• My research focuses on the synthesis of modified nucleosides, oligonucleotides, metallated oligonucleotides, and their conjugation to develop hybridization probes. (utu.fi)
  • Modified nucleosides and nucleic acids, Oligonucleotide chemistry, developing covalently mercurated hybridization probes. (utu.fi)
  • The short-oligonucleotide-based Affymetrix GeneChip ® arrays utilize multiple probes for each gene with an automated control for the experimental process from hybridization to quantification and thus provide reliable and comparable data [ 2 ]. (biomedcentral.com)
  • Existing methods for measuring transcript levels in single cells include RT-qPCR (1), single molecule counting using digital PCR (2) or hybridization probes (3, 4), and next generation sequencing (5). (justia.com)
  • Cy3 can also be used to label DNA oligos for use as hybridization probes in other applications, such as Fluorescent In-Situ Hybridization (FISH). (genelink.com)
  • This Double Labeling of Oligonucleotide Probes for Fluorescence In Situ Hybridization (DOPE-FISH 0 strategy may provide an effective solution to the problem of low signal intensity, which is commonly observed when using corresponding singly-labeled FISH probes for microbe identification. (genelink.com)
  • Also known as a genotypic assay, techniques include PCR, DNA fragment analysis, allele specific oligonucleotide (ASO) probes, DNA sequencing, and nucleic acid hybridization to DNA microarrays or beads. (biostars.org)
  • The technology utilizes fluorogenic oligonucleotide signaling probes and flow cytometry to detect and isolate individual living cells expressing one or more genes. (genelink.com)
  • The method is based upon the broadly-applicable principles of fluorescence-resonance energy transfer (FRET) and nucleic acid hybridization using fluorogenic oligonucleotide signaling probes originally reported for in tubo qRT-PCR applications, transfected into living cells. (genelink.com)
  • CHROMOVERT® PROCESS a) cDNAs are subcloned for expression of mRNAs comprising 3' untranslated plasmid-encoded Chromo-Tag™ sequences for detection using fluorogenic oligonucleotide signaling probes. (genelink.com)
  • Cell engineering method using fluorogenic oligonucleotide signaling probes and flow cytometry. (genelink.com)
  • The intensity of fluorescence is measured to quantify the amount of hybridization that has occurred between the probes and the target molecules. (tutorialspoint.com)
  • The probes can be cDNA fragments or oligonucleotides, depending on the type of microarray. (tutorialspoint.com)
  • The hybridization occurs between the complementary sequences of the probes and the target molecules. (tutorialspoint.com)
  • The cDNA microarray uses complementary DNA as probes, while the oligonucleotide microarray uses short DNA sequences as probes. (tutorialspoint.com)
  • In ECHO probes, a hybridization-dependent fluorescent nucleotide regulated by the H-aggregation of thiazole orange organic dyes (D 514 ) is incorporated into specific sequence contexts and serves as fluorescent detection readout for target nucleic acids. (ne.jp)
  • The target of ECHO probes is only the complementary single-stranded nucleic acid. (ne.jp)
  • If you have the data on the secondary structure of the target nucleic acid, it would give a hint for the design of probes. (ne.jp)
  • Locked Nucleic Acid in PCR primers, qPCR probes, and other types of oligonucleotides is soluble in water and standard buffers as well as follows Watson-Crick base-pairing rules. (sigmaaldrich.com)
  • Locked Nucleic Acid Dual-Labeled Probes discriminate better than DNA Dual-Labeled Probes in SNP genotyping analysis9. (sigmaaldrich.com)
  • Locked Nucleic Acid PCR primers and qPCR probes are compatible with all real-time thermocyclers and end-point analytical detection instruments. (sigmaaldrich.com)
  • The accuracy of T m calculations requires consideration of various physical properties of oligonucleotides, such as sequence length and composition, and accounts for experimental conditions, including the concentration of primers/probes, target oligo molecules, and salt/ionic strength. (idtdna.com)
  • Gene probes are used in various blotting and in situ hybridization (ISH) techniques for the detection of nucleic acid sequences in food industry, environmental, medical, and veterinary applications to improve the specificity of the analyses. (enzolifesciences.com)
  • Molecular probes can be broadly categorized into DNA probes and RNA probes, cDNA probes, and synthetic oligonucleotide probes. (enzolifesciences.com)
  • Nucleic acid probes are either a single stranded DNA or RNA with a strong affinity towards a specific DNA or RNA target sequence. (enzolifesciences.com)
  • Probes labeled by nick translation can be used in many different hybridization techniques including: chromogenic in situ hybridization (CISH), fluorescent in situ hybridization (FISH), screening gene banks by colony or plaque hybridization, DNA or RNA transfer hybridization, and re-association kinetic studies. (enzolifesciences.com)
