We found a significant negative correlation between FFE of the 2nd codon residue and the helix content of protein structures, which was not expected even though this pos- sibility is mentioned in the literature . Our previous work on a Common Periodic Table of Codons and Nucleic Acids  indicated that the second codon resi- due is intimately coupled with the known physico-chem- ical properties of the amino acids. Almost all amino acids show significant positive or negative correlation to the helix content of proteins. Therefore, the real biological meaning and significance of any connection between the FFE of the 2nd codon residue and the propensity towards a protein structural element is highly questionable. A working hypotheses grew out of these observations, namely that (a) partial, local reverse complementarity exists in nucleic acids and forms the nucleicacidstructure; (b) there is some degree of similarity between the folding of nucleic acids and proteins; (c) nucleicacidstructure determines the amino acid co-locations; (d) as a conse- quence, amino acids encoded by the interacting (partially reverse complementary) codons might show preferential co-locations in the protein structures.
Targeting nucleic acids in a structure- or sequence-specific manner with small molecules remains a significant challenge in chemical biology. The ability to modulate a particular nucleicacidstructure would allow for the specific control of cellular processes. Nucleicacid junctions are important structural motifs involved in several biological processes found in DNA and RNA. Three-way junctions (3WJs) occur at replication forks, in triplet repeat expansions, viral genomes, bacterial temperature sensors, as well as riboswitches and building blocks in nanotechnology. We have developed a new class of nucleicacid junction binders based on the small molecule triptycene. These triptycene-based molecules were shown to significantly stabilize a model system junction. After establishing their selectivity towards junctions over other secondary structures, these molecules were applied to biologically relevant junctions. Triptycenes were demonstrated to bind to a d(CAG)•(CTG) repeat implicated in the pathogenesis of triplet repeat expansion diseases, including Huntington’s disease. These molecules may serve as probes to study diseases associated with these repeats. Additionally, we have
sibility makes the idea of wobble base regulation of nucleicacidstructure even more interesting, because it indicates that the excess information in the redundant codon (carried by the wobble bases) may be used to mod- ify or regulate the protein structure. To explore this possi- bility we compared the TFEs of intact and wobble base- modified mRNA sequences to the propensity towards dif- ferent structural elements in the coded proteins (Figure 2). There is a positive correlation between mRNA TFE and the frequency of helices in the coded proteins. In contrast, the correlation between dG and beta sheet frequency is nega- tive. This means that RNA complexity is proportional to beta sheet-type and other amino acid collocations, but inversely related to alpha helix frequency. The relation- ship between mRNA and protein structure will definitely be the subject of further evaluation because of its funda- mental importance for further understanding the transla- tion process and protein folding. The correlation between nucleicacid composition (sequence), nucleicacid folding energy (structure) and protein structural elements (helix, sheet) is a strong indication that protein-folding informa- tion is present in the redundant exon bases [8,21], and coding sequences function as chaperons .
The present invention provides functional nucleicacid probes, and methods of using functional nucleicacid probes, for binding a target to carry out a desired function. The probes have at least one functional nucleicacid, at least one regulating nucleicacid, and at least one attenuator. The functional nucleicacid is maintained in an inactive state by the attenuator and activated by the regulating nucleicacid only in the presence of a regulating nucleicacid target. In its activated state the functional nucleicacid can bind to its target to carry out a desired function, such as generating a signal, cleaving a nucleicacid, or catalyzing a reaction.
The three dimensional structure of four PNA complexes have been determined so far (Figure 4). A hexamer PNA-RNA duplex (14) and an octamer PNA-DNA duplex (15) were solved by NMR methods, while an undecamer 2PNA/DNA triplex (16) and a hexamer PNA/PNA duplex (17) were solved by X-ray crystallography. It can be concluded from these structures, that PNA is able to adapt well to its nucleicacid partner, as the RNA strand in the RNA/PNA duplex is essentially in a A-form conformation, while the DNA strand in the PNA/DNA duplex adopts a B-like conformation. It is, however, equally clear that PNA prefers to adopt a helical conformation (named the P-form [16,17]) that is distinctly different from other nucleicacid helices. This conformation is dominating in the 2PNA/DNA triplex (16), and is clearly seen in the PNA/PNA duplex which is a very wide helix (28 Å) with almost twice the pitch (18 base pairs per turn) of an A- or B-form helix (10-11 base pairs per turn).
The polymeric strand is stabilized by N-H···O intramolecular interaction between the cytosine base and the phosphate oxygen atom. The cytosine base also interacts with the axial Chlorine atom to form N-H···Cl hydrogen bond. The structure is stabilized through the extensive network of N-H···O, C-H···O and O-H···O hydrogen bond interactions between the water molecules and polymerizing, making the sheets to run in third direction. The chlorine atom Cl1 at the same time along with the water molecule O1W and O8W of the phosphate group forms an envelope shape five membered ring [Cl1-O2W-O8-O1W-O3W-Cl1] via hydrogen bond. Thus the water molecules, the phosphate oxygen atoms, the chlorine atoms and the nitrogen atoms of the base make the network of hydrogen bonds in three dimension. In the three dimensional network the copper atoms, the base and the sugar with the phosphate are running anti parallel direction pushing the bipyridyl ring on the outer side, thus remaining as the back bone of the sheet. Additionally, there is a presence of slipped π···π stacking
Nucleicacid vaccine is one of the hot spot of PCV2 vaccine researches. DNA vaccines may be capable of in- ducing immunity regardless of maternally derived anti- bodies [14, 15] and they have induced protective cellular and humoral immunity in preclinical models of infec- tious diseases. PCV2 Nucleicacid vaccine was first re- ported by Kamstrup , they developed and investigated the potential of DNA vaccination approach to against PCV2. Mice were vaccinated three times by gene gun and all mice responded serologically by raising antibodies against PCV2. They found that vaccination based on DNA might offer opportunities for vaccination of piglets against PCV2.
