Sequence optimisation

Sequence optimisation here at BaseClear will boost gene expression in the desired host organism. Many factors can determine the success or failure of your gene expression. BaseClear will try to eliminate factors that will have a negative effect on the genes translation or expression and optimise the sequence for maximum expression, furthermore we can provide you with tools to help you clone your gene:

Restriction sites:

Adding extra restriction sites 5" and 3" for cloning purposes.

Codonoptimization:

Change the codon usage to favour the codon usages of your favourite organism and eliminate rarely used codon sequences. We can also include a threshold or specific select certain AZ codons per gene. By doing so, all very rare and rare AZ codon sequences will be avoided, which will improve gene transcription and will adapt a foreign gene to suit the amino acid codon distribution found in the host organism.

Addition and removal of restriction sites.

Some restrictions sites in a gene can cause problems particularly if further cloning steps are necessary. BaseClear can change the codons of these anino acids, so that the amino acids encoded are unchanged but the problematic restrictions sites are removed. Addition of restriction sites is also possible, again without alterning the amino acids sequence which is encoded.

Removing motives:

Certain motives can destabilize mRNA structures, or can harbour a specific initiation site, which must to be avoided to maximize the gene expression. BaseClear can search for and remove such motives, the customer can also specify motives which are to be avoided

Removing Repeats.

Repeats can give problems during cell growth or during transcription/translation. We can remove such repeat by changing the codon sequence, thus eliminating the problem

Stabilizing mRNA motives.

Secondary structures/hairpins and other mRNA structures can potentially destabilize gene expression. Therefore BaseClear can optimise the gene sequence to avoid such mRNA structures.

Removing Cryptic splice sites.

Another destabilizing element in a gene are potential slice sites. For a number of organisms we can detect and remove the splice site sequences. On request we can also train our program to recognize cryptic splice sites from organisms not in our list.

Adding special sequences.

BaseClear has an easy to use list of sequences and tags, which can be added to any gene sequence. In this way you don’t have to search for the sequence, just tell us were you want the specific DNA sequence (like his tags etc) to be added. Additionally the customer can also specify specific sequences themselves which they would like added