Molecular Modeling as a Visualization Tool in Design of DNA Crosslinked Polyacrylamide

2004 ◽  
Author(s):  
Karin Rafaels ◽  
John Kerrigan ◽  
Noshir Langrana ◽  
David Lin
Keyword(s):  
Mechanical Properties ◽  
Critical Concentration ◽  
Computer Assisted ◽  
Nanoscale Structures ◽  
Dna Oligonucleotides ◽  
Dna Crosslinks ◽  
Sequence Of Events ◽  
Modified Dna ◽  
Dna Strands ◽  
Gel Composition

Polymers such as polyacrylamide form a diverse class of biomaterials in use today. The experimental research performed by our group has demonstrated how a critical concentration of crosslinking DNA strands can lead to gel formation in the polyacrylamide. The removal or addition of DNA strands can reverse or significantly increase the stiffness and strength of the gel. DNA is a versatile material for the exploration of nanoscale structures because its hybridization chemistry is very specific. DNA crosslinked gels use end-modified DNA oligonucleotides in the gels. The ability to choose the base sequence in the DNA crosslinks offers an opportunity to engineer the nanoscale structure of this material. However, it is extremely difficult to visualize the sequence of events that occurs when DNA is crosslinked with polyacrylamide. Computer modeling is a tool that enables the researchers to study the structural aspects of the newly engineered DNA crosslinkers. In this study, polyacrylamide gel crosslinked with DNA has been assayed with respect to energy and size using AMBER 7.0 software [1]. Since DNA-crosslinked gels are likely to find a range of applications it is important to know how to tailor the gel composition for a particular application. It is also of interest to know what the composition is that would induce the greatest change in stiffness. The molecular models generated in AMBER survey the mechanical properties of the gel as a function of crosslinker density, polyacrylamide density, and crosslinker length. The structure of an equilibrium state is computed using an explicitly solvated model. Visual inspection of the model determines other mechanical properties of the gel and helps predict chemical interactions. A long-term goal of this work is to use computer assisted modeling techniques to guide the experiments, to predict linker stiffness, and to examine other mechanical properties of the DNA crosslinker.

DNA Nanotechnologies for the Design of Bio-Inspired Soft Nanocomposites With Reversible Rigidity

2019 ◽  
Author(s):  
Theo Calais ◽  
Thileepan Stalin ◽  
Vincent S. Joseph ◽  
Pablo Valdivia y Alvarado
Keyword(s):  
Mechanical Properties ◽  
Dna Hybridization ◽  
Limited Range ◽  
Robot Locomotion ◽  
Dna Oligonucleotides ◽  
Dna Strands ◽  
Shape Memory Effects ◽  
Order Of Magnitude ◽  
Helicoidal Structure ◽  
Novel Strategy

Abstract Structures and mechanisms in soft robotics are primarily based on chemically versatile species such as hydrogels, polymers, or elastomers, thus offering great potential for the design of adaptive core properties. In particular, tunable rigidity is highly desirable to enable control of soft grippers or for advanced robot locomotion. However, most of the strategies explored so far rely on mechanisms, such as phase transitions or shape memory effects, that require heavy external hardware or have a limited range of tunable rigidity. In this work, we propose a novel strategy inspired by the sea cucumber dermis mechanism. High aspect ratio carbon nanotubes (CNTs) are reversibly interconnected by DNA oligonucleotides within a polyacrylamide (PAAm) hydrogel. The combination of the excellent mechanical properties of CNTs and the reversible hybridization of DNA strands into a stable double-helicoidal structure allowed the reversible tunability of mechanical properties over one order of magnitude (from ∼100 Pa to ∼1 kPa) within minutes by increasing the temperature beyond the melting temperature of DNA strands (∼50 °C). First, the functionalization strategy of CNTs with DNA strands is described and characterized. The aggregation of CNTs driven by the DNA hybridization is then demonstrated. The mechanical properties of hydrogels functionalized with CNTs are finally analyzed using rheology measurements.

