Hierarchical Assembly of DNA Origami Nanostructures Using Coiled-coil Peptides

2019 ◽  
Author(s):  
Alex Buchberger ◽  
Chad Simmons ◽  
Nour Fahmi ◽  
Ronit Freeman ◽  
Nicholas Stephanopoulos
Keyword(s):  
Self Assembly ◽  
Coiled Coil ◽  
Dna Origami ◽  
Hybrid Nanostructures ◽  
Hierarchical Assembly ◽  
Alternating Copolymer ◽  
Self Assembling ◽  
Potential Applications ◽  
Multiple Routes ◽  
Stepwise Assembly

DNA and peptides are two of the most commonly used biomolecules for building self-assembling materials, but few examples exist of hybrid nanostructures that contain both components. Here we report the modification of two peptides that comprise a coiled-coil heterodimer pair with orthogonal DNA handles in order to link DNA origami nanostructures bearing complementary strands into micrometer long one-dimensional arrays. We probed the effect of number of coils on self-assembly and demonstrated the formation of self-assembled structures through multiple routes, to form dimers and trimers, an alternating copolymer of two different origami bundles, and stepwise assembly of purified structures with coiled-coil conjugates. Our results demonstrate the successful merging of two distinct self-assembly modes to create hybrid bionanomaterials expected to have a range of potential applications in the future.

Hierarchical Assembly of DNA Origami Nanostructures Using Coiled-coil Peptides

2019 ◽  
Author(s):  
Alex Buchberger ◽  
Chad Simmons ◽  
Nour Fahmi ◽  
Ronit Freeman ◽  
Nicholas Stephanopoulos
Keyword(s):  
Self Assembly ◽  
Coiled Coil ◽  
Dna Origami ◽  
Hybrid Nanostructures ◽  
Hierarchical Assembly ◽  
Alternating Copolymer ◽  
Self Assembling ◽  
Potential Applications ◽  
Multiple Routes ◽  
Stepwise Assembly

DNA and peptides are two of the most commonly used biomolecules for building self-assembling materials, but few examples exist of hybrid nanostructures that contain both components. Here we report the modification of two peptides that comprise a coiled-coil heterodimer pair with orthogonal DNA handles in order to link DNA origami nanostructures bearing complementary strands into micrometer long one-dimensional arrays. We probed the effect of number of coils on self-assembly and demonstrated the formation of self-assembled structures through multiple routes, to form dimers and trimers, an alternating copolymer of two different origami bundles, and stepwise assembly of purified structures with coiled-coil conjugates. Our results demonstrate the successful merging of two distinct self-assembly modes to create hybrid bionanomaterials expected to have a range of potential applications in the future.

scholarly journals A Structurally Variable Hinged Tetrahedron Framework from DNA Origami

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
David M. Smith ◽  
Verena Schüller ◽  
Carsten Forthmann ◽  
Robert Schreiber ◽  
Philip Tinnefeld ◽  
...  
Keyword(s):  
Self Assembly ◽  
Gel Electrophoresis ◽  
Imaging Techniques ◽  
Building Blocks ◽  
Dna Origami ◽  
Microscopy Technique ◽  
Wire Frame ◽  
Wide Range ◽  
Potential Applications ◽  
Linker Molecules

Nanometer-sized polyhedral wire-frame objects hold a wide range of potential applications both as structural scaffolds as well as a basis for synthetic nanocontainers. The utilization of DNA as basic building blocks for such structures allows the exploitation of bottom-up self-assembly in order to achieve molecular programmability through the pairing of complementary bases. In this work, we report on a hollow but rigid tetrahedron framework of 75 nm strut length constructed with the DNA origami method. Flexible hinges at each of their four joints provide a means for structural variability of the object. Through the opening of gaps along the struts, four variants can be created as confirmed by both gel electrophoresis and direct imaging techniques. The intrinsic site addressability provided by this technique allows the unique targeted attachment of dye and/or linker molecules at any point on the structure's surface, which we prove through the superresolution fluorescence microscopy technique DNA PAINT.

