DIY: Gene synthesis codon optimization

Do not use free codon optimization algorithm provided by some
"leading" companies, such as GeneArt, Genscript,  IDT etc. A
company has recently synthesized ~ 100 genes using GeneArt software, or
sequences provided by Genscript and IDT, 90% of the synthetic genes
could not be expressed in E coli, or expressed at extremely low
level (compared to wt).

Save money to do your own optimization for expression of your gene in
E coli:

1. Analyse wild type DNA sequence using
this website:

Red = rare Arg codons AGG, AGA, CGA

Green = rare Leu codon CTA

Blue = rare Ile codon ATA

Orange = rare Pro codon CCC

for the following input sequence:

gga cca aac aca gaa ttt gca CTA
tcc ctg tta agg
aaa aac ATA
atg act ATA
aca acc tca aag gga gag ttc aca ggg tta ggc ATA

cat gat cgt gtc tgt gtg ATA
aca cac gca cag cct ggt gat gat gta CTA
gtg aat ggt cag aaa att aga
gtt aag gat aag tac aaa tta gta gat cca gag aac att aat CTA
gag ctt aca gtg ttg act tta gat aga
aat gaa aaa ttc aga
gat atc agg
gga ttt ATA
tca gaa gat CTA
gaa ggt gtg gat gcc act ttg gta gta cat tca aat aac ttt acc aac act atc
tta gaa gtt ggc cct gta aca atg gca gga ctt att aat ttg agt agc acc CCC
act aac aga
atg att cgt tat gat tat gca aca aaa act ggg cag tgt gga ggt gtg ctg tgt
gct act ggt aag atc ttt ggt att cat gtt ggc ggt aat gga aga
caa gga ttt tca gct caa ctt aaa aaa caa tat ttt gta gag aaa caa

The length is: 546 nucleotides

Number of total single rare Arg codons:


occurring at codons:
12, 55, 79, 84, 87, 133, 166

Number of tandem rare Arg codon double repeats:

Number of tandem rare Arg codon triple repeats:

Too lazy to beautify this new part right now…Results are in order for
Arginine, Leucine, Isoleucine, and Proline, respectively (delimited by
1.1, 2.1, 3.1, 4.1 for singles; 1.2, 2.2, 3.2, 4.2 for doubles; etc.).
Single rare codons at positions:
12 55 79 84 87 133 166 (agg)|(aga)|(cga)1.1 8 48 70 94 cta2.1 15 18 30
37 90 ata3.1 38 130 ccc4.1


Double rare codons at positions:
(agg)|(aga)|(cga)1.2 cta2.2 ata3.2 ccc4.2

Triple rare codons at positions:
(agg)|(aga)|(cga)1.3 cta2.3 ata3.3 ccc4.3


2. Change  rare codons 
Ile: ATA
Leu: CTA
Pro: CCC
Arg: AGG, AGA, CGG, and CGA
based on this
E coli codon usage table:

For example:

cta –> CTG

ata –> ATC or ATT

aga –> CGC or CGT
cgg –> CGC or CGT

cga–> CGC or CGT
agg –> CGC or CGT

ccc –> CCG



3. Change second amino acid to A (gct, gca), K (aaa) or S (agc, tcc, tct)

4. Change G and C to A and T at the 5'-end.
A high GC content in the 5'-end of the gene of interest –> formation of secondary structure in the mRNA —> Inefficient translation —> low expression

5.  Remove cis-acting DNA sequences such as internal TATA-boxes, chi-sites, and ribosomal entry sites; AT-rich or GC-rich sequence stretches; repeat sequences; and RNA secondary structures. Remove internal Shine-Dalgarno sequences such as AAGGAG(nnnnn)ATG, GAAGGAGA(nnnnn)ATG, AAGGAGG(nnnnn)ATG, AAGGAGGT(nnnnn)ATG, GGAG, GAGG, and AGGA.



6. Add two stop codons TAATAA

7. Append another strong terminator to the end of your DNA sequence



December 22, 2012 at 3:59 pm


  1. Elva said,

    August 19, 2014 @ 2:53 pm

    Thank you for the good writeup. It actually was once a entertainment account it.
    Glance advanced to more introduced agreeable from you!

    However, how could we keep up a correspondence?

  2. Ft Best Best Fort Lauderdale Plumbers said,

    August 21, 2014 @ 1:38 am

    A person having little expertise meanwhile can handle
    these issues before a professional comes in frame.
    The possibilities are endless with today’s line of hardware, woodworking and project supplies.
    So wiping water into the sink and cleaning up is quicker.

  3. Boca Raton CPAs said,

    August 25, 2014 @ 7:19 am

    When using such a solution, you will be asked to talk about the events that affected you in the year,
    marriage, new baby, move to a new house, started college,
    changed employment status, etc. They come to the picture even in divorce cases in order to
    establish compensation that is needed for child support or spouses.
    For a common judgment creditor lien to outrank an IRS lien the lien needs to get recorded before the IRS’s lien is recorded, and be a “Choate” lien; which means it is a final lien circumstance, and that lien specifically lists what’s attached.

  4. said,

    August 25, 2014 @ 5:38 pm

    Ce sont vraiment vraiment merveilleux sur le thème de blogging.

    Vous avez touché quelques belles exigeants ici. Toute façon suivre wrinting.

  5. white widow autoflowering said,

    August 27, 2014 @ 7:55 pm

    Excellent post. I definitely love this website.
    Continue the good work!

