In vitro generation of genetic diversity for directed evolution by error-prone artificial DNA synthesis.

Generating genetic diversity lies at the heart of directed evolution which has been widely used to engineer genetic parts and gene circuits in synthetic biology. With the ever-expanding application of directed evolution, different approaches of generating genetic diversity are required to enrich the traditional toolbox. Here we show in vitro generation of genetic diversity for directed evolution by error-prone artificial DNA synthesis (epADS). This approach comprises a three-step process which incorporates base errors randomly generated during chemical synthesis of oligonucleotides under specific conditions into the target DNA. Through this method, 200 ~ 4000 folds of diversification in fluorescent strength have been achieved in genes encoding fluorescent proteins. EpADS has also been successfully used to diversify regulatory genetic parts, synthetic gene circuits and even increase microbial tolerance to carbenicillin in a short time period. EpADS would be an alternative tool for directed evolution which may have useful applications in synthetic biology.

[Current status and prospect of DNA synthesis in industrial biotechnology].

DNA synthesis is one of the most basic, widely-used tools in life science as well as a key enabling technology in synthetic biology. The rapid development of industrial biotechnology promoted by synthetic biology is creating an insatiable demand for large-scale DNA synthesis from more convenient, economical and safe sources. Industrial DNA synthesis platforms have remarkable advantages in terms of throughput, cost and speed. The research and development processes of industrial biotechnology benefit from these advantages, achieving a higher efficiency and lower cost. However, challenges in DNA manufacturing process remain, such as the use of large amounts of organic reagents, waste of resources and so on. With the continuous and rapid increase of DNA synthesis scale, the hazard of toxic chemicals, cost burden and environmental burden are becoming prominent. Based on our practical work on DNA synthesis, we discuss the demand and strategies for large-scale DNA synthesis in industrial biotechnology as well as the issues and potential solutions for sustainable development.

MASSIS: a mass spectrum simulation system. 2: Procedures and performance.

The use of the mass spectral simulation system, MASSIS, is reported and its performance has been evaluated. The search for substructures matching with fragments stored in four pivot databases was realised using the Ullmann algorithm. Special cleavage rules, such as the McLafferty rearrangement, the retro-Diels-Alder reaction, elimination of a neutral small molecule and oxygen migration, are processed through shortest path and depth-first search algorithms. For a search in the database of small fragments, the key step is to determine the tautomeric fragments; then a match can be obtained using a subgraph isomorphism algorithm. A string match is used to determine peak intensity. If the limited environment of an atom is the same as that found in the database of relationships between fragment and intensity, this intensity value is assigned to the query atom. Performance in a set of tests is very important in evaluating the system performance. A comparison of peaks with an intensity greater than 5% (relative) shows that our system has a very high performance figure (> 90% ) for routine organic compounds.

3-deoxy-3,3-difluoro-D-arabinofuranose: first stereoselective synthesis and application in preparation of gem-difluorinated sugar nucleosides.

The design and synthesis of gem-difluorinated sugar nucleosides were described. The key intermediate, 3-deoxy-3,3-difluoro-d-arabinofuranose 9, was first stereoselectively prepared from the chiral gem-difluorohomoallyl alcohol 12. The kinetic formation of single anti-14 in the benzylation of 12 could be accomplished by controlling the amount of sodium hydride used. The dihydroxylation of 14 (a mixture of anti and syn isomers) followed by deprotection and oxidation stereoselectively afforded furanose 9 with the arabino configuration at the C2 position. N(1)-(3-Deoxy-3,3-difluoro-beta-D-arabinofuranosyl)cytosine 6 was prepared from 9 by the glycosylation reaction. 4'-Thiofuranose 25 was easily synthesized from 9. The oxidation of 25 followed by the condensation with silylated N(4)-benzoylcytosine (Pummerer reaction) failed to give our desired protected nucleoside l-3'-deoxy-3',3'-difluoro- 4'-thiocytidine 27', but the regioisomer 27 was obtained. The regiochemistry of the Pummerer reaction was determined by the kinetic acidity of the alpha-proton of 4'-thiofuranose 25.

MASSIS: a mass spectrum simulation system 1. Principle and method.

A mass spectrum simulation system was developed. The simulated spectrum for a given target structure is computed based on the cleavage knowledge and statistical rules established and stocked in pivot databases: cleavage rule knowledge, function groups, small fragments and fragment-intensity relationships. These databases were constructed from correlation charts and statistical analysis of large population of organic mass spectra using data mining techniques. Since 1980, several systems were proposed for mass spectrum simulation, but in present there is no any commercial software available. This shows the complexity and difficulties in the development of a such system. The reported mass spectral simulation system in this paper could be the first general software for organic chemistry use

On the 6-exo atom transfer radical cyclization reactions of 3-butenyl 2-iodoalkanoates.

Bis(tributyltin)-initiated atom transfer cyclization reactions of 3-butenyl iodoalkanoates in the presence of BF3.OEt2 as the catalyst afforded the 6-exo cyclization products as a mixture of 3,4-cis- and trans-substituted tetrahydro-2H-pyran-2-ones in 53-71% yield with the major isomers being the cis ones. Ab initio calculations at the B3LYP/6-31G level on the transition states of the radical cyclization and on the cyclized products revealed that the reactions are kinetically controlled and the transition states for the 6-exo radical cyclization are in boat conformations. Moreover, the cis-oriented transition states are of lower energy than the corresponding trans-oriented ones, which are in excellent agreement with experimental results.