Functional self-assembling polypeptide bionanomaterials

2012 ◽  
Vol 40 (4) ◽  
pp. 629-634 ◽  
Author(s):  
Tibor Doles ◽  
Sabina Božič ◽  
Helena Gradišar ◽  
Roman Jerala
Keyword(s):  
Self Assembly ◽  
Biological Systems ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Chemical Properties ◽  
Building Blocks ◽  
External Signal ◽  
Form Complex ◽  
Cell Factories ◽  
Self Assembling

Bionanotechnology seeks to modify and design new biopolymers and their applications and uses biological systems as cell factories for the production of nanomaterials. Molecular self-assembly as the main organizing principle of biological systems is also the driving force for the assembly of artificial bionanomaterials. Protein domains and peptides are particularly attractive as building blocks because of their ability to form complex three-dimensional assemblies from a combination of at least two oligomerization domains that have the oligomerization state of at least two and three respectively. In the present paper, we review the application of polypeptide-based material for the formation of material with nanometre-scale pores that can be used for the separation. Use of antiparallel coiled-coil dimerization domains introduces the possibility of modulation of pore size and chemical properties. Assembly or disassembly of bionanomaterials can be regulated by an external signal as demonstrated by the coumermycin-induced dimerization of the gyrase B domain which triggers the formation of polypeptide assembly.

Biomolecular templating of functional hybrid nanostructures using repeat protein scaffolds

2015 ◽  
Vol 43 (5) ◽  
pp. 825-831 ◽  
Author(s):  
David Romera ◽  
Pierre Couleaud ◽  
Sara H. Mejias ◽  
Antonio Aires ◽  
Aitziber L. Cortajarena
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Hybrid Nanostructures ◽  
Biological Molecules ◽  
Complex Structures ◽  
Tetratricopeptide Repeats ◽  
Molecular Building Blocks ◽  
Potential Applications ◽  
Experimental Approaches ◽  
Nano Patterning

The precise synthesis of materials and devices with tailored complex structures and properties is a requisite for the development of the next generation of products based on nanotechnology. Nowadays, the technology for the generation of this type of devices lacks the precision to determine their properties and is accomplished mostly by ‘trial and error’ experimental approaches. The use of bottom-up approaches that rely on highly specific biomolecular interactions of small and simple components is an attractive approach for the templating of nanoscale elements. In nature, protein assemblies define complex structures and functions. Engineering novel bio-inspired assemblies by exploiting the same rules and interactions that encode the natural diversity is an emerging field that opens the door to create nanostructures with numerous potential applications in synthetic biology and nanotechnology. Self-assembly of biological molecules into defined functional structures has a tremendous potential in nano-patterning and the design of novel materials and functional devices. Molecular self-assembly is a process by which complex 3D structures with specified functions are constructed from simple molecular building blocks. Here we discuss the basis of biomolecular templating, the great potential of repeat proteins as building blocks for biomolecular templating and nano-patterning. In particular, we focus on the designed consensus tetratricopeptide repeats (CTPRs), the control on the assembly of these proteins into higher order structures and their potential as building blocks in order to generate functional nanostructures and materials.

Control of the stepwise assembly–disassembly of DNA origami nanoclusters by pH stimuli-responsive DNA triplexes

Nanoscale ◽  
2019 ◽  
Vol 11 (39) ◽  
pp. 18026-18030 ◽  
Author(s):  
Shuo Yang ◽  
Wenyan Liu ◽  
Risheng Wang
Keyword(s):  
Self Assembly ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Stimuli Responsive ◽  
Dna Triplexes ◽  
Stepwise Assembly

We demonstrate the pH-regulated, multistep self-assembly of DNA nanostructures by employing DNA triplexes as dynamic linkers in a stepwise, selective, and reversible fashion.

FORMATION OF REVERSED MICELLE NANORING BY A DESIGNED SURFACTANT-LIKE PEPTIDE

NANO ◽  
2012 ◽  
Vol 07 (04) ◽  
pp. 1250024 ◽  
Author(s):  
FENG QIU ◽  
YONGZHU CHEN ◽  
CHENGKANG TANG ◽  
YANRONG LU ◽  
JINGQIU CHENG ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Self Assembly ◽  
Molecular Model ◽  
Intermolecular Hydrogen Bond ◽  
Reversed Micelle ◽  
System A ◽  
Self Assembling ◽  
Potential Applications ◽  
Ft Ir ◽  
Novel Strategy

Designing self-assembling peptides as nanomaterials has been an attractive strategy in recent years, however, these peptides were usually studied in aqueous solutions for their self-assembling behaviors and applications. In this study, we have designed a surfactant-like peptide AGD with a wedge-like shape and studied its self-assembling behaviors in aqueous solution or nonpolar system. By analyzing the intermolecular hydrogen bond using FT-IR and characterizing the nanostructures with DLS, AFM and TEM, it was confirmed that AGD could not undergo self-assembly in aqueous solution while could self-assemble into well-ordered nanorings in nonpolar system. A molecular model has been proposed to explain how the nanorings were formed in the manner of reversed micelle. These results suggested a novel strategy to fabricate self-assembling peptide nanomaterials in nonpolar system, which could have potential applications in many fields.

