During the DNA replication process, a polymerization reaction takes place in which the reactants are deoxyribonucleoside triphosphates. In order to make the process happen, the nucleotides need to have three groups of phosphate whose energy allows the reaction that results in just one phosphate being incorporated into the filament.
Other discriminating factors for initiating replication are the presence of a single strand that acts as a template for the new strands, which will be the copy of it; and the denaturising of certain types of proteins of double helix DNA. This takes place through two processes:
One in which double helix strands are separated using enzymes called Helicases, another process in which the single strands are stabilised by denaturing non-enzymatic proteins to which they bond selectively. These processes create a replication fork which, through its migration along the leading strands, is able to be replicated continuously through exposure, while the other, lagging strand is disseminated into newly synthesised fragments called Okazaki fragments which trigger the RNA primer.
The resulting strands therefore have primers and gaps and must be completed by the endonucleases removing the primers, and the reparative polymerases filling in the gaps. Subsequently, the DNA ligase will bind together the newly synthesised fragments of the lagging strand.
Replication, which is a semi-conservative process, therefore produces two identical double helices made up of one existing strand and one new one.
In terms of its dimensions, structure, length and rigidity, the DNA molecule is highly compatible with nanotechnologies used for top-down systems, in which the manipulation of atoms or molecules leads to the formation of new structures, and bottom-up systems, where the molecules self-assemble based on the recognition characteristics.
In the case of bottom-up systems, given the cohesive structure of the helices which bind together through tiny complementary single strand terminals, these extremities can be precisely programmed according to a very high number of types of interaction.
Single DNA strands can interact with certain types of nanotubes, creating a stable hybrid whose induced component (the symbiotic nanotube) can be dissolved in aqueous solution.
It is possible to cause stable errors during the process of replication of pure and hybrid strands; this can lead to the appearance of mutations, which are programmable and controllable through nanomachines that can also influence and guide protein synthesis processes.
A single strand DNA sequence is able to self-assemble into a helicoid structure which wraps around the nanotubes, leading to new hybrids with characteristics that depend on the atomic structure of the hybridizing factor and its electronic properties. Using anion exchange chromatography, it is possible to separate the metal nanotubes from the semi-conductor nanotubes, to assist the development of electronic applications.
Through nanotechnologies it is possible to reproduce symbiotic agents between the ribosome and the basic ribonucleic acid, each time modifying and conditioning the process of information and exchange with the aminoacids for building proteins. The nanomachine (developed on the molecular structure of the hybrid) is therefore able to monitor, from the level of atomic processes, the process of acquiring the information needed for the chemical catalysis of the proteins, and to modify its content.
The cells of the immune and nervous systems communicate with each other through a network of channels used for exchanging information. Some cells, namely the dendritic cells and macrophages, use nanotubes to transmit molecular messages.
So by triggering a process of information acquisition in a nanomachine, it is possible to exploit the cellular communication channels to provoke learning by cells situated at a significant distance in a very short time-span, allowing chemical-physical transformations and transformations in response to stimuli, in the same way as neuronal communication.
The nanomachine is able to intervene at the level of atomic processes, in the process of acquiring information needed for protein catalysis, and is able to modify its content if necessary.
The nanomachine is made up of biomineral materials which behave, due to the presence of organic macromolecules, symbiotically with the protein assembly processes.
The creation process of the biomineral material takes place through a study of the cellular processes that characterise the four stages of the creation mechanism, and the composite materials present in living organisms:
- Supermolecular organisation
- Molecular recognition of the interface
- Vectorial regulation of the growth of the crystal
- The cellular process
Through biomimetic chemistry it is possible to imitate these creation processes to produce the nanomachine; the latter, having induced and programmable characteristics, and exploiting the molecular processes of hybridization, is compatible with the organic apparatus (symbiosis induced by processes between catalyser and assembler).
By engineering materials with regular structures in terms of size of particles, morphology (or selected polymorphism), oriented enucleation and organised growth, it is possible to achieve structures that are capable of not interacting with the medium of propagation of the second generation of assemblers. By the controlled monitoring of biomineralisation processes, particularly of crystallization in the presence of biological macromolecules, we are able to add assembled monostrates and functionalised polymer substrates. By adding small organic molecules, peptides (which interact with the brain’s opiate receptors imitating drugs such as heroin or morphine) and above all, certain polymers via condensation (polyacrylate – PS), we obtain a biomaterial such as hydroxyapatite, which is used for building the biomachine.
The assemblers allow us to modify, manage and sample the activity of the “D” type amino acid when assembling proteins. Assemblers are able to make copies of themselves, and therefore to replicate themselves.
An assembler is a functionalised nanomachine that is programmed to interact with the protein synthesis processes and to provide indications useful to the amino acid which is designated to carry out the function of assembly.
This is an external element which, once it has been inserted through absorption, samples and instructs the amino acid (up to 700,000 operations per second), conditioning the synthesis process. The assembler becomes a second source of information for the “D” type amino acid, as it actually enters into symbiosis with the RNA. The nanomachine is able to condition the polymerase of the HnRNA (heterogeneous RNA which must mature to become mRNA), which matures in such a way that the mRNA (messenger) produced contains corresponding information, deriving from the previously modified DNA (transcription).
Protein synthesis starting from a modified DNA and a sampled RNA involves the nanomechanical assembler as the evolutive and conditioning agent of the process.
To ensure that the host organism quickly modifies its synthesis capacities, the nanomachine must be able to replicate by a number that varies according to the number of synthesis processes needed by the organism itself.
Ingeneo designs nanomachines called “SEME”; they contain a nanocomputer (a hybrid system on a mathematical-logical base of atomic-scale dimensions) and through self-replication they create a number of assemblers defined by the messenger RNA, by its starter strands. These assemblers therefore interface with the modified mRNA and as they have been previously programmed, they condition its synthesis results. Once the protein synthesis process has been modified, they gather information on the growth activity of the resulting polypeptidic chain, sampling the speed and type of bond.
At this point, the assembler is programmed to share this information with other assemblers, and to self-replicate to create the second generation of nanomachines.
The aim of Ingeneo’s research in the field of nanotechnologies is to organise biomineral and organometalloid matter so as to stimulate the debate on the risks of potentially destructive technologies, attempting to select materials for the development of self-replicating nanomachines. In the field of molecular genetics the only route possible for the production of efficient products in the medical and biomechanics field is that of nanotechnology that is able to self-replicate in a way that is non-destructive for the host organism; this means it is “able to understand” what its expressible functions are, intervening in the assembly processes of the very matter of the organism, as they are constructed with the same material and chemical logic.
The increasingly faint boundaries between the organic and the inorganic point to the need to design self-replication so that assemblers and nanomachines do not go haywire and exploit their potential for reproduction and interference in molecular processes in a way that would be uncontrollable, destructive and therefore ethically wrong.
