proprietary library and barcoding approach.ResultsWe evaluated Pf-SMARRT using control mocked dried blood spots (DBS) at varying levels of parasitemia and a mixture of 3D7 and Dd2 strains at known frequencies, showing the ability to genotype at low parasite density and recall within-sample allele frequencies. …”
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BAC-browser: the tool for synthetic biology by Tatiana A. Semashko, Gleb Y. Fisunov, Georgiy Y. Shevelev, Vadim M. Govorun

“…To assemble DNA sequences, a fragmentation tool was created: regular breakdown into oligonucleotides of a certain length and breakdown into oligonucleotides with thermodynamic alignment. …”
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Application of the weighted histogram method for calculating the thermodynamic parameters of the formation of oligodeoxyribonucleotide duplexes by I. I. Yushin, V. M. Golyshev, D. V. Pyshnyi, A. A. Lomzov

“…Some of the most important physicochemical properties of oligonucleotides are thermodynamic parameters of the formation of their duplexes with DNA and RNA. …”
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Making Sense of Antisense by Bruce R Yacyshyn, William R Shanahan

“…A recent report on the use of systemically administered oligonucleotides in human Crohn’s disease is reviewed. …”
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Capture-SELEX: Selection of DNA Aptamers for Aminoglycoside Antibiotics by Regina Stoltenburg, Nadia Nikolaus, Beate Strehlitz

“…The oligonucleotides of these binding complexes were amplified, purified, and immobilized via the docking sequence to the magnetic beads as the starting point of the following selection round. …”
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Fluorescent DNA Stabilized Silver Nanoclusters as Biosensors by Alfonso Latorre, Romina Lorca, Álvaro Somoza

“…Moreover, since oligonucleotides can be designed to have binding properties (aptamers) a variety of sensors for proteins and cells have been developed using silver nanoclusters. …”
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