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Journal of Molecular Biology May 1974
Topics: Animals; Base Sequence; DNA; DNA, Single-Stranded; Ducks; Electrophoresis, Polyacrylamide Gel; Genotype; Hemoglobins; Molecular Weight; Nucleic Acid Denaturation; Nucleic Acid Hybridization; Poly A-U; Poly U; Polynucleotides; RNA, Messenger; Ribonucleases; Temperature; Tritium
PubMed: 4835728
DOI: 10.1016/0022-2836(74)90130-2 -
Bulletin of Mathematical Biology Apr 2006The study of genetic sequences is of great importance in biology and medicine. Mathematics is playing an important role in the study of genetic sequences and, generally,...
The study of genetic sequences is of great importance in biology and medicine. Mathematics is playing an important role in the study of genetic sequences and, generally, in bioinformatics. In this paper, we extend the work concerning the Fuzzy Polynucleotide Space (FPS) introduced in Torres, A., Nieto, J.J., 2003. The fuzzy polynucleotide Space: Basic properties. Bioinformatics 19(5); 587-592 and Nieto, J.J., Torres, A., Vazquez-Trasande, M.M. 2003. A metric space to study differences between polynucleotides. Appl. Math. Lett. 27:1289-1294: by studying distances between nucleotides and some complete genomes using several metrics. We also present new results concerning the notions of similarity, difference and equality between polynucleotides. The results are encouraging since they demonstrate how the notions of distance and similarity between polynucleotides in the FPS can be employed in the analysis of genetic material.
Topics: Algorithms; Codon; DNA; Fuzzy Logic; Genome; Models, Genetic; Polynucleotides; RNA
PubMed: 16794951
DOI: 10.1007/s11538-005-9020-5 -
Systematic and Applied Microbiology Jan 2021Recent developments in fluorescence in situ hybridization (FISH) methods allow the detection and visualization of the genes/genomic regions of bacteria, archaea and...
Recent developments in fluorescence in situ hybridization (FISH) methods allow the detection and visualization of the genes/genomic regions of bacteria, archaea and infecting viruses at the single cell level. These methods use mixtures of polynucleotides as probes to specifically detect the target of interest. Gene-PROBER enables the design of polynucleotide mixtures for targeting genes or genomic regions in microorganisms. It has four workflows, depending on the availability of non-target sequences and the choice of probe synthesis, either by chemical synthesis or by PCR. It outputs polynucleotides that are spread along the target sequence and have similar melting properties. Therefore, such a polynucleotide mixture can be used as a single probe, in a single hybridization reaction. Gene-PROBER is a freely available web service that can be accessed at http://gene-prober.icbm.de/, and is implemented in the R language using the Shiny package.
Topics: Archaea; Bacteria; Bacterial Typing Techniques; In Situ Hybridization, Fluorescence; Internet; Nucleic Acid Hybridization; Oligonucleotide Probes; Polynucleotides; Software
PubMed: 33352459
DOI: 10.1016/j.syapm.2020.126173 -
The Journal of Physical Chemistry. B Mar 2018The assembly of stacked dyes on DNA is of interest for electron transfer, light harvesting, sensing, and catalysis applications. A combination of UV/vis absorption,...
The assembly of stacked dyes on DNA is of interest for electron transfer, light harvesting, sensing, and catalysis applications. A combination of UV/vis absorption, linear dichroism (LD), and circular dichroism (CD) was applied to characterize thoroughly the aggregation with DNA of the phenothiazine dyes methylene blue, azure B, and thionine. Aggregates of each dye with [poly(dG-dC)], [poly(dA-dT)], and calf thymus DNA were explored at high dye:DNA binding ratios, where excess dye groove-binds after all intercalation sites are filled. The organization of the aggregates (dimers, trimers, and multimers) with polydeoxynucleotides displays a structural diversity that depends on DNA sequence, extent of methylation of dye exocyclic amine groups, and ionic strength. The dyes typically form right-handed H-aggregates having negative LD, consistent with stepped stacking along the minor groove. However, aggregates in some dye:DNA aggregates show left-handed chirality or positive LD, indicating unusual modes of aggregation such as formation of adventitious dimers between intercalated and minor groove bound dye. In terms of sequence-dependence, methylene blue shows more extensive aggregation with [poly(dA-dT)], while thionine aggregates more with [poly(dG-dC)]. Azure B has distinctive behavior that is unlike either other dyes. Thus, although these phenothiazine dyes possess a common tricyclic framework, the organization of their polynucleotide-facilitated aggregates depends sensitively on the extent of methylation of the exocyclic amines.
