KW - Oligonucleotide microarray
Microarray analysis using disiloxyl 70mer oligonucleotides
OligoCalc: an online oligonucleotide properties calculator
Several methods for fabricating DNA arrays have been described (). These fall into two groups: in situ synthesis (), or deposition and immobilization of pre-synthesized DNA sequences (). Immobilization of pre-synthesized oligonucleotides offers the flexibility needed to quickly make low and medium-density arrays containing anywhere from several dozen to several hundred features per array. Although the technologies and skills needed to prepare low density arrays are readily available to a large number of researchers, there is an increasing need for high-throughput array-based analyses with high density arrays (>50 000 features per square centimeter). Both photolithographic and ink-jet array synthesis methods prepare arrays in a combinatorial manner, one nucleotide at a time. This permits the end user to create a high-density array with a greater diversity of sequences in less time and at a lower cost than spotting pre-synthesized oligonucleotides.
Since oligonucleotide probes are synthesized in known locations on the array, the hybridization patterns and signal intensities can be interpreted in terms of gene identity and relative expression levels by Affymetrix GeneChip Operating Software.
Microarrays: the use of oligonucleotides and ..
Figure Model of Cancer Classification. In this model, the Phenotype is represented by Morphological Characteristics/and subtypes; Proteomic profile can be derived from high-throughput tissue microarrays and immunohistochemistry plus automated computer-assisted quantitation with normalized intensities, protein microarrays and mass spectrometry; array comparative genomics for Copy Number Variation(CNV) and chromosomal aberrations, Genomic profiling using cDNA microarrays, and finally microRNA profiling. This provides protein profile and cDNA profiles for Gene Ontology and functional annotation. Signally pathways active or repressed can be derived. The CNV and microRNA data provide information to explain active oncogene induced pathways and miRNA targeted pathways that impact proliferation, cell survival, metastasis etc.
We demonstrate a new method for making oligonucleotide microarrays by synthesis in situ. The method uses conventional DNA synthesis chemistry with an electrochemical deblocking step. Acid is delivered to specific regions on a glass slide, thus allowing nucleotide addition only at chosen sites. The acid is produced by electrochemical oxidation controlled by an array of independent microelectrodes. Deblocking is complete in a few seconds, when competing side-product reactions are minimal. We demonstrate the successful synthesis of 17mers and discrimination of single base pair mismatched hybrids. Features generated in this study are 40 μm wide, with sharply defined edges. The synthetic technique may be applicable to fabrication of other molecular arrays.
Oligonucleotide Array - YouTube
Single-stranded DNA oligonucleotide synthesized directly on the surface of the GeneChip array using photolithography and combinatorial chemistry.
All information of the oligonucleotide DNA synthesis orders will be managed by our integrated LIMS and is able to share with other services (DNA Sequencing, MicroArray, Next-Gen Sequencing) for your research.
In Situ Synthesis of Oligonucleotide Microarrays | …
(2004), In situ synthesis of oligonucleotide microarrays
05/11/2014 · In oligonucleotide microarrays, short DNA oligonucleotides are spotted onto the array
oligonucleotide microarray; DNA chip; parallel synthesis;
In situ oligonucleotide synthesis on carbon materials: Stable substrates for microarray fabrication
Microarray oligonucleotide probe designer: a Web …
23/09/2011 · Microarray Generation of Thousand-Member Oligonucleotide ..
Bionexus DNA marker,Protein Marker,Gene-Peptide Synthesis
The PEG capping was implemented in DNA chip synthesis and the comparison chip was synthesized using regular AC capping. The goals in these experiments were to compare hybridization results when the two DNA chips were treated with cDNA samples labeled with Cy3 (universal total RNA sample) or Cy5 (skeletal muscle total RNA sample) fluorescent dye. The two samples were co-hybridized to the chip and the ratio of Cy3 to Cy5 is shown in color ranging from green (Cy3 > Cy5) to yellow (Cy3 = Cy5) to red (Cy5 > Cy3). The color ratio image comparison of the PEG capping versus the AC capping chip is shown in . This experiment validates that PEG capping is applicable to DNA microarray synthesis for the improvement of capping efficiency, which is critical for the initial synthesis steps of in situ oligonucleotide synthesis on glass surfaces. In addition, the capping reaction time using the PEG capping reagent is several fold shorter than that of AC capping.
Peptide Library Generation | Peptide Library Screening Tool
DNA microarrays are increasingly used in the biological sciences to help interpret the data emerging from large-scale genome sequencing. They are used for the analysis and comparison of gene expression levels (–), resequencing genes to identify mutations (–), analysis of sequence polymorphism on a large scale (,), optimization of antisense oligonucleotides (), basic studies of molecular hybridization (,) and analysing DNA–protein interactions (). Several methods have been developed to fabricate arrays. One set of methods deposits spots of presynthesized nucleic acids on the surface of the support (), or on microbeads (). In others, probes are synthesized in situ (–). Each method has its strengths and weaknesses. An ideal method of array fabrication would be rapid so that an array could be designed and made within a few hours, would have high spatial resolution to reduce the size and hence the amounts of reagents used in hybridization, would allow the use of different chemistries so that probes could be made with different backbones and bases, would allow 3′ or 5′ attachment so that probes could be used in enzymatic extension as well as hybridization based tests and would be programmable so that a computer file would direct defined sequences to defined sites on the array. No existing method of array fabrication meets all these criteria. A photolithographic method provides high spatial resolution () and has proven successful for repeat manufacture of the same oligonucleotide sets. But as each oligonucleotide set requires a new mask set, the method is less suitable for custom designs. A new light-directed method (), which uses programmable microarrays of mirrors rather than masks, may eliminate this problem and new photolabile protecting groups may improve coupling yields (), which are reported to be lower than conventional oligonucleotide synthesis yields at present (,). Physical masking using mechanical flow cells and conventional synthetic chemistry gives high coupling yields and also provides high resolution, but is best used for sets of probes with related sequences, such as all sequences of a predetermined length (), or tiling paths of all oligonucleotides complementary to a gene of known sequence (). Ink jet fabrication is rapid, highly flexible and has a high throughput (–). However, its resolution is limited by the accuracy in aiming droplets of reagents and by their spread upon surface impact ().
Locked Nucleic Acid (LNA™) Technology - Exiqon
An oligonucleotide microarray containing 3888 sequences, which are selected from human cancer related genes, was synthesized as described previously.5 One chip synthesis used a regular protocol with acetic anhydride (AC) capping and the other chip used the same protocol except for UniCap Phosphoramidite (PEG) capping.
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