Which is the most suitable type of purification for my oligo?
For some applications, such as PCR or sequencing, desalination is a suitable standard and is the normal choice, but other applications require more pure oligos. How to choose and decide? Your choice of purification must be based on several factors, including the application you will be using the oligo in, the oligo length, and if you have any modifications to add.
During the synthesis cycles, for each addition of a new base, about ~ 1% of the oligos being synthesized will not add the appropriate basis. This leads to the formation of particles smaller in size, sub-bases or deletion mutants. This can happen anywhere within the sequence and leads to a mixture of oligos with different overall lengths, truncated products, and oligos with internal deletions.
For some applications, such as PCR or sequencing, desalination is a suitable standard and is the normal choice, but other applications require more pure oligos. How to choose and decide? Your choice of purification must be based on several factors, including the application you will be using the oligo in, the oligo length, and if you have any modifications to add.
During the synthesis cycles, for each addition of a new base, about ~ 1% of the oligos being synthesized will not add the appropriate basis. This leads to the formation of particles smaller in size, sub-bases or deletion mutants. This can happen anywhere within the sequence and leads to a mixture of oligos with different overall lengths, truncated products, and oligos with internal deletions.
As a general rule, any oligonuclotide more than 40 bases in length must receive further purification steps, always keeping in mind that further purification will result in a decrease in the yield of the final oligonucleotide.
Your application is simple PCR or sequencing? Desalination is enough and perfectly adequate. Your results will not be affected by the inevitable existence of low amounts of shorter oligos and deletion mutants.
Do you want to order a large unmodified oligo? Probably you should ask cartdrige purification, since the shorter fragments and salts are eliminated. Our experience shows us that the purification achieved by these methods are quite comparable to that observed after HPLC purification for oligonucleotides up to 30 bases. The result is a purified oligonucleotide, saltfree
Your application is simple PCR or sequencing? Desalination is enough and perfectly adequate. Your results will not be affected by the inevitable existence of low amounts of shorter oligos and deletion mutants.
Do you want to order a large unmodified oligo? Probably you should ask cartdrige purification, since the shorter fragments and salts are eliminated. Our experience shows us that the purification achieved by these methods are quite comparable to that observed after HPLC purification for oligonucleotides up to 30 bases. The result is a purified oligonucleotide, saltfree
For other applications, such as cloning or mutagenesis the total length of the final product is of the utmost importance, and PAGE purification should be strongly considered. PAGE result in the highest level of purity in terms of full-length product, and your oligos will be at least 90% of the entire body. However, we note that PAGE purification can damage some modifications, including fluorophores and many modifications used for fixation. PAGE purification should be avoided for the following modifications: any fluorophore, Acrydite, amino modifiers, biotin, digoxigenin, I Linker, spacer 18, thiol modifiers (HPLC or IE-HPLC purification would be the choice in this case)
If you need a clean product, but also need a higher yield, you should choose HPLC for oligos up to 50nts and in some cases even more. The purification process is controlled and documented by UV spectroscopy. This allows the maximum concentration of the pure product by collecting the desired peak, which is the "cutting quality," so that any peak shoulders will not be collected. RP-HPLC for modified oligonucleotides is also the appropriate method of choice.
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