  • Hybridization capture-based enrichment, which uses small bits of nucleic acid termed oligonucleotides as capture probes, is one method that allows for targeted sequencing. (qsstudy.com)
  • However, while hybridization capture-based enrichment is an effective method for targeted sequencing, commercially produced biotinylated capture probes are costly and can only be utilized for a limited number of reactions, making the per-sample cost for each capture process prohibitive. (qsstudy.com)
  • This process is repeated to build specific oligonucleotide sequences. (medscape.com)
  • The microarray technology is based on the hybridization of labelled DNA or RNA molecules to complementary sequences that are immobilized on a solid substrate. (tutorialspoint.com)
  • The principle of DNA microarray technology is based on the hybridization of complementary sequences of nucleic acid molecules. (tutorialspoint.com)
  • The oligonucleotides are designed to be complementary to specific DNA or RNA sequences that are to be analysed. (tutorialspoint.com)
  • Incorporating Locked Nucleic Acid into oligonucleotides increases thermal duplex stability 2 and improves the specificity of oligonucleotide hybridization to target sequences. (sigmaaldrich.com)
  • The bold letters in the sequences denote Locked Nucleic Acid bases. (sigmaaldrich.com)
  • Specifically, Locked Nucleic Acid oligonucleotides can be designed to address traditionally problematic target sequences, such as AT- or GC-rich regions. (sigmaaldrich.com)
  • Random priming is a type of primer extension in which a mixture of small oligonucleotide sequences, acting as primers, anneal to a heat-denatured double-stranded template. (enzolifesciences.com)
  • Detection of the rRNA amplification product sequences is achieved using nucleic acid hybridization (HPA). (cdc.gov)
  • These oligonucleotides (also known as "oligos") are biotin-tagged and intended to hybridize to their targets based on nucleic acid sequence complementarity, allowing enabling simple capture and isolation of target sequences from biological samples. (qsstudy.com)
  • Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. (bvsalud.org)
  • The 2 most common microarray technologies in use are the oligonucleotide microarrays and the robotically spotted complementary DNA (cDNA) microarrays. (medscape.com)
  • Oligonucleotide microarrays are manufactured by Affymetrix (Santa Clara, Calif) using photolithographic techniques. (medscape.com)
  • There are two main types of DNA microarrays: cDNA microarrays and oligonucleotide microarrays. (tutorialspoint.com)
  • Oligonucleotide microarrays are prepared by synthesizing oligonucleotides directly on the microarray chip. (tutorialspoint.com)
  • Gillespie and Spiegelman (1) observed that single stranded DNA binds strongly to nitrocellulose membranes in a manner that minimises the two strands reassociating with each other, but allows the hybridisation to complementary RNA. (ddw-online.com)
  • The ratio of quantum yields between after and before addition of the complementary nucleic acid strands showed a strong relationship with the number of possible Watson-Crick base pairs formed within two bases from D 514 in the 'self-dimer' of the probe. (ne.jp)
  • T m of duplex between an oligonucleotide and its complementary sequence. (sigmaaldrich.com)
  • The T m of an oligonucleotide duplex is the temperature at which half of the oligo molecules are single-stranded (and thus "melted") and half are double-stranded (i.e., annealed to its complementary strand). (idtdna.com)
  • Target amplification assays are based on the ability of complementary oligonucleotide primers to specifically anneal and allow enzymatic amplification of the target nucleic acid strands. (cdc.gov)
  • The method is based on a magnetic barcoding strategy: PCR-amplified target MTB genes are captured and magnetically labeled by a pair of complementary oligonucleotides conjugated to microspheres and magnetic nanoprobes. (cdc.gov)
  • The clear change in fluorescence intensity depending on hybridization is useful for visible gene analysis. (ne.jp)
  • The principle of DNA microarray is based on the hybridization of DNA strands. (tutorialspoint.com)
  • Therefore, an understanding of melting temperature (T m ) provides information on when and how the DNA or RNA strands are going to hybridize and defines the rules for hybridization. (idtdna.com)
  • While folding of a single oligonucleotide is concentration independent, the T m is strongly influenced by oligo concentration when 2 or more nucleic acid strands interact. (idtdna.com)
  • Examples of methods utilizing such non-radioactive detection methods include DNA sequencing, oligonucleotide probe methods, detection of polymerase-chain-reaction products, immunoassays, and the like. (justia.com)
