Controlled Assembly of SNAP–PNA–Fluorophore Systems on DNA Templates To Produce Fluorescence Resonance Energy Transfer

Gholami, Zahra; Hanley, Quentin S.

doi:10.1021/bc500319p

Cited by 8 publications

(15 citation statements)

References 72 publications

(158 reference statements)

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“…Supramolecular protein polymers therefore are important synthetic targets with a wide variety of potential applications in biology, medicine, and catalysis. However, with natural biological polymerization events, the organization and reorganization pathways for assembly are carefully orchestrated by a host of complex binding events, which are challenging to mimic in vitro . , Therefore, while methods have been developed to synthesize protein polymers, the ability to deliberately control the pathways by which they form is not currently available. − …”

Section: Introductionmentioning

confidence: 99%

Programming Protein Polymerization with DNA

et al. 2018

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A strategy that utilizes DNA for controlling the association pathway of proteins is described. This strategy uses sequence-specific DNA interactions to program energy barriers for polymerization, allowing for either step-growth or chaingrowth pathways to be accessed. Two sets of mutant green fluorescent protein (mGFP)−DNA monomers with single DNA modifications have been synthesized and characterized. Depending on the deliberately controlled sequence and conformation of the appended DNA, these monomers can be polymerized through either a step-growth or chain-growth pathway. Cryoelectron microscopy with Volta phase plate technology enables the visualization of the distribution of the oligomer and polymer products, and even the small mGFP−DNA monomers. Whereas cyclic and linear polymer distributions were observed for the step-growth DNA design, in the case of the chain-growth system linear chains exclusively were observed, and a dependence of the chain length on the concentration of the initiator strand was noted. Importantly, the chain-growth system possesses a living character whereby chains can be extended with the addition of fresh monomer. This work represents an important and early example of mechanistic control over protein assembly, thereby establishing a robust methodology for synthesizing oligomeric and polymeric protein-based materials with exceptional control over architecture.

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Section: Introductionmentioning

confidence: 99%

Programming Protein Polymerization with DNA

et al. 2018

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“…Subsequent studies on structurally similar constructs placed on solid substrates under cryogenic conditions demonstrated that these efficiencies could be increased by ≈3‐fold by minimizing the number of alternative and parasitic relaxation pathways . Work realized by the Hanley group used DNA templates to align fluorescent proteins (monomeric teal fluorescent protein or labeled bovine serum albumin) to also look at HomoFRET transfer, finding that the total fluorescence was not the sum of the individual components and confirming the existence of parasitic traps . Liedl and collaborators looked at HomoFRET within the context of a DNA origami that displayed non‐linearly arranged HomoFRET regions (see Figure D) .…”

Section: Fluorescently Labeled Dna Materialsmentioning

confidence: 99%

“…The theoretical applicability of incorporating HomoFRET sections into MPWs is, in general quite large, but increased dye density is still required for optimal transfer. Paradoxically, increasing dye density (and therefore the total number of dyes) has its own inherent limitations as the possibility of energetic traps increases and if the dyes are brought too close together the dye can no longer be considered a point‐dipole and FRET assumptions may break down 154b,157b. Moreover, increasing an acceptor dye's density increases its direct absorption cross‐section and thus its ability to be directly excited at the more blue‐shifted donor excitation wavelength.…”

Section: Fluorescently Labeled Dna Materialsmentioning

confidence: 99%

Utilizing the Organizational Power of DNA Scaffolds for New Nanophotonic Applications

Bui

Dı́az

Fontana

et al. 2019

Advanced Optical Materials

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Rapid development of DNA technology has provided a feasible route to creating nanoscale materials. DNA acts as a self‐assembled nanoscaffold capable of assuming any three‐dimensional shape. The ability to integrate dyes and new optical materials such as quantum dots and plasmonic nanoparticles precisely onto these architectures provides new ways to exploit their near‐ and far‐field interactions. A fundamental understanding of these optical processes will help drive development of next‐generation photonic nanomaterials. This review is focused on latest progress in DNA‐based photonic materials and highlights DNA scaffolds for rapidly assembling and prototyping nanoscale optical devices. Three areas are discussed including intrinsically active DNA structures displaying chiral properties, DNA scaffolds hosting plasmonic nanomaterials, and fluorophore‐labeled DNAs that engage in Förster resonance energy transfer and give rise to complex molecular photonic wires. An explanation of what is desired from these optical processes when harnessed sets the tone for what DNA scaffolds are providing toward each focus. Examples from the literature illustrate current progress along with a discussion of challenges to overcome for further improvements. Opportunities to integrate diverse classes of optically active molecules including light‐generating enzymes, fluorescent proteins, nanoclusters, and metal–chelates in new structural combinations on DNA scaffolds are also highlighted.

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“…Moreover, FRET permits the complex state to be monitored at a range of temperatures not easily studied by traditional techniques in the field such as gel-shift assays and size exclusion chromatography. In one recent example, Gholami et al used FRET to verify heterodimer assembly induced using a DNA template . Green fluorescent protein (GFP) and its derivatives such as ECFP and EYFP can form homodimers both in solution and in crystals with a dissociation constant of approximately 100 μM .…”

Section: Introductionmentioning

confidence: 99%

“…In one recent example, Gholami et al used FRET to verify heterodimer assembly induced using a DNA template. 14 Green fluorescent protein (GFP) and its derivatives such as ECFP and EYFP can form homodimers both in solution and in crystals with a dissociation constant of approximately 100 μM. 15 This tendency of GFP to weakly interact with itself is attributed to a conserved hydrophobic patch on the protein surface.…”

Section: ■ Introductionmentioning

confidence: 99%

Controlled Assembly of Artificial Protein–Protein Complexes via DNA Duplex Formation

et al. 2015

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DNA-protein conjugates have found a wide range of applications. This study demonstrates the formation of defined, non-native protein-protein complexes via the site specific labeling of two proteins of interest with complementary strands of single-stranded DNA in vitro. This study demonstrates that the affinity of two DNA-protein conjugates for one another may be tuned by the use of variable lengths of DNA allowing reversible control of complex formation.

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Controlled Assembly of SNAP–PNA–Fluorophore Systems on DNA Templates To Produce Fluorescence Resonance Energy Transfer

Cited by 8 publications

References 72 publications

Programming Protein Polymerization with DNA

Programming Protein Polymerization with DNA

Utilizing the Organizational Power of DNA Scaffolds for New Nanophotonic Applications

Controlled Assembly of Artificial Protein–Protein Complexes via DNA Duplex Formation

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