  6. bandage dress bebe kardashian said,

    September 11, 2014 @ 3:26 am

    Yellow bridesmaid dresses are great for summer and spring weddings because they add flair and class to your
    wedding. After washing the clip-in extensions, simply air dry them and store in a safe place.
    If a celebrity trend is meant to be repeated by
    the general public, you will be able to compliment rather
    than stare with horror at the woman in front of you at the local grocery store check-out line.

  7. online said,

    September 20, 2014 @ 2:25 am

    It’s not my first time to pay a quick visit this site, i
    am browsing this website dailly and obtain nice data from here daily.

  8. my hcg weight loss journey said,

    September 20, 2014 @ 4:24 am

    ” He had been admitted to the ER due to a heart attack. Warrants have been issued for his arrest in Europe and he lives in hiding outside the E. It is a bit pricey, but is well worth the extra money.

  9. free criminal defense attorneys said,

    September 20, 2014 @ 1:41 pm

    If some one needs to be updated with most up-to-date technologies then he must be visit this site and be up to date everyday.

  10. legis said,

    September 20, 2014 @ 3:16 pm

    The actual worry is not how much money is obtainable, most partners don’t truly comprehend money difficulties
    and have no idea how to take care of them.
    The Advantages of Online Courses – There are several advantages of online courses.

    * How to notice shots that most people wouldn’t normally even think about – to help make your pictures stay ahead of the crowd.

  11. hcg weight loss omaha Ne said,

    September 21, 2014 @ 7:49 am

    Homeopathic HCG drops for weight loss work by preserving your muscle tissue
    first. However, in just short span of time, the HCG drops have gained so much prominence and popularity that they are being sought after by numerous people all over the world.
    These suggestions are provided to assist you in optimizing your meal plans with approved foods with these quick weight loss diets.

  12. said,

    September 22, 2014 @ 1:14 pm

    I’m amazed, I must say. Rarely do I encounter a blog that’s both
    educative and interesting, and let me tell you, you’ve hit the
    nail on the head. The problem is something too
    few people are speaking intelligently about.
    I am very happy that I stumbled across this during my hunt for something concerning this.

  13. celebrity dress up party ideas said,

    September 25, 2014 @ 2:07 am

    The revealing and additionally strapless mermaid wedding dress outline is the most famous
    one. Firstly, you have access to millions of online stores worldwide at the click
    of a button. These steeply-priced shoes are demure, yet captivating.

  14. best hcg drops for sale said,

    September 25, 2014 @ 2:18 pm

    If you decide you must eat something totally not
    on your diet, you will be in effect doing a.
    Indeed, it has been found that men using HCG to lose weight have even better outcomes than female users in several instances.

    A typical HCG program involves combining a low calorie diet and HCG usage.

  15. said,

    September 26, 2014 @ 10:05 pm

    If some onne waqnts exoert view about blogging
    after that i recommend him/her to visit this blog, Keep up the good

  16. best moving Company uk to usa said,

    September 27, 2014 @ 11:13 am

    While doing the resettlement work shifters
    get confused in between the puzzling works. For the young professional families that can no longer afford King
    William have chosen Mahncke Park and have started refurbishing the run down homes with wraparound porches.

    Moving interstate will cause you some stress although it will also
    be exciting. In fact, all such equity release calculator is very
    useful for the senior citizens as these help them in understanding all about the equity release UK
    schemes. When transporting the car to Egypt port, it is very important
    that you look into the details of the customs fee
    and port fee. Functional and striking, track lighting fixtures can be found
    in different shapes and sizes according to your choices
    and needs, from ultra modern to that which resembles turn-of-the century, any style to fit any dcor.
    Leading organizations specializing in datacenter solutions
    offer their clients and customers with authentic warranties.

    Professional call answering services enable offices everywhere to take advantage of the
    latest technology while maintaining a professional image.
    They follow customer oriented approach in their business process.
    A good facility management company has an industry-specific expertise
    and performs its duties through proven methodologies, techniques and tools.

  17. hcg weight loss killeen tx said,

    September 30, 2014 @ 12:53 am

    The fast fatigue state that most skinny get into is very common. Not only are they best for reducing
    weight and to better your physical condition, but also to make you slender and generally more desirable.
    He is not just some dude who wanted to get affluent with the naive
    overweight population, or gain profits of people with more money than they knew
    what to do with.

  18. fall skin said,

    October 2, 2014 @ 1:00 am

    If you know your hair loss is likely to be permanent then there are
    some very stylish and flattering wigs available today, which look so realistic no one would be able to
    tell the difference. Also sign up for my pet blog and let me know if you have questions or concerns regarding your
    pets. Using natural treatment for hair loss just makes good sense.

  19. perdi peso said,

    October 6, 2014 @ 3:17 am

    In fact, all the reasons mentioned above are applicable too all men and
    women. It is advisable to do some research on the product and as far as the diet pills are concerned oxyelite are one of the best and most effective.
    Ingredients of this herbal slimming suplplement are completely natural such as
    Babuna (Matricaria Chamomilla), Jwasa (Alhagi Maurorum), Bair (Zizyphus Jujuba), Bhadradanti (Jatropha Multifida),
    Pashanbhed (Coleus Aromaticus), Katha (Acacia
    Catechu), Chandras (Veteria Indica), Kulthi (Dolichos Biflorus), Kaligiri (Vernonia Anthelmintica),
    Babool (Acacia Arabica Wild), Gurlu (Coix Lachryma), Laksha (Cocus
    Lacca), Piplamool (Piper longum), Samudra Shosh (Argyreia Speciosa), Haritki (Terminalia Chebula),
    and Chitrak (Plumbags Zeylanica).

RSS feed for comments on this post · TrackBack URI

Leave a Comment