DNA nanomachines and their functional evolution

Liu, Huajie; Li, Dongsheng

doi:10.1039/b822719e

Cited by 145 publications

(131 citation statements)

References 105 publications

Supporting

Mentioning

129

Contrasting

Unclassified

Order By: Relevance

“…There has, for example, been a rapid development of various artificial nanomotors with the aim of mimicking the performance of biological machines [4][5][6].…”

Section: Introductionmentioning

confidence: 99%

A minimal model of an autonomous thermal motor

Fogedby¹,

Imparato²

2017

EPL

View full text Add to dashboard Cite

We consider a model of a Brownian motor composed of two coupled overdamped degrees of freedom moving in periodic potentials and driven by two heat reservoirs. This model exhibits a spontaneous breaking of symmetry and gives rise to directed transport in the case of a nonvanishing interparticle interaction strength. For strong coupling between the particles we derive an expression for the propagation velocity valid for arbitrary periodic potentials. In the limit of strong coupling the model is equivalent to the Büttiker-Landauer model [1-3] for a single particle diffusing in an environment with position dependent temperature. By using numerical calculations of the Fokker-Planck equation and simulations of the Langevin equations we study the model for arbitrary coupling, retrieving many features of the strong coupling limit. In particular, directed transport emerges even for symmetric potentials. For distinct heat reservoirs the heat currents are well-defined quantities allowing a study of the motor efficiency. We show that the optimal working regime occurs for moderate coupling. Finally, we introduce a model with discrete phase space which captures the essential features of the continuous model, can be solved in the limit of weak coupling, and exhibits a larger efficiency than the continuous counterpart. IntroductionThere is currently numerous scientific investigations aimed at characterizing the functioning of micro and nano-motors. There has, for example, been a rapid development of various artificial nanomotors with the aim of mimicking the performance of biological machines [4][5][6].From the point of view of man-made engineered micro and nano-motors, ideally one would like to design autonomous machines which are able to cyclically extract energy from the resources available in the environment and convert it to useful work. Similarly to their macroscopic counterparts, such machines must be driven outof-equilibrium by means of one or more thermodynamic forces.In the present paper we focus in particular on a motor driven by temperature gradients. A Brownian motor has long been the paradigmatic model for a microscopic machine, working either in time-dependent or steady state conditions. One well known example is a Brownian particle moving in a periodic and asymmetric potential, a so-called ratchet potential. In such a spatially periodic system, the breaking of the spatial inversion symmetry and of thermal equilibrium, obtained by modulating the force acting on the particle, results in the emergence of directed transport [7][8][9]. Another typical example is represented by a Brownian particle driven by both a periodic temperature variation and an external parameter, periodically changing the system energy [10,11]. This model, which mimics the operation of a heat engine cyclically in contact with different heat reservoirs, has been implemented in a recent experiment [12]. In all these models there is an external agent that changes periodically some parameters, typically a thermodynamic force, according to the moto...

show abstract

“…There has, for example, been a rapid development of various artificial nanomotors with the aim of mimicking the performance of biological machines [4][5][6].…”

Section: Introductionmentioning

confidence: 99%

A minimal model of an autonomous thermal motor

Fogedby¹,

Imparato²

2017

EPL

View full text Add to dashboard Cite

show abstract

“…On the other hand, flexible nature of a single-stranded DNA allows them to find application in machine components such as hinges or nano-actuators. 18 For utility purpose DNA generally finds advantage due to high ability for molecular recognition and to self-assemble. Due to complementary hydrogen bond formation as Adenosine-Thyamine, Guanine-Cytosine pairs, two complementary single strands of DNA in a solution recognizes each other to form double strand in specific manner.…”

Section: Biological Molecular Machinesmentioning

confidence: 99%

Introduction to Molecular Machines

Baruah¹

2017

Concepts for Molecular Machines

View full text Add to dashboard Cite

“…The highly specific binding through Watson-Crick base-pairing of oligonucleotides facilitates convenient creation of defined assemblies by molecular recognition. One strategy is to induce defined conformational changes by DNA hybridization to realize complex molecular machines in liquids [2,3]. A popular example is the design of molecular tweezers, which can be actuated by DNA hybridization, as reported by Yurke et al [4].…”

Section: Introductionmentioning

confidence: 99%

Properties of amphiphilic oligonucleotide films at the air/water interface and after film transfer

Keller

Kwak

Vries

et al. 2013

Colloids and Surfaces B: Biointerfaces

View full text Add to dashboard Cite

Properties of amphiphilic oligonucleotide films at the air/water interface and after film transfer Keller, R.; Kwak, M.; de Vries, J. W.; Sawaryn, C.; Wang, J.; Anaya, M.; Muellen, K.; Butt, H. -J.; Herrmann, A.; Berger, R. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. b s t r a c tThe self-assembly of amphiphilic hybrid materials containing an oligonucleotide sequence at the air/water interface was investigated by means of pressure-molecular area (˘-A) isotherms. In addition, films were transferred onto solid substrates and imaged using scanning force microscopy. We used oligonucleotide molecules with lipid tails, which consisted of a single stranded oligonucleotide 11mer containing two hydrophobically modified 5-(dodec-1-ynyl)uracil nucleobases (dU11) at the 5 -end of the oligonucleotide sequence. The air/water interface was used as confinement for the self-assembling process of dU11. Scanning force microscopy of films transferred via Langmuir-Blodgett technique revealed mono-, bi-(˘ ≥ 2 mN/m) and multilayer formation (˘ ≥ 30 mN/m). The first layer was 1.6 ± 0.1 nm thick. It was oriented with the hydrophilic oligonucleotide moiety facing the hydrophilic substrate while the hydrophobic alkyl chains faced air. In the second layer the oligonucleotide moiety was found to face the air. The second layer was found to cover up to 95% of the sample area. Our measurements indicated that the rearrangement of the molecules into bi-and multiple bilayers happened already at the air/water interface. Similar results were obtained with a second type of oligonucleotide amphiphile, an oligonucleotide block copolymer, which was composed of an oligonucleotide 11mer covalently attached at the terminus to polypropyleneoxide (PPO).

show abstract

DNA nanomachines and their functional evolution

Cited by 145 publications

References 105 publications

A minimal model of an autonomous thermal motor

A minimal model of an autonomous thermal motor

Introduction to Molecular Machines

Properties of amphiphilic oligonucleotide films at the air/water interface and after film transfer

Contact Info

Product

Resources

About