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From Computational RNA Structure Prediction to the Design of Biologically Active RNA-Based Nanostructures
Published in Peixuan Guo, Kirill A. Afonin, RNA Nanotechnology and Therapeutics, 2022
W.K. Kasprzak, Bruce A. Shapiro
From the structural point of view RNA is a polymer chain containing a combination of four nucleotides with a directionality corresponding to the natural order of RNA chain synthesis (transcription), from the 5′ to 3′ end. The bases that give nucleotides their names, usually referred to by the single letters A, G, C, and U, are Adenine, Guanine, Cytosine, and Uracil. A primary structure of RNA is defined by a sequence of nucleotides. Conceptually single-stranded, RNA chains are sufficiently flexible to fold onto themselves and base pair Gs with Cs and As with Us in the canonical, Watson-Crick scenario. An additional, so-called “wobble” base pair G-U is also frequent. In general, all kinds of non-canonical interactions are found in natural RNAs. The pattern of paired and unpaired nucleotides defines the secondary structure of a sequence. Pairing interactions stabilize the folded RNA. Unpaired regions, out of which emanate two or more helices (or branches), are called loops, and they tend to destabilize the secondary structure.
Pre-programmed Self-assembly
Published in Klaus D. Sattler, st Century Nanoscience – A Handbook, 2019
Carlos I. Mendoza, Daniel Salgado-Blanco
As previously discussed, particles with directional interactions can be used to program self-assembly. Directionality in DNA-grafted nanoparticles can be incorporated in a number of different ways, for example, by chemically patterning particles with patches of DNA or using DNA-encoded nanoparticles assembled on a solid support (Maye et al. 2009). Also, directionality arises naturally from shape anisotropy; specific orientations between particles can be favored enthalpically if they permit the formation of additional DNA bridges or entropically if they increase the configurational freedom of the system (Jones et al. 2010, Lu et al. 2015 and O’Brien et al. 2015). Recently, nanoparticles (about 100 nm in size) that combine chemical and geometrical directionality have been fabricated (Désert et al. 2013). Shape and sequence complementarity are promising strategies that are being currently investigated to maximize specificity of DNA-grafted particles; however, the number of different species that can be built is still far from what can be obtained using DNA tiles.
Classifications and typical examples of biomotors
Published in Peixuan Guo, Zhengyi Zhao, Biomotors: Linear, Rotation, and Revolution Motion Mechanisms, 2017
The FtsK family has many varied members, but the majority share the same three components: a N-terminal domain with four transmembrane segments that anchor the motor to the cytoplasmic membrane, a C-terminal domain consisting of about 512 amino acids, and a highly variable linker that connects the N- and C-domains and is rich in amino acids glutamine and proline. While the N-terminal domain plays a major role in cell division, the C-terminal domain functions in chromosome segregation and DNA translocation. The latter is divided into three segments: α, β, and γ. The first two parts are the motor portion of FtsK, and they assemble into a hexameric ring with a central channel through which dsDNA passes. The γ subdomain provides for directionality of the DNA. It has been found that the C-terminal domain of FtsK uses the γ subdomain to bind to DNA at sites of 8 base pair sequences called KOPS, which direct the rapid translocation of DNA. As with many other biomotors, it is the hydrolysis of ATP that powers this process, allowing FtsK to translocate up to 17,000 bp/sec (Lee et al., 2012). FtsK is often grouped in the same superfamily as SpoIIIE, and members of this large family are involved in DNA conjugation, segregation, and translocation as well as protein transport. The FtsK/SpoIIIE family of proteins belongs to the additional strand conserved E (ASCE) superfamily, which are hexameric dsDNA translocases found in many bacterial species. Within the ASCE class, the FtsK/HerA clade is present throughout bacteria and archaea. The large FtsK-HerA family (Iyer et al., 2004) also contains the motor proteins of various conjugative plasmids and transposons such as the single-strand translocase protein TrwB (Gomis-Ruth and Coll, 2001; Gomis-Ruth et al., 2001).
Biomolecules of Similar Charge Polarity Form Hybrid Gel
Published in Soft Materials, 2022
Pankaj Pandey, Vinod Kumar Aswal, Joachim Kohlbrecher, Himadri B. Bohidar
This ratio is on the order of ~103, hence FA molecules were in propensity in the solution. Since, FA was dissolved in DMSO solvent, there was a hydration layer mostly comprising of DMSO and, therefore, a water depletion region prevailed in the vicinity of the FA–solvent interface (Scheme 1). Because of this directionality requirement, these solvated FA moieties specifically locate themselves closer to the DNA strands where intermolecular hydrogen bonding possibility exists, thereby forcing the reorganization of DNA strands in the solvent medium. Due to the propensity of FA molecules nearly all hydrogen bonding sites on DNA will get saturated with firm binding. Therefore, FA molecules play the role of pseudo crosslinker in this process. This eventually leads to the dynamic arrest of the DNA strands and the concomitant formation of the network structure. It is well known that above 90° C, dsDNA exists as ssDNA. Since our sol was at a temperature well above this temperature, it was reasonable to argue that ssDNA interacted with FA forming interpolymer complexes which prohibited formation of dsDNA upon cooling. Further DMSO is shown to be a denaturation agent for DNA.[28] This is depicted in Scheme 1.