Self‐Assembly of Perylenediimide–Single‐Strand‐DNA Conjugates: Employing Hydrophobic Interactions and DNA Base‐Pairing To Create a Diverse Structural Space

2017 ◽  
Vol 23 (43) ◽  
pp. 10328-10337 ◽  
Author(s):  
Ashutosh Kumar Mishra ◽  
Haim Weissman ◽  
Elisha Krieg ◽  
Kevin A. Votaw ◽  
Martin McCullagh ◽  
...  
Keyword(s):  
Self Assembly ◽  
Hydrophobic Interactions ◽  
Single Strand ◽  
Base Pairing ◽  
Dna Conjugates ◽  
Dna Base ◽  
Structural Space

scholarly journals Controlling the Self-Assembly of Biomolecules into Functional Nanomaterials through Internal Interactions and External Stimulations: A Review

Nanomaterials ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 285 ◽  
Author(s):  
Li Wang ◽  
Coucong Gong ◽  
Xinzhu Yuan ◽  
Gang Wei
Keyword(s):  
Self Assembly ◽  
Electrostatic Interactions ◽  
Materials Science ◽  
Hydrophobic Interactions ◽  
The Self ◽  
Functional Nanomaterials ◽  
Light Stimulation ◽  
Dna Base ◽  
Wide Range ◽  
Structure And Functions

Biomolecular self-assembly provides a facile way to synthesize functional nanomaterials. Due to the unique structure and functions of biomolecules, the created biological nanomaterials via biomolecular self-assembly have a wide range of applications, from materials science to biomedical engineering, tissue engineering, nanotechnology, and analytical science. In this review, we present recent advances in the synthesis of biological nanomaterials by controlling the biomolecular self-assembly from adjusting internal interactions and external stimulations. The self-assembly mechanisms of biomolecules (DNA, protein, peptide, virus, enzyme, metabolites, lipid, cholesterol, and others) related to various internal interactions, including hydrogen bonds, electrostatic interactions, hydrophobic interactions, π–π stacking, DNA base pairing, and ligand–receptor binding, are discussed by analyzing some recent studies. In addition, some strategies for promoting biomolecular self-assembly via external stimulations, such as adjusting the solution conditions (pH, temperature, ionic strength), adding organics, nanoparticles, or enzymes, and applying external light stimulation to the self-assembly systems, are demonstrated. We hope that this overview will be helpful for readers to understand the self-assembly mechanisms and strategies of biomolecules and to design and develop new biological nanostructures or nanomaterials for desired applications.

Crystallization and self-assembly of shape-complementary sequence-defined peptoids

2021 ◽  
Author(s):  
Sunting Xuan ◽  
Xi Jiang ◽  
Nitash P. Balsara ◽  
Ronald N. Zuckermann
Keyword(s):  
Protein Binding ◽  
Self Assembly ◽  
Biological Systems ◽  
Base Pairing ◽  
Complementary Sequence ◽  
Binding Interactions ◽  
Crystal Lattices ◽  
Shape Complementarity ◽  
Dna Base

Shape complementarity between polymers is a hallmark of biological systems (e.g. DNA base pairing and protein binding interactions). Here we explore the role of shape complementarity between sequence-defined N-alkyl peptoids in crystal lattices.

scholarly journals The Research of G–Motif Construction and Chirality in Deoxyguanosine Monophosphate Nucleotide Complexes

2021 ◽  
Vol 9 ◽  
Author(s):  
Yanhong Zhu ◽  
Zhongkui Li ◽  
Pengfei Wang ◽  
Qi–Ming Qiu ◽  
Hongwei Ma ◽  
...  
Keyword(s):  
Solid State ◽  
Self Assembly ◽  
Genetic Diseases ◽  
Dna Interaction ◽  
Wave Direction ◽  
Base Pairing ◽  
X Ray Crystallography ◽  
Mismatched Dna ◽  
H Nmr ◽  
Guanine Base

A detailed understanding of the mismatched base-pairing interactions in DNA will help reveal genetic diseases and provide a theoretical basis for the development of targeted drugs. Here, we utilized mononucleotide fragment to simulate mismatch DNA interactions in a local hydrophobic microenvironment. The bipyridyl-type bridging ligands were employed as a mild stabilizer to stabilize the GG mismatch containing complexes, allowing mismatch to be visualized based on X-ray crystallography. Five single crystals of 2′-deoxyguanosine–5′–monophosphate (dGMP) metal complexes were designed and obtained via the process of self-assembly. Crystallographic studies clearly reveal the details of the supramolecular interaction between mononucleotides and guest intercalators. A novel guanine–guanine base mismatch pattern with unusual (high anti)–(high anti) type of arrangement around the glycosidic angle conformations was successfully constructed. The solution state 1H–NMR, ESI–MS spectrum studies, and UV titration experiments emphasize the robustness of this g–motif in solution. Additionally, we combined the methods of single-crystal and solution-, solid-state CD spectrum together to discuss the chirality of the complexes. The complexes containing the g–motif structure, which reduces the energy of the system, following the solid-state CD signals, generally move in the long-wave direction. These results provided a new mismatched base pairing, that is g–motif. The interaction mode and full characterizations of g–motif will contribute to the study of the mismatched DNA interaction.

