Abstract DNA origami is a mainstay of nanotechnology and several efforts have been devoted to understanding how various factors the self-assembly reaction affect final yield target structure. This study analyses base sequence affects through generation off-target side reactions during selfassembly. Off-target bindings are an under-explored phenomenon can potentially introduce unwanted assembly barriers kinetic traps in folding pathway. We developed multi-objective computational approach that...

Binary light-up aptamers are intriguing and emerging tools with potential in different fields. Herein, we demonstrate the versatility of a split Broccoli aptamer system able to turn on fluorescence signal only presence complementary sequence. First, an RNA three-way junction harbouring is assembled E. coli-based cell-free TX-TL where folding functional demonstrated. Then, same strategy introduced into 'bio-orthogonal' hybrid RNA/DNA rectangle origami characterized by atomic force microscopy:...

In addressing the origins of Darwinian evolution, recent experimental work has been focussed on discovery simple physical effects which would provide a relevant selective advantage to protocells competing with each other for limited supply lipid. particular, data coming from Szostak's lab suggest that transition prebiotically plausible lipid membranes more complex and heterogeneous ones, closer real biomembranes, may have driven by changes in fluidity membrane its affinity available...

Artificial protocellular compartments and lipid vesicles have been used as model systems to understand the origins requirements for early cells, well design encapsulated reactors biotechnology. One prominent feature of is semi-permeable nature their membranes, able support passive diffusion individual solute species into/out compartment, in addition an osmotic water flow opposite direction net concentration gradient. Crucially, this affects internal aqueous volume vesicle response...

The scaffolded origami technique is an attractive tool for engineering nucleic acid nanostructures. This paper demonstrates RNA folding in vitro which, the first time, all components are transcribed simultaneously a single-pot reaction. Double-stranded DNA sequences by T7 polymerase into scaffold and staple strands able to correctly fold high synthesis yield nanoribbon. Synthesis successfully confirmed atomic force microscopy, unpurified transcription reaction mixture analyzed gel-imaging...

Conceiving the process of biogenesis as evolutionary development highly dynamic and integrated protocell populations provides most appropriate framework to address difficult problem how prebiotic chemistry bridged gap full-fledged living organisms on early Earth. In this contribution we briefly discuss implications taking dynamic, functionally systems (rather than complex reaction networks in bulk solution, sets artificially evolvable replicating molecules, or even these same molecules...

Design of experiments (DOE) enables scientists to explore complex, multidimensional spaces against a background experimental variability with the minimum resource. While these methods are most successful when combined expert knowledge define design space and capture dimensionality problem, many believe, often quite strongly, that they can deliver insights into without recourse DOE tools. Many believe small experiments, guided by scientific intuition alone, exploring changes as each variable...

Abstract DNA-based memory systems are being reported with increasing frequency. However, dynamic DNA data structures able to store and recall information in an ordered way, be interfaced external nucleic acid computing circuits, have so far received little attention. Here we present vitro implementation of a stack structure using polymers. The is record combinations two different signals, release the signals into solution reverse order, then re-record. We explore accuracy limits through...

Our PCR Simulator is a web-based application designed to introduce concepts of multi-factorial experimental design and support teaching the polymerase chain reaction. Learners select settings receive results their simulated reactions quickly, allowing rapid iteration between data generation analysis. This enables student perform complex iterative strategies within short session. Here we provide overview user interface underpinning model, describe our experience using this tool in environment.

The concept of identity is used both (i) to distinguish a system as particular material entity that conserved such in given environment (token-identity: i.e., permanence or endurance over time), and (ii) relate with other members set (type-identity: an equivalence relationship). Biological systems are characterized, minimal universal sense, by highly complex dynamic, far-from-equilibrium organization very diverse molecular components transformation processes (i.e., 'genetically instructed...

How did natural systems develop the first mechanisms of regulation and what for? could they turn into adaptive agents in a minimal (though deeply meaningful) biological sense? A novel simulation platform, "Araudia", has been implemented to address these questions, which are interrelated, prebiotic scenario where metabolically diverse protocells allowed modify their dynamic behaviour response changes boundary conditions (e.g., nutrient concentrations medium) and/or activity other protocells,...

An intermediate step between simple models of protocells having no membrane structure and the current, complex organization modern cells considers forms change that interact with protocell dynamics in predictable ways. Here we analyse a kinetic model system: bioreactor vesicle involving mechanosensitive channels. This is closed lipid bilayer which hosts minimal metabolism X +E! W +E inside its internal (variable volume) water pool, channels anchored membrane. The reactor can swell, opening...

We recently reported the design for a DNA nano-device that can record and store molecular signals. Here we present an evolutionary algorithm tailored to optimising nucleic acid sequences predictively fold into our desired target structures. In approach, device is first specified abstractly: topology of individual strands their foldings multi-strand complexes are described at domain-level. Initially, this decomposed set pairwise strand interactions. Then, optimize candidate domains, such...

Chemical reaction networks can exhibit interesting non- linear dynamics in contexts with variable solvent volume (Pawowski and Zielenkiewicz, 2004; Lizana et al., 2008), although this possibility has received little atten- tion the literature. Lipid vesicles, standard chas- sis for many prebiotic protocell models, are compartments which enclose a water pool of volume. The semi- permeable nature lipid bilayer membrane facilitates, by mechanism osmosis, flow entering or leaving internal...

Chemical reaction networks can exhibit interesting non- linear dynamics in contexts with variable solvent volume (Pawowski and Zielenkiewicz, 2004; Lizana et al., 2008), although this possibility has received little atten- tion the literature. Lipid vesicles, standard chas- sis for many prebiotic protocell models, are compartments which enclose a water pool of volume. The semi- permeable nature lipid bilayer membrane facilitates, by mechanism osmosis, flow entering or leaving internal...

An intermediate step between simple models of protocells having no membrane structure and the current, complex organization modern cells considers forms change that interact with protocell dynamics in predictable ways. Here we analyse a kinetic model system: bioreactor vesicle involving mechanosensitive channels. This is closed lipid bilayer which hosts minimal metabolism X +E! W +E inside its internal (variable volume) water pool, channels anchored membrane. The reactor can swell, opening...

Designs for scaffolded DNA origami nanostructures are commonly and minimally published as the list of staple scaffold sequences required. In nearly all cases, high-level editable design files (e.g. caDNAno) which generated low-level not made available. This de facto ‘raw sequence’ exchange format allows designs to be re-attempted in laboratory by other groups, but effectively stops from being significantly modified or re-purposed new future applications. To make raw sequence more accessible...

ABSTRACT The scaffolded origami technique has provided an attractive tool for engineering nucleic acid nanostructures. This paper demonstrates RNA folding in vitro which all components are transcribed simultaneously a single-pot reaction. Double-stranded DNA sequences by T7 polymerase into scaffold and staple strands able to correctly fold high yield the nanoribbon. Synthesis is successfully confirmed atomic force microscopy unpurified transcription reaction mixture analyzed gel-imaging...