  • Nucleic acid labeling is widely used by end-users for the detection of molecular infectious diseases. (technavio.com)
  • The advent of the nucleic acid labeling technique, coupled with the development of genomics, has significantly increased the use of molecular biology enzymes, kits, and reagents for the detection of pathogenic events at the genomic level. (technavio.com)
  • The lack of adequate training and courses on nucleic acid labeling tests available for the detection and staging of a disease is one of the prime factors limiting the number of students graduating to become laboratory technicians. (technavio.com)
  • In this web page, recent advances in nucleic acid detection using exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probe technologies are introduced to you. (ne.jp)
  • Solid phase hybridisation-based microplate assays have been uncovered to combine an excellent limit of detection (LOD) with outstanding assay performance at lower limit of quantification (LLOQ). (hum-molgen.org)
  • Other typical applications are: inflammation response monitoring (total and subclass IgG, IgE, IgA, IgM, cytokines, etc), assays for immunogenicity detection to your nucleic acid drugs or therapeutic monoclonal antibodies), complement activation monitoring, pathogen pharmacodynamics in antibiotics research (detection by ELISA or Real-Time qPCR), biomarker quantification as surrogate markers in preclinical or clinical drug developmen. (hum-molgen.org)
  • In theory, any nucleic acid can be used as a probe provided it can be labeled to permit detection and quantitation of the hybrid molecules formed between the probe and sequence to be identified. (enzolifesciences.com)
  • Here we introduce a platform for the detection of nucleic acids based on a magnetic barcoding strategy. (cdc.gov)
  • Nucleic acid amplification tests, in particular, have emerged as a preferred approach for TB detection. (cdc.gov)
  • Most recently, GeneXpert MTB/RIF (Cepheid) advanced nucleic acid-based detection by integrating PCR and a highly sensitive molecular-beacon assay into a single, automated system. (cdc.gov)
  • We herein report on the development of a nucleic acid platform designed to provide fast and portable detection, and demonstrated the utility by detecting MTB DNA from mechanically processed TB patient sputum samples. (cdc.gov)
  • Bacterial artificial chromosome-comparative genomic hybridization (BAC-CGH) has been used to look for genomic amplifications and deletions which may also contribute to expression changes. (ox.ac.uk)
  • Array comparative genomic hybridization analysis of colorectal cancer cell lines and primary carcinomas. (ox.ac.uk)
  • Array comparative genomic hybridization, with a genome-wide resolution of approximately 1 Mb, has been used to investigate copy number changes in 48 colorectal cancer (CRC) cell lines and 37 primary CRCs. (ox.ac.uk)
  • GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. (nih.gov)
  • The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. (nih.gov)
  • Another recently developed application of Real-Time qPCR uncovers an appealing area of increasing interest: the quantification of nucleic acid therapeutics in preclinical development. (hum-molgen.org)
  • The two main types of DNA microarray are the cDNA microarray and the oligonucleotide microarray. (tutorialspoint.com)
  • This temperature reduction allows hybridization to occur between the deoxyadenosine region on the capture oligomer and the poly-deoxythymidine molecules that are covalently attached to the magnetic particles. (cdc.gov)
  • DNA is a long chain of linear polymers containing deoxyribose sugars and their covalently bonded bases known as nucleic acids. (wikibooks.org)
  • These same assays have also been leveraged for highly parallel quantitative investigations of the structure-function relationships of nucleic acid interactomes. (nature.com)
  • Our services range from hybridisation assays to Real-Time qPCR to detect your investigational new drug based on nucleic acids chemistry (RNA/DNA). (hum-molgen.org)
  • We also offer immunology assays to investigate immune response to nucleic acids therapeutics. (hum-molgen.org)
  • Accelerō Bioanalytics comprehensive service portfolio provides sandwich hybridisation assays of any kind: hybridisation assays for aptamers, CpG oligonucleotides, or antisense therapeutics, hybridisation-ligation assays, competitive hybridisation assays for antisense therapeutics, ligation assay/qPCR combinations to detect viral point mutations, branched DNA probe assays for transcript quantification, and many more. (hum-molgen.org)
  • 20fold more sensitive than for conventional sandwich hybridisation assays. (hum-molgen.org)
  • Accelerō Bioanalytics offers custom-made quantitative Real-Time RT-qPCR assays for your investigational new nucleic acid drug like siRNA, micro RNA, or RNA aptamers. (hum-molgen.org)
  • Many new nucleic acid-based diagnostic tools or assays have been developed that allow analysis of DNA and RNA molecules in clinical samples. (enzolifesciences.com)