Recent advances in the fabrication and bio-medical applications of self-assembled dipeptide nanostructures

Nanomedicine ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. 139-163
Author(s):  
Sonika Chibh ◽  
Jibanananda Mishra ◽  
Avneet Kour ◽  
Virander S Chauhan ◽  
Jiban J Panda
Keyword(s):  
Significant Role ◽  
Self Assembly ◽  
Biomedical Applications ◽  
Building Blocks ◽  
Natural Phenomenon ◽  
Medical Applications ◽  
Self Assembling ◽  
Recent Advances ◽  
Potential Applications ◽  
Self Assembled

Molecular self-assembly is a widespread natural phenomenon and has inspired several researchers to synthesize a compendium of nano/microstructures with widespread applications. Biomolecules like proteins, peptides and lipids are used as building blocks to fabricate various nanomaterials. Supramolecular peptide self-assembly continue to play a significant role in forming diverse nanostructures with numerous biomedical applications; however, dipeptides offer distinctive supremacy in their ability to self-assemble and produce a variety of nanostructures. Though several reviews have articulated the progress in the field of longer peptides or polymers and their self-assembling behavior, there is a paucity of reviews or literature covering the emerging field of dipeptide-based nanostructures. In this review, our goal is to present the recent advancements in dipeptide-based nanostructures with their potential applications.

Bioinspired Artificial Protein Materials: Self-Assembly and Order from Nano to Macroscale

2011 ◽  
Vol 1301 ◽  
Author(s):  
Min Dai ◽  
Jennifer S. Haghpanah ◽  
Carlo Yuvienco ◽  
Jin Kim Montclare
Keyword(s):  
Self Assembly ◽  
Matrix Protein ◽  
Coiled Coil ◽  
Supramolecular Assembly ◽  
Stimuli Responsive ◽  
Block Polymers ◽  
Self Assembling ◽  
Assembly Behavior ◽  
Protein Block

ABSTRACTWe describe the biosynthesis and characterization of protein materials comprised of two distinct self-assembling domains (SADs): elastin (E) found in tissue for its elastic properties and cartilage oligomeric matrix protein coiled-coil (COMPcc, C) predominantly locatedin joint and in bones. Based on earlier studies on protein block polymers comprised these two SADs, orientation and number of blocks play a crucial role in the overall stimuli-responsive supramolecular assembly behavior. Here we fabricate a range of EnC and CEn block polymers in which the E domain is systematically truncated to explore the effects of the E domain on the overall physicochemical behavior.

scholarly journals Self-assembly of bioactive peptides, peptide conjugates, and peptide mimetic materials

2017 ◽  
Vol 15 (28) ◽  
pp. 5867-5876 ◽  
Author(s):  
Charlotte J. C. Edwards-Gayle ◽  
Ian W. Hamley
Keyword(s):  
Self Assembly ◽  
Bioactive Peptides ◽  
Peptide Conjugates ◽  
Amphiphilic Peptides ◽  
Peptide Mimetic ◽  
Self Assembling ◽  
Potential Applications

Self-assembling peptide and peptide conjugates have attracted great attention due to their biocompatibility, biodegradability and biofunctionality. This review covers self-assembly of amphiphilic peptides and peptide mimetic materials, as well as their potential applications.

scholarly journals DNA Ring Motif with Flexible Joints

Micromachines ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 987 ◽  
Author(s):  
Shiyun Liu ◽  
Satoshi Murata ◽  
Ibuki Kawamata
Keyword(s):  
Self Assembly ◽  
Dna Origami ◽  
Molecular Devices ◽  
Dna Nanostructures ◽  
Geometric Complexity ◽  
Flexible Joints ◽  
Self Assembling ◽  
Complementary Sequences ◽  
Novel Method ◽  
Ring Motif

The invention of DNA origami has expanded the geometric complexity and functionality of DNA nanostructures. Using DNA origami technology, we develop a flexible multi-joint ring motif as a novel self-assembling module. The motif can connect with each other through self-complementary sequences on its segments. The flexible joints can be fixed in a straightened position as desired, thereby allowing the motif to take various shapes. We can adjust the number of flexible joints and the number of connectable segments, thereby enabling programmable self-assembly of the motif. We successfully produced the motif and evaluated several self-assembly patterns. The proposed multi-joint ring motif can provide a novel method for creating functional molecular devices.

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