Heteropolydeoxynucleotides synthesized with terminal deoxyribonucleotidyltransferase. II. Nearest neighbor frequencies and extent of digestion by micrococcal deoxyribonuclease

Template-Independent Enzymatic Oligonucleotide Synthesis (TiEOS): Its History, Prospects, and Challenges

There is a growing demand for sustainable methods in research and development, where instead of hazardous chemicals, an aqueous medium is chosen to perform biological reactions. In this Perspective, we examine the history and current methodology of using enzymes to generate artificial single-stranded DNA. By using traditional solid-phase phosphoramidite chemistry as a metric, we also explore criteria for the method of template-independent enzymatic oligonucleotide synthesis (TiEOS). As its key component, we delve into the biology of one of the most enigmatic enzymes, terminal deoxynucleotidyl transferase (TdT). As TdT is found to exponentially increase antigen receptor diversity in the vertebrate immune system by adding nucleotides in a template-free manner, researchers have exploited this function as an alternative to the phosphoramidite synthesis method. Though TdT is currently the preferred enzyme for TiEOS, its random nucleotide incorporation presents a barrier in synthesis automation. Taking a closer look at the TiEOS cycle, particularly the coupling step, we find it is comprised of additions > n+1 and deletions. By tapping into the physical and biochemical properties of TdT, we strive to further elucidate its mercurial behavior and offer ways to better optimize TiEOS for production-grade oligonucleotide synthesis.

Sequence analysis of heteropolymeric DNA synthesized in vitro by the enzyme terminal deoxynucleotidyl transferase and cloned in Escherichia coli

We have synthesized in vitro single strands of DNA in reaction mixtures containing the terminal deoxynucleotidyl transferase (Bollum's enzyme), an oligo-dG as primer, the four common deoxynucleoside triphosphates and both Mg and Co ions. The resulting heteropolymers have been converted into double strands, tailed with oligo-dC sequences, annealed with an oligo-dG tailed plasmid vector and cloned in E. coli. Six recombinant plasmids have been isolated and characterized. Two of them have been sequenced. The heteropolymeric chains produced by the terminal transferase, ranging in size between 200 and 400 nucleotides, are richer in purines than in pyrimidines, except in the last portions. Open reading frames for 7-20 amino acids with repeated, in phase translational stop codons are present in these sequences and in their complements.

Reactions induced in vitro between model DNA and benzo[a]pyrene by near-ultraviolet radiation

Near-ultraviolet (300--480 nm wavelength) irradiation of the single-strand polydeoxynucleotide poly[d(A,C,G,T)] and carbon-14 labeled benzo[alpha]-pyrene (B[alpha] P) in aqueous dimethylsulfoxide (DMSO) solution led to appreciable binding of labeled hydrocarbon to the polynucleotide. Nuclease digests of polydeoxynucleotide-B[alpha]P complexes were examined by chromatography on Sephadex LH-20; at high fluences of near-ultraviolet light deoxyguanosine (dG) residues of the polymer were largely destroyed when the hydrocarbon was present. Approximately 85% of the B[alpha] P of the digests were recovered as hydrophilic derivatives not adsorbed by Sephadex LH-20. Elution of the columns with an aqueous-methanol gradient indicated that substances similar to the covalent deoxynucleoside-B[alpha] P adducts formed between microsomally-oxidized B[alpha] P and DNA were likewise present in the digests. When the deoxyadenosine (dA), deoxycytidine (dC) or dG moieties of the polymer were tritium-labeled, substances doubly-labeled with tritium and carbon-14 were found; ratios of the two radioactivities indicated that equimolar amounts of deoxynucleoside and hydrocarbon were present.