scholarly journals Hierarchical coassembly of DNA–triptycene hybrid molecular building blocks and zinc protoporphyrin IX

2016 ◽  
Vol 7 ◽  
pp. 697-707 ◽  
Author(s):  
Rina Kumari ◽  
Sumit Singh ◽  
Mohan Monisha ◽  
Sourav Bhowmick ◽  
Anindya Roy ◽  
...  
Keyword(s):  
Self Assembly ◽  
Polyacrylamide Gel Electrophoresis ◽  
Protoporphyrin Ix ◽  
Building Blocks ◽  
Ros Generation ◽  
Zinc Protoporphyrin ◽  
Dna Nanostructures ◽  
Native Page ◽  
Dna Nanostructure ◽  
Molecular Building Blocks

Herein, we describe the successful construction of composite DNA nanostructures by the self-assembly of complementary symmetrical 2,6,14-triptycenetripropiolic acid (TPA)–DNA building blocks and zinc protoporphyrin IX (Zn PpIX). DNA–organic molecule scaffolds for the composite DNA nanostructure were constructed through covalent conjugation of TPA with 5′-C12-amine-terminated modified single strand DNA (ssDNA) and its complementary strand. The repeated covalent conjugation of TPA with DNA was confirmed by using denaturing polyacrylamide gel electrophoresis (PAGE), reverse-phase high-performance liquid chromatography (RP-HPLC) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). The biologically relevant photosensitizer Zn PpIX was used to direct the hybridization-mediated self-assembly of DNA–TPA molecular building blocks as well as a model guest molecule within the DNA–TPA supramolecular self-assembly. The formation of fiber-like composite DNA nanostructures was observed. Native PAGE, circular dichroism (CD) and atomic force microscopy (AFM) have been utilized for analyzing the formation of DNA nanofibers after the coassembly. Computational methods were applied to discern the theoretical dimension of the DNA–TPA molecular building block of the nanofibers. A notable change in photocatalytic efficiency of Zn PpIX was observed when it was inside the TPA–DNA scaffold. The significant increase in ROS generation by Zn PpIX when trapped in this biocompatible DNA–TPA hybrid nanofiber may be an effective tool to explore photodynamic therapy (PDT) applications as well as photocatalytic reactions.

scholarly journals Constructing Large 2D Lattices Out of DNA-Tiles

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1502
Author(s):  
Johannes M. Parikka ◽  
Karolina Sokołowska ◽  
Nemanja Markešević ◽  
J. Jussi Toppari
Keyword(s):  
Self Assembly ◽  
Dna Nanotechnology ◽  
Building Blocks ◽  
High Yield ◽  
Dna Nanostructures ◽  
Liquid Interfaces ◽  
Basic Principles ◽  
Dna Tiles ◽  
One Step ◽  
Solid Liquid

The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.

scholarly journals Inverse Design of Nanoporous Crystalline Reticular Materials with Deep Generative Models

2020 ◽  
Author(s):  
Zhenpeng Yao ◽  
Benjamin Sanchez-Lengeling ◽  
N. Scott Bobbitt ◽  
Benjamin J. Bucior ◽  
Sai Govind Hari Kumar ◽  
...  
Keyword(s):  
Self Assembly ◽  
Metal Organic Framework ◽  
Internal Surface ◽  
Building Blocks ◽  
Structural Features ◽  
Generative Models ◽  
Combinatorial Design ◽  
Surface Areas ◽  
Molecular Building Blocks ◽  
Metal Organic

Reticular frameworks are crystalline porous materials that form <i>via</i> the self-assembly of molecular building blocks (<i>i.e.</i>, nodes and linkers) in different topologies. Many of them have high internal surface areas and other desirable properties for gas storage, separation, and other applications. The notable variety of the possible building blocks and the diverse ways they can be assembled endow reticular frameworks with a near-infinite combinatorial design space, making reticular chemistry both promising and challenging for prospective materials design. Here, we propose an automated nanoporous materials discovery platform powered by a supramolecular variational autoencoder (SmVAE) for the generative design of reticular materials with desired functions. We demonstrate the automated design process with a class of metal-organic framework (MOF) structures and the goal of separating CO<sub>2</sub> from natural gas or flue gas. Our model exhibits high fidelity in capturing structural features and reconstructing MOF structures. We show that the autoencoder has a promising optimization capability when jointly trained with multiple top adsorbent candidates identified for superior gas separation. MOFs discovered here are strongly competitive against some of the best-performing MOFs/zeolites ever reported. This platform lays the groundwork for the design of reticular frameworks for desired applications.

scholarly journals Inverse Design of Nanoporous Crystalline Reticular Materials with Deep Generative Models

2020 ◽  
Author(s):  
Zhenpeng Yao ◽  
Benjamin Sanchez-Lengeling ◽  
N. Scott Bobbitt ◽  
Benjamin J. Bucior ◽  
Sai Govind Hari Kumar ◽  
...  
Keyword(s):  
Self Assembly ◽  
Metal Organic Framework ◽  
Internal Surface ◽  
Building Blocks ◽  
Structural Features ◽  
Generative Models ◽  
Combinatorial Design ◽  
Surface Areas ◽  
Molecular Building Blocks ◽  
Metal Organic

