EGNAS: an exhaustive DNA sequence design algorithm

Kick, Alfred; Bönsch, Martin; Mertig, Michael

doi:10.1186/1471-2105-13-138

Cited by 20 publications

(32 citation statements)

References 35 publications

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“…In the CESS evaluation steps, the possible formation of aberrant stem-loop or bulge formations is not considered, contrary to other, similar programs (8). This is because such structures, if present, are likely to be superseded by competing proper pairings of full-length USPs, which always have longer base-pair stretches than seed pairs.…”

Section: Resultsmentioning

confidence: 99%

GENESUS: A two-step Sequence Design Program for DNA Nanostructure Self-Assembly

Tsutsumi

Asakawa

Kanegami³

et al. 2014

BioTechniques

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DNA has been recognized as an ideal material for bottom-up construction of nanometer scale structures by self-assembly. The generation of sequences optimized for unique self-assembly (GENESUS) program reported here is a straightforward method for generating sets of strand sequences optimized for self-assembly of arbitrarily designed DNA nanostructures by a generate-candidates-and-choose-the-best strategy. A scalable procedure to prepare single-stranded DNA having arbitrary sequences is also presented. Strands for the assembly of various structures were designed and successfully constructed, validating both the program and the procedure.

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Section: Resultsmentioning

confidence: 99%

GENESUS: A two-step Sequence Design Program for DNA Nanostructure Self-Assembly

Tsutsumi

Asakawa

Kanegami³

et al. 2014

BioTechniques

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“…For polycistronic constructs spacer DNA sequences (between genes) were designed with EGNAS (version 1158). 51 For a list of all constructs see Table S1.…”

Section: Methodsmentioning

confidence: 99%

Dodecin as carrier protein for immunizations and bioengineering applications

Bourdeaux

Kopp

Lautenschlaeger

et al. 2020

Preprint

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In bioengineering, scaffold proteins have been increasingly used to recruit molecules to parts of a cell, or to enhance the efficacy of biosynthetic or signaling pathways. For example, scaffolds can be used to make weak or non-immunogenic small molecules immunogenic by attaching them to the scaffold, in this role called carrier. Here, we present the dodecin from Mycobacterium tuberculosis (mtDod) as a new scaffold protein. MtDod is a homododecameric complex of spherical shape, high stability and robust assembly, which allows the attachment of cargo at its surface. We show that mtDod, either directly loaded with cargo or equipped with domains for non-covalent and covalent loading of cargo, can be produced recombinantly in high quantity and quality in Escherichia coli. Fusions of mtDod with proteins of up to four times the size of mtDod, e.g. with monomeric superfolder green fluorescent protein creating a 437 kDa large dodecamer, were successfully purified, showing mtDod's ability to function as recruitment hub. Further, mtDod equipped with SYNZIP and SpyCatcher domains for post-translational recruitment of cargo was prepared of which the mtDod/SpyCatcher system proved to be particularly useful. In a case study, we finally show that mtDod peptide fusions allow producing antibodies against human heat shock proteins and the Cterminus of heat shock cognate 70 interacting protein (CHIP).One application of protein carriers is their conjugation with peptides for the generation of antibodies (AB) utilizing the increased immunogenicity of the carrier-peptide conjugate. 6 Such ABs can identify proteins, which contain the peptides used for AB generation, in complex samples, and allow the specific labeling of proteins of interest in their spatiotemporal distribution; e.g. by immunofluorescence imaging or western blotting. As ABs preferentially recognize surface-exposed regions, termini of target proteins are usually a good source for exposed epitopes and their sequences are used as peptides for conjugation. In order to produce high-quality anti-peptide ABs, the peptide is ideally displayed at the carrier surface in similar orientation as in the intact protein. A dense packing of peptides at carrier surfaces is thought to be advantageous during immunization, because highly repetitive epitopes on particle surface facilitate B-cell activation through increased cell surface receptor oligomerization. 1,2 In a typical process for forming peptide-carrier conjugates for AB production, an about 20 amino acid-long peptide is coupled to residues at the surface of a carrier protein by a chemical reaction. 7-9 Commonly used carrier proteins are keyhole limpet hemocyanin (KLH), bovine serum albumin (BSA) and rabbit serum albumin (RSA), but also other proteins, e.g. tetanus toxoid (TT), and artificial carrier-systems, e.g. multiple antigen peptides (MAP) or virus-like particles (VLP), are used. 10,11 While BSA bears typical carrier properties (likely also other albumins) and exposes the peptides at the surface at a potentially high density,...

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“…Single‐stranded overhangs were optimized by means of the program EGNAS . DNA concentrations were determined by UV/Vis measurements using a NanoPhotometer™ Pearl (Implen, Germany).…”

Section: Methodsmentioning

confidence: 99%

“…200 nm) to which the DNA objects under investigation were bound. Among others, variations in SPR signals can be caused by temperature changes, structural reorganizations close to the gold surface, or adsorption/desorption of material to/from the gold surface .…”

Section: Design Of Structures and Experimentsmentioning

confidence: 99%

Concept, synthesis, and structural characterization of DNA origami based self-thermophoretic nanoswimmers

Herms

Günther

Sperling

et al. 2017

Phys. Status Solidi A

Self Cite

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We present a novel concept for the synthesis of a selfthermophoretic nanoswimmer, a construct consisting of a gold nanoparticle as a heating element and an artificial DNA structure as a thermophoretic active part. For the latter, DNA origami technique was applied to design and synthesize rodlike bundle structures as well as a more complex 2-leg construct. This novel concept is based on the versatile and easy-to-apply DNA origami toolbox to realize Janus particlelike structures with various geometries. We synthesized a variety of different nanoswimmers and characterized them in terms of structure, yield, and thermal stability.Schematic representation of the construction principle of a self-thermophoretic nanoswimmer consisting of a DNA origami structure and a gold nanoparticle. Inset: TEM image of such a nanoswimmer structure.

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EGNAS: an exhaustive DNA sequence design algorithm

Cited by 20 publications

References 35 publications

GENESUS: A two-step Sequence Design Program for DNA Nanostructure Self-Assembly

GENESUS: A two-step Sequence Design Program for DNA Nanostructure Self-Assembly

Dodecin as carrier protein for immunizations and bioengineering applications

Concept, synthesis, and structural characterization of DNA origami based self-thermophoretic nanoswimmers

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