scholarly journals Rules for the self-assembly of ESCRT-III on endosomes

2021 ◽  
Author(s):  
Simon Sprenger ◽  
Simona M. Migliano ◽  
Florian Oleschko ◽  
Marvin Kobald ◽  
Michael Hess ◽  
...  
Keyword(s):  
Self Assembly ◽  
Hydrophobic Interactions ◽  
The Self ◽  
Amino Acid Residues ◽  
Lateral Expansion ◽  
Endosomal Sorting ◽  
Aaa Atpase ◽  
Charged Amino Acids ◽  
Membrane Budding ◽  
Positively Charged

ABSTRACTThe endosomal sorting complexes required for transport (ESCRT) mediate various membrane remodeling processes in cells by mechanism that are incompletely understood. Here we combined genetic experiments in budding yeast with site-specific cross-linking to identify rules that govern the self-assembly of individual ESCRT-III proteins into functional ESCRT-III complexes on endosomes. Together with current structural models of ESCRT-III, our findings suggest that, once nucleated, the growing Snf7 protofilament seeds the lateral co-assembly of a Vps24 - Vps2 heterofilament. Both Vps24 and Vps2 use positively charged amino acid residues in their helices α1 to interact with negatively charged amino acids in helix α4 of Snf7 subunits of the protofilament. In the Vps24 - Vps2 heterofilament, the two subunits alternate and interact with each other using hydrophobic interactions between helices α2/α3. The co-assembly of the Vps24 - Vps2 heterofilament restricts the lateral expansion of Snf7 protofilaments and leads the immediate recruitment of the AAA-ATPase Vps4. This self-assembly process of three ESCRT-III subunits results in the formation of a Snf7 protofilament and the co-assembly of a Vps24 - Vps2 heterofilament. This sets the stage for Vps4 recruitment and the subsequent ATP-driven dynamic self-organization of ESCRT-III / Vps4 assemblies and the ensuing membrane budding and scission events.

scholarly journals Supercoiling and looping promote DNA base accessibility and coordination among distant sites

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonathan M. Fogg ◽  
Allison K. Judge ◽  
Erik Stricker ◽  
Hilda L. Chan ◽  
Lynn Zechiedrich
Keyword(s):  
Mechanical Stress ◽  
Genomic Instability ◽  
Base Pair ◽  
Base Pairing ◽  
Complex Interplay ◽  
Site Specific ◽  
Torsional Strain ◽  
Dna Base ◽  
Dna Backbone ◽  
Negative Supercoiling

AbstractDNA in cells is supercoiled and constrained into loops and this supercoiling and looping influence every aspect of DNA activity. We show here that negative supercoiling transmits mechanical stress along the DNA backbone to disrupt base pairing at specific distant sites. Cooperativity among distant sites localizes certain sequences to superhelical apices. Base pair disruption allows sharp bending at superhelical apices, which facilitates DNA writhing to relieve torsional strain. The coupling of these processes may help prevent extensive denaturation associated with genomic instability. Our results provide a model for how DNA can form short loops, which are required for many essential processes, and how cells may use DNA loops to position nicks to facilitate repair. Furthermore, our results reveal a complex interplay between site-specific disruptions to base pairing and the 3-D conformation of DNA, which influences how genomes are stored, replicated, transcribed, repaired, and many other aspects of DNA activity.

Self-assembly of gold nanoparticles in a block copolymer aggregate template driven by hydrophobic interactions

2019 ◽  
Vol 10 (46) ◽  
pp. 6269-6277
Author(s):  
Jong Dae Jang ◽  
Sang-Woo Jeon ◽  
Young-Jin Yoon ◽  
Joona Bang ◽  
Young Soo Han ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Block Copolymer ◽  
Self Assembly ◽  
Hydrophobic Interactions ◽  
Self Assembled

We report various self-assembled structures of gold nanoparticles in a block copolymer aggregate template, which are easily driven by hydrophobic interactions.

scholarly journals A Deep Dive into DNA Base Pairing Interactions Under Water

2020 ◽  
Vol 124 (27) ◽  
pp. 5559-5570
Author(s):  
Rongpeng Li ◽  
Chi H. Mak
Keyword(s):  
Base Pairing ◽  
Deep Dive ◽  
Dna Base ◽  
Pairing Interactions

scholarly journals Identification and nanomechanical characterization of the fundamental single-strand protofilaments of amyloid α-synuclein fibrils

2018 ◽  
Vol 115 (28) ◽  
pp. 7230-7235 ◽  
Author(s):  
Francesco Simone Ruggeri ◽  
Fabrizio Benedetti ◽  
Tuomas P. J. Knowles ◽  
Hilal A. Lashuel ◽  
Sergey Sekatskii ◽  
...  
Keyword(s):  
Single Molecule ◽  
Self Assembly ◽  
Amyloid Fibrils ◽  
Molecular Assembly ◽  
Single Strand ◽  
Force Microscopy ◽  
Atomic Force ◽  
Presynaptic Protein ◽  
Polypeptide Chains

The formation and spreading of amyloid aggregates from the presynaptic protein α-synuclein in the brain play central roles in the pathogenesis of Parkinson’s disease. Here, we use high-resolution atomic force microscopy to investigate the early oligomerization events of α-synuclein with single monomer angstrom resolution. We identify, visualize, and characterize directly the smallest elementary unit in the hierarchical assembly of amyloid fibrils, termed here single-strand protofilaments. We show that protofilaments form from the direct molecular assembly of unfolded monomeric α-synuclein polypeptide chains. To unravel protofilaments’ internal structure and elastic properties, we manipulated nanomechanically these species by atomic force spectroscopy. The single-molecule scale identification and characterization of the fundamental unit of amyloid assemblies provide insights into early events underlying their formation and shed light on opportunities for therapeutic intervention at the early stages of aberrant protein self-assembly.

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