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Long DNA synthesis from oligonucleotide mixtures by …

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process.

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Solid-phase oligonucleotide synthesis - ATDBio

Mispriming can be minimized by keeping the melting temperatures of the oligos as high as possible, and by keeping the oligos as long as possible. Unfortunately, doing so will also increase the possibility of introducing errors from oligonucleotide synthesis. Gene synthesis is very much a balancing act.

Each tandem synthesis was prepared using our long oligonucleotide synthesis protocol.

The original version of DNAWorks was restricted to oligos being immediately adjacent to each other. This was primarily due to my belief that the oligos should be as short as possible. However, increases in the efficiency of oligonucleotide synthesis and user demands warranted the ability to gap oligos. In version 2, oligos can be as long as the user wants, but no smaller than 20 nt.

custom oligo synthesis, oligonucleotides ..

After spending so much time getting a synthetic gene put together, wouldn't it be simple to make 1-3 new oligos for each site-directed mutation and be sure the new oligos will not create problems in the PCR? Well, now you can! Clicking on "mutant sequence" will display the entry form for doing just that. Enter a job name, the mutated sequence (make sure it is the same length as the original sequence), the original logfile and trial number (used for original gene synthesis). The parameters will be set to the same as that of the trial number from the original logfile. Once everything is entered, clicking "Design oligos" will generate the replacement oligos, along with an evaluation of scores for the mutated sequence. The mutation is printed in lowercase font, and it is highlighted in the oligonucleotide assembly.

DNAWorks is a computer program that automates the design of oligonucleotides for gene synthesis by PCR-based gene assembly. The program requires simple input information: an amino acid sequence of the target protein or a DNA sequence, and a desired annealing temperature. Additionally, codons can be optimized for an organism of choice, sequences (such as restriction sites) can be excluded from the protein coding region, and flanking sequences (for subsequent cloning or integration) can be added to the protein coding region. The program outputs a set of oligonucleotide sequences with highly homogeneous annealing temperatures, minimal size, and low tendencies for hairpin formation and mispriming by both short and long range repeats. With the help of DNAWorks and a two-step PCR method, synthetic genes of up to 3000 basepairs can be successfully constructed.

TriLink BioTechnologies - Oligo Synthesis, mRNA, …

The oligo length parameter provides a limit to the length in nucleotides any one of a set of synthetic oligonucleotides can attain. The synthesis of oligonucleotides is subject to errors, mainly deletions, but occasionally mismatches and insertions. The error rate of oligonucleotide synthesis is primarily dependent on length; longer oligonucleotides tend to have more errors (although operator methodology can play a strong role as well -- DNAWorks cannot address technical sloppiness!). To minimize the number of errors in synthetic genes, it is best to keep the oligonucleotide lengths to a minimum.

The annealing temperature parameter sets an ideal annealing temperature for a set of synthetic oligonucleotides. At this temperature, under normal PCR conditions (ionic strength ~100 mM, [Mg2+] = 1-4 mM), all of the oligonucleotides will anneal and assemble cooperatively. The uniformity of annealing temperatures prevents mispriming and/or lack of priming prior to the elongation step, and helps to assure a single uniform PCR product.

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  • FAM (fluorescein), HEX, JOE, ROX, TAMRA, TET, Texas …

    - Gene Link

  • DNA & RNA & ZNA Oligonucelotide Synthesis | …

    About Us - Bio-Synthesis

  • 15/01/2015 · Original Article

    TriLink manufactures oligonucleotides, modified nucleoside triphosphates, mRNA and long RNA.

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FDA-Approved Oligonucleotide Therapies in 2017: …

This article by Eugene Lukhtanov of ELITechGroup Molecular Diagnostics introduces the tripeptide of dihydropyrroloindole-carboxylate (CDPI3), which is a minor groove binding (MGB) moiety derived from the natural product CC-1065 and exhibits strong DNA binding properties. Synthetic oligonucleotides with covalently-attached CDPI3 moieties have enhanced DNA affinity and have improved the hybridization properties of sequence-specific DNA probes. Short CDPI3-oligonucleotides hybridize with single-stranded DNA to give more stable DNA duplexes than unmodified oligonucleotides of similar length. The author describes the general properties of CDPI3 MGB-oligonucleotide conjugates in detail, along with some specific applications:

Click Chemistry -- Publications

Enter a job name, email address (optional), the mutated sequence(s) (make sure they are the same length(s) as the original sequence(s)), the original logfile and trial number (used for original gene synthesis). The parameters will be set to the same as that of the trial number from the original logfile. Once everything is entered, clicking "Design Oligos" will generate the replacement oligos, along with an evaluation of scores for the mutated sequence. The mutation is printed in lowercase font, and it is highlighted in the oligonucleotide assembly.

Oncogenic Role of THOR, a Conserved Cancer/Testis Long Non-coding RNA

While this method is simple in principle, in practice numerous complications can lead to errors in the synthesis. To reduce the possibility of errors during oligonucleotide synthesis, the oligonucleotides should be rather short, yet they must still be long enough to provide stable priming overlaps. Any deleterious secondary structures in the oligonucleotides and gene also need to be avoided. Further, the presence of internal repeats within the sequence can cause mispriming, and any overlooked sequences (such as restriction sites or integration-specific sequences) can cause downstream difficulties with subcloning. Therefore, for large proteins with coding sequences of >300 nt, the process of designing these oligonucleotides is tedious and confusing. In the case of a single gene, the problem can be attacked by manual design, but for projects where high throughput is required (i.e. structural genomics) an automated strategy for synthetic gene design is needed.

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