Topics: Animals; Cattle; Circular Dichroism; DNA; Fluorescent Dyes; Molecular Structure; Polynucleotides
PubMed: 29481085
DOI: 10.1021/acs.jpcb.7b12835 -
Scientific Reports Jul 2017The safe and effective delivery of therapeutic genes into target cell interiors is of great importance in gene therapy. Chitosan has been extensively studied as a gene...
The safe and effective delivery of therapeutic genes into target cell interiors is of great importance in gene therapy. Chitosan has been extensively studied as a gene delivery carrier due to its good biocompatibility and biodegradability. Understanding the atomic interaction mechanism between chitosan and DNA is important in the design and application of chitosan-based drug and gene delivery systems. In this work, the interactions between single-stranded polynucleotides and different types of chitosan were systematically investigated by using molecular dynamics (MD) simulation. Our results demonstrate that the functional groups of chitosan, the types of base and length of polynucleotides regulate the interaction behavior between chitosan and polynucleotides. The encapsulation capacity of polynucleotide by chitosan is mainly balanced by two factors: the strength of polynucleotide binding to chitosan and the tendency of self-aggregation of polynucleotide in the solution. For -NH chitosan, due to the strong electrostatic interaction, especially the H-bond between -NH groups in chitosan and phosphate groups in polynucleotide, the aggregation effect could be partially eliminated. The good dispersal capacity of polynucleotides may improve the encapsulation of polynucleotides by chitosan, and hence increase the delivery and transfection efficiency of chitosan-based gene carrier.
Topics: Chitosan; DNA; Hydrogen Bonding; Molecular Dynamics Simulation; Polynucleotides; Static Electricity; Thermodynamics
PubMed: 28698591
DOI: 10.1038/s41598-017-05197-0 -
Applied and Environmental Microbiology Jan 2021Much of virus fate, both in the environment and in physical/chemical treatment, is dependent on electrostatic interactions. Developing an accurate means of predicting... (Review)
Review
Much of virus fate, both in the environment and in physical/chemical treatment, is dependent on electrostatic interactions. Developing an accurate means of predicting virion isoelectric point (pI) would help to understand and anticipate virus fate and transport, especially for viruses that are not readily propagated in the lab. One simple approach to predicting pI estimates the pH at which the sum of charges from ionizable amino acids in capsid proteins approaches zero. However, predicted pIs based on capsid charges frequently deviate by several pH units from empirically measured pIs. Recently, the discrepancy between empirical and predicted pI was attributed to the electrostatic neutralization of predictable polynucleotide-binding regions (PBRs) of the capsid interior. In this paper, we review models presupposing (i) the influence of the viral polynucleotide on surface charge or (ii) the contribution of only exterior residues to surface charge. We then compare these models to the approach of excluding only PBRs and hypothesize a conceptual electrostatic model that aligns with this approach. The PBR exclusion method outperformed methods based on three-dimensional (3D) structure and accounted for major discrepancies in predicted pIs without adversely affecting pI prediction for a diverse range of viruses. In addition, the PBR exclusion method was determined to be the best available method for predicting virus pI, since (i) PBRs are predicted independently of the impact on pI, (ii) PBR prediction relies on proteome sequences rather than detailed structural models, and (iii) PBR exclusion was successfully demonstrated on a diverse set of viruses. These models apply to nonenveloped viruses only. A similar model for enveloped viruses is complicated by a lack of data on enveloped virus pI, as well as uncertainties regarding the influence of the phospholipid envelope on charge and ion gradients.
