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Properties of DNA

Nucleic acids are information containing macromolecules in living matter consisting of several building blocks: sugar (ribose in the case of RNA; deoxyribose in the case of DNA), phosphate, and the four bases Adenine, Guanine, Cytosine, and Thymine (in RNA Thymine is replaced by Uracil). Sugar and phosphate form the backbone in which the A, C, G, T, or U bases are attached. The sequence of the bases is the essential code for biological information of the organism. Thus, for translation into an amino acid sequence of a protein the bases are grouped together into triplets called codons (there are 64 (43) possible triplets or codons). This genetic code is universal for all known living organisms. Its properties and tendencies are what drive the biotechnology industry today.

The first unique feature of nucleic acids is its ability to carry information. The second feature is to form specific antiparallel heteroduplexes. This is based upon the possibility that Adenine can form a pair with Thymine (or Uracil in RNA) and Guanine can form a pair with Cytosine. The base pairing ability is the reason for identical replication, for information interchange and information transport, and for the identification of specific sequences by probing them with complementary nucleic acids.

Synthetic DNA and a few of its Applications

Synthesizer

Some of the most tra­di­tion­ally impor­tant appli­ca­tions are probes for hybrid­i­za­tion (for con­fir­ma­tion of the pre­sence of a spe­ci­fic tar­get sequence), pri­mers for DNA sequen­cing and/or PCR, DNA or RNA for struc­tural stu­dies of mole­cules, and DNA frag­ments for site directed muta­ge­ne­sis.

There are several key com­po­nents essent­ial to the chem­istry of build­ing an oligo­nu­cle­o­tide on an auto­mated syn­the­sizer.

First, the start­ing mono­mer must con­tain one distinct coup­ling site. Other pos­si­ble bin­ding sites must be blocked effic­iently by pro­tect­ing groups. The start­ing the monomer is usually in the form of a solid sup­port such as a succ­inyl CPG.

The first monomer to be coupled must be added. Like the start-monomer it must be efficiently blocked by protecting groups except for the coupling site. The site where the next monomer is going to be attached must of course also be protected and chemically active at the phosphorous site such as a phosphoramidite.

Synthesizer

Coup­ling must be allowed under appro­pri­ate con­di­tions and the newly syn­the­sized dimer must be iso­la­ted and every­thing else must be removed.

The coup­ling site of the dimer to the next mono­mer must be depro­tected without affect­ing any one of the other pro­tect­ing groups.

Again the now depro­tected dimer must be iso­lated, then the next mono­mer must be added and so on.

Once syn­the­sis of the appro­pri­ate length is com­plete, all pro­tect­ing groups must be cleaved off of the pro­duct and the pro­duct off of the sup­port to yield bio­log­ic­ally act­ive DNA.

In auto­mated syn­the­sis these men­tioned steps are bro­ken down as fol­lows:

  • Detritylation
  • Coupling
  • Capping
  • Oxidation

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