  • This nucleic acid labeling market research report provides valuable insights on the post COVID-19 impact on the market, which will help companies evaluate their business approaches. (technavio.com)
  • What will the Nucleic Acid Labeling Market Size be During the Forecast Period? (technavio.com)
  • The increasing research and development (R&D) activities at academic institutes and medical organizations is notably driving the nucleic acid labeling market growth, although factors such as a lack of skilled workforce may impede the market growth. (technavio.com)
  • Our research analysts have studied the historical data and deduced the key market drivers and the COVID-19 pandemic impact on the nucleic acid labeling industry. (technavio.com)
  • One of the key factors driving growth in the nucleic acid labeling market is the increasing research and development (R&D) activities at academic institutes and medical organizations. (technavio.com)
  • Such research studies on genome sequencing and genetics, in turn, increase the adoption of nucleic acid labeling by research laboratories. (technavio.com)
  • These institutes make use of nucleic acid labeling techniques to conduct their R&D activities. (technavio.com)
  • Such factors are thus expected to propel the growth of the global nucleic acid labeling market. (technavio.com)
  • The increasing investment in the development of new biotechnological techniques is a nucleic acid labeling market trend that is expected to have a positive impact in the coming years. (technavio.com)
  • In recent years, end-users such as hospitals, diagnostic centers, academic institutes, and research organizations have been increasingly opting for nucleic acid labeling techniques for disease diagnosis. (technavio.com)
  • Such increasing use of nucleic acid labeling for exploring disease-related genes and management of infectious diseases is expected to positively impact the growth of the global nucleic acid labeling market. (technavio.com)
  • The lack of a skilled workforce will be a major challenge for the nucleic acid labeling market during the forecast period. (technavio.com)
  • Nucleic acid labeling needs skilled professionals such as pathologists and clinicians who can perform nucleic acid labeling tests, genotyping tests, and predisposition diagnostic tests. (technavio.com)
  • In addition, the improved hybridization of the PCR primer or qPCR probe to its target may increase the melting temperature (T m ) by up to 8 °C per Locked Nucleic Acid monomer substitution in medium salt conditions compared to native-state DNA oligonucleotides 4 ( Table 1 ). (sigmaaldrich.com)
  • To address these unknowns, we employ steady-state and time-resolved infrared spectroscopy to measure the influence of cytosine modification on the thermodynamics and kinetics of hybridization by assessing the impact on local base pairing dynamics, shifts in the stability of the duplex state, and changes to the hybridization transition state. (acs.org)
  • Read this advice from our own thermodynamics specialist, Dr Richard Owczarzy, on the effects of probe and primer melting temperature (T m ) on hybridization. (idtdna.com)
  • Dr Richard Owczarzy (Ohv-char'-zee), a Principal Scientist at IDT and an extensively published expert on nucleic acid thermodynamics, confirms that many researchers are still under the illusion that they can use a simple formula to calculate T m -multiplying the number of GC and AT bases by a given constant. (idtdna.com)
  • In contrast, strong emission is observed when the ECHO probe binds to its target nucleic acid, because the aggregate is dissolved and each dye independently intercalates into the nascent duplex structure. (ne.jp)
  • The presence of a single base mismatch has a greater destabilizing effect on the duplex formation between an Locked Nucleic Acid oligonucleotide and its target than with a native-state DNA oligonucleotide. (sigmaaldrich.com)
  • Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation. (harvard.edu)
  • This increase in hybridization creates a significant broadening in the scope of assay conditions and allows for more successful multiplexing. (sigmaaldrich.com)
  • Dot blotting and dot hybridisation (4) evolved out of the filter hybridisation technique and provided the basic concept for DNA arrays. (ddw-online.com)
  • During the hybridization step, the sequence specific regions of the capture oligomers bind to specific regions of the target molecules. (cdc.gov)
  • The introduction of solid supports for DNA hybridisation/reassociations greatly broadened the range of applications of nucleic acid hybridisations, and provided the basis for solid-based methods being used today. (ddw-online.com)
  • [ 7 ] They consist of a glass surface onto which oligonucleotides consisting of 25 bases are built a single nucleotide at a time. (medscape.com)
