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Multistep synthesis in the laboratory ..
Multistep synthesis in the laboratory typically requires numerous reaction vessels, each containing a different set of reactants. In contrast, cells are capable of performing highly efficient and selective multistep biosynthesis under mild conditions with all reactants simultaneously present in solution. If the latter approach could be applied in the laboratory, it may improve the ease, speed, and efficiency of multistep reaction sequences. Here we show that a DNA mechanical device— a DNA walker moving along a DNA track— can be used to perform a series of amine acylation reactions in a single solution without any external intervention. The multistep products generated by this primitive ribosome mimetic are programmed by the sequence of the DNA track, are unrelated to the structure of DNA, and are formed with speeds and overall yields significantly greater than those previously achieved by multistep DNA-templated small-molecule synthesis.
To confirm that multistep synthesis mediated by the DNAsome proceeds in an ordered manner programmed by the nucleotide sequence of the track (in the above example, I-C1-C2-C3), we repeated the above experiment using three different DNA tracks, or omitting T altogether. Since S3 lacks an amine group, it effectively serves as a translation terminator. When the experiment described above was repeated using an I-C1-C3-C2 track, W was again entirely consumed and the predominant product observed by mass spectrometry was consistent with the reaction of W+S1+S3 (). The absence of products containing S2 is consistent with the ordered, sequence-dependent nature of DNAsome-mediated multistep synthesis. Likewise, using an I-C2-C3-C1 track resulted in the formation of a predominant product consistent with the reaction of W+S2+S3 (), and using an I-C3-C2-C1 track yielded only W+S3 product (). Finally, omission of the track altogether resulted in the formation of a complex mixture of minor products consistent with the uncontrolled random intermolecular reaction of W, S1, S2, and S3 (). Taken together, these results establish that artificial translation mediated by the DNAsome proceeds in a manner programmed by the order of codons on the DNA track.
A fully automated, multistep flow synthesis of 5-amino …
Recent advances in engineering DNA-based devices- have resulted in nanometer-scale DNA machines that are capable of autonomously changing their physical location over time.- For example, Mao and coworkers recently reported a DNA “nanowalker” that moves unidirectionally along a DNA track from station to station. We envisioned that the ability of a DNA walker to translocate could be integrated with DNA-templated synthesis to enable a specific chemical reaction to take place upon arrival of the walker at each station. Because the reaction product remains linked to the walker and serves as the starting material for the next reaction, this strategy results in a progressively more advanced synthetic reaction product as the walker moves along its track. Here we report the development of an autonomous DNA walker that performs a series of amine acylation reactions as it moves from station to station along a DNA track. The resulting machine mediates multistep synthesis of an oligoamide in a single isothermal solution programmed by the sequence of a DNA track, conceptually resembling an artificial ribosome. The system can generate multistep products in overall yields that are much higher than those of previous DNA-templated small-molecule syntheses,, and in total reaction times of only a few hours. This work also represents one of the first DNA devices that manipulates the covalent structure of non-nucleic acid molecules,,- and thus expands the functional scope of DNA-based devices.
Two approaches have been developed for the regiospecific continuous-flow synthesis of 1-substituted benzotriazoles. They begin with either an SNAr reaction at high temperature or Pd catalysis and involve consecutive multiphase processes, allowing the multistep synthesis of benzotriazoles to take place in an efficient manner.
A fully automated, multistep flow synthesis of 5 ..
Two subsequent cycles of walker translocation, DNA-templated amine acylation, DNAzyme-catalyzed cleavage, and dissociation of the 5’ fragment of the expended substrate result in the walker resting at the final station on the template covalently linked to the final multistep reaction product (in this case, a triamide containing three amino acid building blocks in a specific T-programmed order). Because each step of this cycle occurs spontaneously under identical conditions, the entire three-step reaction sequence proceeds autonomously, requiring no changes in temperature or pH, and no intervention from the researcher.
In the absence of enzymes, laboratory reaction sequences to generate multistep synthetic products generally proceed in multiple reaction vessels, such that each vessel exposes a different set of substrates to a different set of reaction conditions. In principle, performing multistep reaction sequences in a single solution programmed by a template could significantly increase the ease, speed, and overall efficiency of multistep syntheses. We previously engineered a DNA template that undergoes a series of secondary structure changes when subjected to a schedule of increasing temperatures. These changes expose hybridization sites for DNA-templated synthesis, an approach to controlling chemical reactivity in which reactions between DNA-linked reagents are triggered by DNA hybridization, enabling a multistep reaction sequence to take place in one solution. While successful, the generality of this approach is significantly limited by requiring a different arrangement of substrates for each step and requiring large changes in temperature during the reaction sequence (for example, 4 °C to 72 °C).
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Organic Chemistry Practice Problems at Michigan State University
The Multistep Synthesis Project is the capstone for the majors organic lab sequence. Information about this experiment is located . Here are the documents to help you prepare for your project:
Products | Zaiput Flow Technologies
We report a semiautomated synthesis of sequence and architecturallydefined, unimolecular macromolecules through a marriage of multistepflow synthesis and iterative exponential growth (Flow-IEG).
Click Chemistry Publications - Scripps Research Institute
The user-friendlynature, scalability, and modularity of Flow-IEG provide a generalstrategy for the automated synthesis of sequence-defined, unimolecularmacromolecules.
1,3-Dioxanes, 1,3-Dioxolanes - Organic Chemistry Portal
The exquisite selectivity and efficiency of many biosynthetic pathways rely on the use of protein or nucleic acid templates to modulate the effective molarities of substrates. For combinatorial biosyntheses including mRNA-templated peptide synthesis during ribosomal translation- as well as pathways that generate polyketides and non-ribosomal peptides,- this strategy enables the sequence of building blocks in a biosynthetic product to be determined by the sequence of mRNA nucleotides or enzyme modules in the template, enabling different multistep reaction products to be generated selectively from a single set of substrates with no external intervention.
Promoter (genetics) - Wikipedia
A major challenge of any effort to perform a multistep reaction sequence in a single solution is to prevent reactive substrates from undergoing any of the many possible reactions other than those on the desired pathway. In the case of transforming amino acid building blocks into a specific oligoamide, each activated amino acid can only react with the nascent product, and not with each other. In nature, the ribosomal machinery modulates the effective molarity of aminoacylated tRNAs with respect to water or other nucleophiles to greatly increase the likelihood than an aminoacylated tRNA in the ribosome's A-site couples with the nascent peptide in the P-site before hydrolysis or errant coupling takes place.- Like the ribosome, the DNAsome system displays multiple activated amino acids on a single track simultaneously. These amino acids each contain a free amine group that can potentially react with the aminoacyl NHS ester on an adjacent substrate station, leading to misordered products or precluding the formation of the desired final product. We hypothesized based on our previous observations,- that the double-stranded nature of the intervening track between adjacent substrates would effectively separate adjacent amino acids, decreasing their effective molarity and preventing side reactions. To test this hypothesis, we performed a model reaction in which a substrate containing a primary amine (S3a) and an NHS ester-linked substrate (S2a) were hybridized at adjacent stations of the same track (). After incubation in 50 mM MOPS buffer, pH 7.5, with 10 mM Mg(OAc)2 for 16 hours, no significant product formation was observed, indicating that adjacently docked substrates are not prone to uncontrolled cross-reaction in the absence of the walker ().
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