Reticular frameworks are crystalline porous materials that form <i>via</i> the self-assembly of molecular building blocks (<i>i.e.</i>, nodes and linkers) in different topologies. Many of them have high internal surface areas and other desirable properties for gas storage, separation, and other applications. The notable variety of the possible building blocks and the diverse ways they can be assembled endow reticular frameworks with a near-infinite combinatorial design space, making reticular chemistry both promising and challenging for prospective materials design. Here, we propose an automated nanoporous materials discovery platform powered by a supramolecular variational autoencoder (SmVAE) for the generative design of reticular materials with desired functions. We demonstrate the automated design process with a class of metal-organic framework (MOF) structures and the goal of separating CO<sub>2</sub> from natural gas or flue gas. Our model exhibits high fidelity in capturing structural features and reconstructing MOF structures. We show that the autoencoder has a promising optimization capability when jointly trained with multiple top adsorbent candidates identified for superior gas separation. MOFs discovered here are strongly competitive against some of the best-performing MOFs/zeolites ever reported. This platform lays the groundwork for the design of reticular frameworks for desired applications.

scholarly journals Self assembled nanocages from DNA–protoporphyrin hybrid molecules

RSC Advances ◽  
2015 ◽  
Vol 5 (108) ◽  
pp. 89025-89029 ◽  
Author(s):  
Vandana Singh ◽  
Mohan Monisha ◽  
Roy Anindya ◽  
Prolay Das
Keyword(s):  
Functional Groups ◽  
Protoporphyrin Ix ◽  
Building Blocks ◽  
Carboxyl Groups ◽  
Dna Oligomers ◽  
Organic Hybrid ◽  
Molecular Building Blocks ◽  
Modified Dna ◽  
Hybrid Molecules ◽  
Self Assembled

DNA–organic hybrid molecular building blocks are generated by covalent conjugation of the carboxyl groups of protoporphyrin IX with the amine functional groups of modified DNA oligomers.

scholarly journals The Assembly of Porphyrin Systems in Well-Defined Nanostructures: An Update

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4307 ◽  
Author(s):  
Gabriele Magna ◽  
Donato Monti ◽  
Corrado Di Natale ◽  
Roberto Paolesse ◽  
Manuela Stefanelli
Keyword(s):  
Self Assembly ◽  
Energy Transport ◽  
Functional Materials ◽  
Building Blocks ◽  
Spatial Arrangement ◽  
Transport Processes ◽  
Internal Electric Field ◽  
Porphyrin Derivatives ◽  
Molecular Building Blocks ◽  
The Individual

The interest in assembling porphyrin derivatives is widespread and is accounted by the impressive impact of these suprastructures of controlled size and shapes in many applications from nanomedicine and sensors to photocatalysis and optoelectronics. The massive use of porphyrin dyes as molecular building blocks of functional materials at different length scales relies on the interdependent pair properties, consisting of their chemical stability/synthetic versatility and their quite unique physicochemical properties. Remarkably, the driven spatial arrangement of these platforms in well-defined suprastructures can synergically amplify the already excellent properties of the individual monomers, improving conjugation and enlarging the intensity of the absorption range of visible light, or forming an internal electric field exploitable in light-harvesting and charge-and energy-transport processes. The countless potentialities offered by these systems means that self-assembly concepts and tools are constantly explored, as confirmed by the significant number of published articles related to porphyrin assemblies in the 2015–2019 period, which is the focus of this review.

Self-Assembly of Proteins into Three-Dimensional Structures Using Bio-Conjugation

2014 ◽  
Vol 1663 ◽  
Author(s):  
Garima Thakur ◽  
Kovur Prashanthi ◽  
Thomas Thundat
Keyword(s):  
Self Assembly ◽  
Three Dimensional ◽  
Gold Surface ◽  
Building Blocks ◽  
Growth Conditions ◽  
Base Layer ◽  
Chemical Structures ◽  
Molecular Building Blocks ◽  
Ring Structures ◽  
Self Assembled

ABSTRACTSelf–assembly of molecular building blocks provides an interesting route to produce well-defined chemical structures. Tailoring the functionalities on the building blocks and controlling the time of self-assembly could control the properties as well as the structure of the resultant patterns. Spontaneous self-assembly of biomolecules can generate bio-interfaces for myriad of potential applications. Here we report self-assembled patterning of human serum albumin (HSA) protein in to ring structures on a polyethylene glycol (PEG) modified gold surface. The structure of the self-assembled protein molecules and kinetics of structure formation entirely revolved around controlling the nucleation of the base layer. The formation of different sizes of ring patterns is attributed to growth conditions of the PEG islands for bio-conjugation. These assemblies might be beneficial in forming structurally ordered architectures of active proteins such as HSA or other globular proteins.

Effect of backbone aspect ratio on the surface-confined self-assembly of tetratopic molecular building blocks

2019 ◽  
Vol 579 ◽  
pp. 123632 ◽  
Author(s):  
Damian Nieckarz ◽  
Wojciech Rżysko ◽  
Valery Lutsyk ◽  
Jakub Lisiecki ◽  
Paweł Szabelski
Keyword(s):  
Aspect Ratio ◽  
Self Assembly ◽  
Building Blocks ◽  
Molecular Building Blocks

Case history of porphyrin J-aggregates: a personal point of view

2009 ◽  
Vol 13 (04n05) ◽  
pp. 461-470 ◽  
Author(s):  
Joaquim Crusats ◽  
Zoubir El-Hachemi ◽  
Carlos Escudero ◽  
Josep M. Ribó
Keyword(s):  
Supramolecular Chemistry ◽  
Self Assembly ◽  
Building Blocks ◽  
Point Of View ◽  
Water Soluble ◽  
The Self ◽  
Molecular Building Blocks ◽  
History Of ◽  
J Aggregates ◽  
The University

The formation and structure of the title aggregates are paradigms of the self-assembly of amphiphilic molecular building blocks in supramolecular chemistry. This review summarizes the research in the University of Barcelona on the homoassociation of the water soluble meso 4-sulfonatophenyl-and phenyl substituted porphyrins.

Sign in / Sign up

Export Citation Format

Share Document