  • Whipple's disease (WD) is a rare chronic systemic infection with a wide range of clinical symptoms, routinely diagnosed in biopsies from the small intestine and other tissues by periodic acid-Schiff (PAS) diastase staining and immunohistological analysis with specific antibodies. (frontiersin.org)
  • Pink) mutant DNA analysis with Locked Nucleic Acid mutant probe (16mer with 3 Locked Nucleic Acid bases). (sigmaaldrich.com)
  • Results of Northern blot analysis revealed that RNA isolated from the liver of mullet collected from the highly contaminated region of Izmir Bay with a dissolved and dispersed petroleum hydrocarbon content of 12.45 mug 1(-1) gave a strong hybridization signal, whereas only a weak hybridization signal was detected in the liver RNA of fish caught from the reference site containing less than 1 mug 1(-1) Of petroleum hydrocarbons. (metu.edu.tr)
  • Where my research was focused on the biomimetic total Synthesis of complex natural products mainly bioactive lactones from carbohydrate scaffolds and Artemisinic acid glycoconjugates synthesis. (utu.fi)
  • I later moved to the University at Albany, State University of New York (SUNY), USA for my postdoctoral research, where I worked on α-functionalization of Cysteine type amino acids with various alkyl halides using photocatalysis and dimeric compounds synthesis through dearomatization reactions. (utu.fi)
  • Despite considerable interest in these modified bases, their impact on the thermodynamic stability of double-stranded DNA (dsDNA) remains ambiguous and their influence on hybridization kinetics and dynamics is even less well-understood. (acs.org)
  • The concentrations of monovalent (sodium, potassium), divalent (magnesium), and polyvalent cations affect the stability of hybridized oligonucleotides [ 3,4 ]. (idtdna.com)
  • In the presence of target sequence, hybridization of the sequence-specific probe results in a fluorogenic conformational change. (genelink.com)
  • Table 1 Increasing the number of Locked Nucleic Acid bases in an oligonucleotide increases the T m . (sigmaaldrich.com)
  • The ability of oligonucleotides to discriminate between alleles via SNPs is greatly enhanced by the incorporation of Locked Nucleic Acid bases 6-8 ( Figure 2 ). (sigmaaldrich.com)
  • Shorter oligonucleotides incorporating Locked Nucleic Acid bases can be used at the same temperatures as longer native-state DNA oligonucleotides. (sigmaaldrich.com)
  • Purple) wild-type DNA with Locked Nucleic Acid mutant Probe (16mer with 3 Locked Nucleic Acid bases). (sigmaaldrich.com)
  • For example, AT-rich native-state DNA oligonucleotides often need to be over 30 bases long (sometimes over 40 bases) to satisfy amplicon design guidelines but may still perform poorly. (sigmaaldrich.com)
  • With Locked Nucleic Acid oligonucleotides, the selective placement of Locked Nucleic Acid bases facilitates the optimal design of highly-specific, shorter oligonucleotides that perform well, even at lengths of only 13 to 20 bases. (sigmaaldrich.com)
  • In DNA a sequence of three bases, which is called a codon, is responsible for the encoding of a single amino acid. (wikibooks.org)
  • The proto-oncogene myc (c-myc) codes for a nuclear protein which is involved in nucleic acid metabolism and in mediating the cellular response to growth factors. (edu.au)
  • The degree of homology between target and probe results in stable hybridization. (enzolifesciences.com)
  • Due to Locked Nucleic Acid's improved hybridization characteristics with accompanied increase in T m , Locked Nucleic Acid oligonucleotides can be synthesized to be shorter, which overcomes certain design limitations that occur with native-state DNA oligonucleotides. (sigmaaldrich.com)
  • In this DECODED™ article, we learn from IDT scientist Dr Richard Owczarzy about oligonucleotide characteristics that impact melting temperature (T m ), a critical factor when planning experiments involving nucleic acid hybridization. (idtdna.com)
  • Important factors that affect T m , including oligo concentration, ion concentration, sequence mismatch, and target strand choice, can all play a signification role in hybridization experiments. (idtdna.com)
  • These nucleic acid polymers encode for the all of the materials an organism needs to live in the form of genes. (wikibooks.org)
  • Also, the design of oligonucleotides for targeting difficult SNPs, such as the relatively stable G:T mismatch, is greatly facilitated by Locked Nucleic Acid. (sigmaaldrich.com)
  • Early studies of DNA melting and reformation were carried out in aqueous solutions and yielded important information about the dependence of melting temperature (Tm) on the G+C composition and salt concentration, as well as information on the dependence of the rate of reassociation on the sequence complexity of the nucleic acid. (ddw-online.com)
  • gene that contains a sequence that hybridizes with an oligonucleotide probe specific for M. tuberculosis complex bacteria. (cdc.gov)