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Benner S.A.,The Westheimer Institute for Science and Technology
Current Opinion in Chemical Biology | Year: 2012

Physicists frequently allow aesthetics to guide their science. Chemists sometimes do. Biologists rarely do. They have encountered too frequently the consequences of the Darwinian 'hack'. The biological parts delivered by Darwinian processes are rarely simple, efficient, or elegant solutions to the biological problems that they address. Nevertheless, as humans, we seek to find aesthetics within our activities. In general, however, it is hard to distinguish what we say is beautiful from what is, in reality, utilitarian. © 2012 Elsevier Ltd.

PubMed | Firebird Biomolecular Sciences, LLC and The Westheimer Institute for Science and Technology
Type: | Journal: Beilstein journal of organic chemistry | Year: 2014

Synthetic biologists wishing to self-assemble large DNA (L-DNA) constructs from small DNA fragments made by automated synthesis need fragments that hybridize predictably. Such predictability is difficult to obtain with nucleotides built from just the four standard nucleotides. Natural DNAs peculiar combination of strong and weak G:C and A:T pairs, the context-dependence of the strengths of those pairs, unimolecular strand folding that competes with desired interstrand hybridization, and non-Watson-Crick interactions available to standard DNA, all contribute to this unpredictability. In principle, adding extra nucleotides to the genetic alphabet can improve the predictability and reliability of autonomous DNA self-assembly, simply by increasing the information density of oligonucleotide sequences. These extra nucleotides are now available as parts of artificially expanded genetic information systems (AEGIS), and tools are now available to generate entirely standard DNA from AEGIS DNA during PCR amplification. Here, we describe the OligArch (for oligonucleotide architecting) software, an application that permits synthetic biologists to engineer optimally self-assembling DNA constructs from both six- and eight-letter AEGIS alphabets. This software has been used to design oligonucleotides that self-assemble to form complete genes from 20 or more single-stranded synthetic oligonucleotides. OligArch is therefore a key element of a scalable and integrated infrastructure for the rapid and designed engineering of biology.

PubMed | The Westheimer Institute for Science and Technology
Type: Journal Article | Journal: Science (New York, N.Y.) | Year: 2010

Lambert et al. (Reports, 19 February 2010, p. 984) reported that silicate ions catalyze the formation and stabilization of four- and six-carbon sugars from simple sugars, suggesting a possible prebiotic pathway for the synthesis of biologically important sugars. Here, we show that silicate has minimal impact in these respects, especially when compared to borate minerals.

PubMed | University of Florida, Firebird Biomolecular Sciences, LLC and The Westheimer Institute for Science and Technology
Type: | Journal: Beilstein journal of organic chemistry | Year: 2014

Many synthetic biologists seek to increase the degree of autonomy in the assembly of long DNA (L-DNA) constructs from short synthetic DNA fragments, which are today quite inexpensive because of automated solid-phase synthesis. However, the low information density of DNA built from just four nucleotide letters, the presence of strong (G:C) and weak (A:T) nucleobase pairs, the non-canonical folded structures that compete with Watson-Crick pairing, and other features intrinsic to natural DNA, generally prevent the autonomous assembly of short single-stranded oligonucleotides greater than a dozen or so.We describe a new strategy to autonomously assemble L-DNA constructs from fragments of synthetic single-stranded DNA. This strategy uses an artificially expanded genetic information system (AEGIS) that adds nucleotides to the four (G, A, C, and T) found in standard DNA by shuffling hydrogen-bonding units on the nucleobases, all while retaining the overall Watson-Crick base-pairing geometry. The added information density allows larger numbers of synthetic fragments to self-assemble without off-target hybridization, hairpin formation, and non-canonical folding interactions. The AEGIS pairs are then converted into standard pairs to produce a fully natural L-DNA product. Here, we report the autonomous assembly of a gene encoding kanamycin resistance using this strategy. Synthetic fragments were built from a six-letter alphabet having two AEGIS components, 5-methyl-2-deoxyisocytidine and 2-deoxyisoguanosine (respectively S and B), at their overlapping ends. Gaps in the overlapped assembly were then filled in using DNA polymerases, and the nicks were sealed by ligase. The S:B pairs in the ligated construct were then converted to T:A pairs during PCR amplification. When cloned into a plasmid, the product was shown to make Escherichia coli resistant to kanamycin. A parallel study that attempted to assemble similarly sized genes with optimally designed standard nucleotides lacking AEGIS components gave successful assemblies of up to 16 fragments, but generally failed when larger autonomous assemblies were attempted.AEGIS nucleotides, by increasing the information density of DNA, allow larger numbers of DNA fragments to autonomously self-assemble into large DNA constructs. This technology can therefore increase the size of DNA constructs that might be used in synthetic biology.

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