Mechanical Properties of a Reversible, DNA-Crosslinked Polyacrylamide Hydrogel

2004 ◽  
Vol 126 (1) ◽  
pp. 104-110 ◽  
Author(s):  
David C. Lin ◽  
Bernard Yurke ◽  
Noshir A. Langrana
Keyword(s):  
Mechanical Properties ◽  
Crosslink Density ◽  
Characteristic Temperature ◽  
Polyacrylamide Hydrogel ◽  
Temperature Dependent ◽  
Temperature Dependent Viscosity ◽  
Dna Crosslinks ◽  
Dna Strands ◽  
Dna Strand ◽  
Dependent Viscosity

Mechanical properties of a polyacrylamide gel with reversible DNA crosslinks are presented. In this system, three DNA strands replace traditional chemical crosslinkers. In contrast to thermoset chemically crosslinked polyacrylamide, the new hydrogel is thermoreversible; crosslink dissociation without the addition of heat is also feasible by introducing a specific removal DNA strand. This hydrogel is characterized by a critical crosslink concentration at which gelation occurs. Below the critical point, a characteristic temperature exists at which a transition in viscosity is observed. Both temperature-dependent viscosity and elastic modulus of the material are functions of crosslink density.

Hybridization effect on mechanical properties of short basalt/jute fiber-reinforced polyester composites

2013 ◽  
Vol 20 (4) ◽  
pp. 343-350 ◽  
Author(s):  
Pandian Amuthakkannan ◽  
Vairavan Manikandan ◽  
Jebbas Thangaiah Winowlin Jappes ◽  
Marimuthu Uthayakumar
Keyword(s):  
Mechanical Properties ◽  
Impact Strength ◽  
Hybrid Composites ◽  
Fiber Composite ◽  
Testing Machine ◽  
Basalt Fiber ◽  
Jute Fiber ◽  
Computer Assisted ◽  
Fiber Reinforced ◽  
Polyester Composites

AbstractMechanical properties of fiber reinforcement that can be obtained by the introduction of basalt fibers in jute fiber-reinforced polyester composites have been analyzed experimentally. Basalt/jute fiber-reinforced hybrid polymer composites were fabricated with a varying fiber percentage by using compression molding techniques. The fabricated composite plates were subjected to mechanical testing to estimate tensile strength, flexural strength and impact strength of the composites. The effect of fiber content on basalt/jute fiber in the composites has been studied. Addition of jute fiber into basalt fiber composite makes it a cost-effective one. Incorporation of basalt fiber into the composites was at approximately 10%, 20%, up to 90%, and the jute fiber percentage was reduced from 90%, 80%, to 10% correspondingly. Mechanical properties were investigated as per ASTM standards. Tensile and flexural strengths were tested by using a computer-assisted universal testing machine, and impact strength by using an Izod impact tester. It has been observed that the addition of jute fiber to the basalt fiber polyester composites enhanced the mechanical properties. Water absorption of hybrid composites was also analyzed and was found to be proportional to fiber percentage.

scholarly journals DNA Origami Nanomachines

Molecules ◽  
2018 ◽  
Vol 23 (7) ◽  
pp. 1766 ◽  
Author(s):  
Masayuki Endo ◽  
Hiroshi Sugiyama
Keyword(s):  
Dna Sequences ◽  
Molecular Motors ◽  
Molecular Machines ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Molecular Systems ◽  
Nanoscale Structures ◽  
Research Fields ◽  
Dna Strands ◽  
External Stimuli

DNA can assemble various molecules and nanomaterials in a programmed fashion and is a powerful tool in the nanotechnology and biology research fields. DNA also allows the construction of desired nanoscale structures via the design of DNA sequences. Structural nanotechnology, especially DNA origami, is widely used to design and create functionalized nanostructures and devices. In addition, DNA molecular machines have been created and are operated by specific DNA strands and external stimuli to perform linear, rotational, and reciprocating movements. Furthermore, complicated molecular systems have been created on DNA nanostructures by arranging multiple molecules and molecular machines precisely to mimic biological systems. Currently, DNA nanomachines, such as molecular motors, are operated on DNA nanostructures. Dynamic DNA nanostructures that have a mechanically controllable system have also been developed. In this review, we describe recent research on new DNA nanomachines and nanosystems that were built on designed DNA nanostructures.

scholarly journals CAMM Techniques for the Prediction of the Mechanical Properties of Tendons and Ligaments Nanostructures

2005 ◽  
Vol 5 ◽  
pp. 564-570
Author(s):  
Simone Vesentini ◽  
Franco M. Montevecchi ◽  
Alberto Redaelli
Keyword(s):  
Mechanical Properties ◽  
Molecular Modeling ◽  
Connective Tissue ◽  
Soft Tissues ◽  
Collagen Molecule ◽  
Computer Assisted ◽  
Mechanical Function ◽  
Top Down ◽  
Structural Constituent ◽  
Structures And Properties