Topics: Isoelectric Point; Models, Biological; Polynucleotides; Static Electricity; Viruses
PubMed: 33188001
DOI: 10.1128/AEM.02319-20 -
International Journal of Molecular... Jan 2024Knee osteoarthritis (OA), an age-related degenerative disease characterized by severe pain and disability, is treated using polynucleotides (PNs) and hyaluronic acid...
Knee osteoarthritis (OA), an age-related degenerative disease characterized by severe pain and disability, is treated using polynucleotides (PNs) and hyaluronic acid (HA). The intra-articular (IA) injection of HA has been studied extensively in both animal models and in humans; however, the efficacy and mechanisms of action remain unclear. In addition, there has been a paucity of research regarding the use of PN alone or in combination with HA in OA. To investigate the effect of the combined injection of PN and HA in vivo, pathological and behavioral changes were assessed in an OA model. Anterior cruciate ligament transection and medial meniscectomy were performed in Sprague-Dawley rats to create the OA animal model. The locomotor activity improved following PNHA injection, while the OARSI grade improved in the medial tibia and femur. In mild OA, TNFα levels decreased histologically in the PN, HA, and PNHA groups but only the PNHA group showed behavioral improvement in terms of distance. In conclusion, PNHA exhibited anti-inflammatory effects during OA progression and improved locomotor activity regardless of the OARSI grade.
Topics: Rats; Humans; Animals; Hyaluronic Acid; Polynucleotides; Rats, Sprague-Dawley; Osteoarthritis, Knee; Anterior Cruciate Ligament; Injections, Intra-Articular
PubMed: 38338992
DOI: 10.3390/ijms25031714 -
Proceedings of the National Academy of... Oct 1968
Topics: Dimethyl Sulfoxide; Kinetics; Methods; Nucleic Acid Denaturation; Phosphorus Isotopes; Poliovirus; Polynucleotides; RNA, Viral; Temperature
PubMed: 4300989
DOI: 10.1073/pnas.61.2.548 -
European Journal of Pharmaceutical... May 2017This review is a comprehensive analysis of the progress made so far on the delivery of polynucleotide-based therapeutics to the eye, using synthetic nanocarriers.... (Review)
Review
This review is a comprehensive analysis of the progress made so far on the delivery of polynucleotide-based therapeutics to the eye, using synthetic nanocarriers. Attention has been addressed to the capacity of different nanocarriers for the specific delivery of polynucleotides to both, the anterior and posterior segments of the eye, with emphasis on their ability to (i) improve the transport of polynucleotides across the different eye barriers; (ii) promote their intracellular penetration into the target cells; (iii) protect them against degradation and, (iv) deliver them in a long-term fashion way. Overall, the conclusion is that despite the advantages that nanotechnology may offer to the area of ocular polynucleotide-based therapies (especially AS-ODN and siRNA delivery), the knowledge disclosed so far is still limited. This fact underlines the necessity of more fundamental and product-oriented research for making the way of the said nanotherapies towards clinical translation.
Topics: Administration, Ophthalmic; Animals; Drug Carriers; Eye Diseases; Genetic Therapy; Humans; Intravitreal Injections; Nanoparticles; Oligonucleotides, Antisense; Particle Size; Polynucleotides; RNA, Small Interfering; Surface Properties
PubMed: 28263915
DOI: 10.1016/j.ejps.2017.03.001 -
Journal of General Microbiology Aug 1974
Topics: Antigens, Bacterial; Base Sequence; Citrobacter; DNA, Bacterial; Escherichia; Genotype; Phenotype; Phosphorus Radioisotopes; Polynucleotides; Serratia; Species Specificity; Spectrophotometry; Temperature
PubMed: 4427101
DOI: 10.1099/00221287-83-2-271