therapeutic strategies, the gene, instead of a protein product, is recognized as drug targets and the modified oligonucleotides (including DNAs and RNAs) are applied as drug candidates. Therefore, nucleic acids related research is essential for better understanding of diseases and identifying novel drug candidate and target for the development of therapeutics with high efficiency to treat some world-wide diseases. Because of the advantages of low toxicity, notable efficacy, and high specificity, numerous nucleicacid-based potential therapeutics are under development or in clinical trials, including nucleoside analog, antisense oligonucleotides, siRNAs, miRNAs, aptamers and ribozymes and DNazymes 7-8 . Instead of the traditional attacking of aberrant proteins, modulating expression of specific diseases’ gene by these nucleic acids therapies can lead to better treatment. Research activities in this area require further development of new nucleicacid analogs with improved properties.
minutes. The extract was then incubated with 5 ml of 5% HCIO^ at 70°C for 40 minutes and then centrifuged. The supernatant was collected. The insoluble pellet was washed once with 1 ml 5% H610^, by centrifuging; this supernatant was added to the first. The pH of the super natant was adjusted approximately to 7 and its volume to 10 ml with HgO and the'^oluble KCIO^ was collected in the cold by centrifugation. The supernatant was read at 260 and at 290 mu. The difference between 260 minus 290 mu reading was multiplied by 57 to obtain yg nucleicacid per ml. DNA content was estimated by the diphenylamine test for deoxyribose. 1 ml of the neutralized acid
substrate turnover, energy stores, oxygen consumption and other physiological measures. Whole-animal composition was determined during development from eggs (NF stage 1) to 2 weeks post-feeding (NF 50–51), which represents two-thirds of the developmental period. Wet and dry masses were found to be highly correlated, with water content remaining constant at 93 % of wet mass. Whole- animal nucleicacid content was linearly correlated with both wet and dry masses, and declined relative to mass as development progressed. Similarly, total protein content
The possibility that the nucleotide sequence itself could modulate translation and hence affect co-translational folding and assembly of proteins has been investigated in a number of studies [5-7]. Studies on the relationships between synonymous codon usage and protein secondary structural units are especially popular [8-10]. The genetic code is redundant (61 codons encode 20 amino acids) and as many as six synonymous codons can encode the same amino acid (Arg, Leu, Ser). The "wobble" base has no effect on the meaning of most codons, but codon usage (wobble usage) is nevertheless not randomly defined [11,12] and there are well-known, stable species- specific differences in codon usage. It seems to be reason- able to search for the meaning (biological purpose) of the wobble bases in association with protein folding. Materials and methods
Figure 2.5 isolates the contributions of hierarchical structure decomposition and defect-weighted sampling to our ensemble defect optimization algorithm by comparing performance to three modified algorithms lacking one or both ingredients. All four methods typically achieve the desired design quality, with hierarchical methods surpassing the quality requirement for the root node as a result of overshooting stop conditions lower in the decomposition tree. Hierarchical methods dramatically reduce design cost relative to their single- scale counterparts (which are not tested for N = 800 due to high cost). Defect-weighted sampling reduces design cost and GC content by focusing mutation effort on the most defective subsequences. For the single- scale methods, the relative cost of design, c des (N )/c eval (N ), increases with N . For hierarchical methods,
depends primarily on the selection of the probe, and secondarily upon the hybridization conditions (mainly the temperature). To date, however, most DNA biosensors are not capable of selectively discriminating against single-base mismatches, as desired for example, for the detection of disease-related point mutations. The ability to recognize a change in a single nucleotide thus represents a major challenge for DNA biosensor technology. Accordingly, a drastically different approach (relying on the use of new probes) is desired to impart higher selectivity onto nucleic-acid biosensors.
Studies of synthetic prions combined with investigations of naturally occurring strains support the thesis that prions are devoid of a prion-specific nucleicacid. A novel strain of prions was produced using mouse (Mo) recombinant PrP composed of residues 89 to 230 (36). The first synthetic prion strain (MoSP1) was inoculated into transgenic 9949 mice expressing N-terminally truncated MoPrP( ⌬ 23–88) and wild-type FVB mice expressing full-length MoPrP. Incubation time measure- ments, neuropathologic lesion profiles, and conformational stability studies using guanidinium HCl denaturation indicate that MoSP1 prions differ from RML and many other prion strains derived from humans with Creutzfeldt-Jakob disease, sheep with scrapie, and cattle with bovine spongiform enceph- alopathy (37).
biosensors could have been applied as a promising approach to some specific issues. They could be used for cheap diagnosis at an early stage of the disease, i.e., immediately after exposure to the pathogen, as well as to monitor the treatment process. SELEX versatility and its susceptibility to modifications, as enhancement of the selective pressure, could allow obtaining aptamers detecting precisely the level of viremia, which is below the threshold of the currently used diagnostic methods. Moreover, an aptamer-based approach ensures a more rapid and cheaper diagnosis . The aptamer structure might be a major constraint in their future application as a diagnostic tool. Many existing aptamers are RNA molecules that are highly susceptible to degradation by nucleases. Consequently, their use as a molecular-recognition element of the biosensors may be limited. This problem can be solved by synthesizing a “mirror” analog of these particles that retains their original properties but are not cleaved by nucleases . The alternative solution includes local modifications of the ribose 2’ sites in the aptamer chain [99,100]. In conclusion, aptamers are molecules potentially attractive for viral diagnostics including the recent pandemic Corona virus disease 19 (COVID-19).