Theoretical prediction of the mechanical properties of soft tissues usually relies on a top-down approach; that is analysis is gradually refined to observe smaller structures and properties until technical limits are reached. Computer-Assisted Molecular Modeling (CAMM) allows for the reversal of this approach and the performance of bottom-up modeling instead. The wealth of available sequences and structures provides an enormous database for computational efforts to predict structures, simulate docking and folding processes, simulate molecular interactions, and understand them in quantitative energetic terms. Tendons and ligaments can be considered an ideal arena due to their well defined and highly organized architecture which involves not only the main structural constituent, the collagen molecule, but also other important molecular “actors” such as proteoglycans and glycosaminoglycans. In this ideal arena each structure is well organized and recognizable, and using the molecular modeling tool it is possible to evaluate their mutual interactions and to characterize their mechanical function. Knowledge of these relationships can be useful in understanding connective tissue performance as a result of the cooperation and mutual interaction between different biological structures at the nanoscale.

Intrafibre distribution of succinate dehydrogenase in cat tibialis anterior motor units

1992 ◽  
Vol 70 (7) ◽  
pp. 970-976 ◽  
Author(s):  
Thomas P. Martin ◽  
V. R. Edgerton
Keyword(s):  
Mechanical Properties ◽  
Enzymatic Activity ◽  
Succinate Dehydrogenase ◽  
Dehydrogenase Activity ◽  
Tibialis Anterior ◽  
Radial Distance ◽  
Motor Units ◽  
Computer Assisted ◽  
Mitochondrial Enzymes ◽  
Succinate Dehydrogenase Activity

Using isolated ventral root filament stimulation and glycogen depletion techniques, 14 motor units from the cat tibialis anterior were studied. Based on their mechanical properties, the units were classified as either slow-fatigue resistant, fast-fatigue resistant, fast-fatigue intermediate, or fast-fatigable. Quantitative histochemical and computer assisted image analysis techniques were used to determine the activity of succinate dehydrogenase in a population of fibres in each unit. In addition, the intrafibre distribution of succinate dehydrogenase activity was measured in those same fibres by calculating the enzymatic activity of circumferential layers every 0.5 μm starting from the fibre edge to its centre. It was established that enzymatic activity and radial distance were linearly related in the fibres. A range in succinate dehydrogenase activity (mean coefficient of variation, 29%) was observed among the fibres of a unit. In contrast, the intrafibre distribution of that activity was rather consistent (mean variation, 4%) across the fibres of a unit. Further, the intrafibre distribution was similar among the fibres of units classified as the same type. However, the intrafibre distribution was disparate among the different unit types. These data suggest that the intrafibre distribution of mitochondrial enzymes may contribute to the mechanical properties of a motor unit. In this regard, a hypothesis is proposed that describes how the absolute activity of a mitochondrial enzyme, and the intrafibre distribution of that activity, may interactively contribute to the fatigue resistance of a unit.Key words: mitochondria, quantitative histochemistry, fatigue.

Selective DNA attachment of micro- and nanoscale particles to substrates

2002 ◽  
Vol 17 (2) ◽  
pp. 473-478 ◽  
Author(s):  
D. M. Hartmann ◽  
M. Heller ◽  
S. C. Esener ◽  
D. Schwartz ◽  
G. Tu
Keyword(s):  
Mechanical Properties ◽  
Solid Supports ◽  
Particulate Materials ◽  
Nanoscale Particles ◽  
Large Particles ◽  
Dna Strands ◽  
Dna Attachment

Materials formed from micro- and nanoscale particles are of interest because they often exhibit novel optical, electrical, magnetic, chemical, or mechanical properties. In this work, a means of constructing particulate materials using DNA strands to selectively attach micro- and nanoparticles to substrates was demonstrated. Unlike previous schemes, the DNA was anchored covalently to the particles and substrates, rather than through protein intermediaries. Highly reproducible selective attachment of 0.11–0.87 mm-diameter particles was achieved, with selective:nonselective binding ratios >20:1. Calculations showed that at most 350 and 4200 DNA strands were involved in the binding of the small and large particles, respectively. Experiments showed that the DNA was bent at an angle, relative to the surfaces of their solid supports.

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