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Drug Discovery Today Aug 2023The novel coronavirus crisis caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) was a global pandemic. Although various therapeutic approaches were... (Review)
Review
The novel coronavirus crisis caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) was a global pandemic. Although various therapeutic approaches were developed over the past 2 years, novel strategies with more efficient applicability are required to target new variants. Aptamers are single-stranded (ss)RNA or DNA oligonucleotides capable of folding into unique 3D structures with robust binding affinity to a wide variety of targets following structural recognition. Aptamer-based theranostics have proven excellent capability for diagnosing and treating various viral infections. Herein, we review the current status and future perspective of the potential of aptamers as COVID-19 therapies.
Topics: Humans; COVID-19; SARS-CoV-2; Oligonucleotides; DNA; RNA; Aptamers, Nucleotide
PubMed: 37315763
DOI: 10.1016/j.drudis.2023.103663 -
Nature Communications Jun 2023Minimally invasive biodegradable implants with regeneration have been a frontier trend in clinic. Degeneration of nucleus pulposus (NP) is irreversible in most of spine...
Minimally invasive biodegradable implants with regeneration have been a frontier trend in clinic. Degeneration of nucleus pulposus (NP) is irreversible in most of spine diseases, and traditional spinal fusion or discectomy usually injure adjacent segments. Here, an innovative minimally invasive biodegradable NP scaffold with function regeneration inspired by cucumber tendril is developed using shape memory polymer poly(glycerol-dodecanoate) (PGD), whose mechanical property is controlled to the similar with human NP by adjusting synthetic parameters. The chemokine stromal cell-derived factor-1α (SDF-1α) is immobilized to the scaffold recruiting autologous stem cells from peripheral tissue, which has better ability of maintaining disc height, recruiting autologous stem cells, and inducing regeneration of NP in vivo compared to PGD without chemokine group and hydrogel groups significantly. It provides an innovative way to design minimally invasive implants with biodegradation and functional recovery, especially for irreversible tissue injury, including NP, cartilage and so on.
Topics: Humans; Glycerol; Nucleus Pulposus; Absorbable Implants; Biodegradation, Environmental; Poly A
PubMed: 37391454
DOI: 10.1038/s41467-023-39604-0 -
Nucleic Acids Research Aug 2023Human PrimPol possesses DNA primase and DNA polymerase activities and restarts stalled replication forks protecting cells against DNA damage in nuclei and mitochondria....
Human PrimPol possesses DNA primase and DNA polymerase activities and restarts stalled replication forks protecting cells against DNA damage in nuclei and mitochondria. The zinc-binding motif (ZnFn) of the C-terminal domain (CTD) of PrimPol is required for DNA primase activity but the mechanism is not clear. In this work, we biochemically demonstrate that PrimPol initiates de novo DNA synthesis in cis-orientation, when the N-terminal catalytic domain (NTD) and the CTD of the same molecule cooperate for substrates binding and catalysis. The modeling studies revealed that PrimPol uses a similar mode of initiating NTP coordination as the human primase. The ZnFn motif residue Arg417 is required for binding the 5'-triphosphate group that stabilizes the PrimPol complex with a DNA template-primer. We found that the NTD alone is able to initiate DNA synthesis, and the CTD stimulates the primase activity of NTD. The regulatory role of the RPA-binding motif in the modulation of PrimPol binding to DNA is also demonstrated.
Topics: Humans; DNA-Directed DNA Polymerase; DNA Primase; DNA Replication; DNA; DNA Primers; Catalysis; Multifunctional Enzymes
PubMed: 37326028
DOI: 10.1093/nar/gkad507 -
Biomacromolecules Sep 2023While biomaterials have become indispensable for a wide range of tissue repair strategies, second removal procedures oftentimes needed in the case of non-bio-based and...
While biomaterials have become indispensable for a wide range of tissue repair strategies, second removal procedures oftentimes needed in the case of non-bio-based and non-bioresorbable scaffolds are associated with significant drawbacks not only for the patient, including the risk of infection, impaired healing, or tissue damage, but also for the healthcare system in terms of cost and resources. New biopolymers are increasingly being investigated in the field of tissue regeneration, but their widespread use is still hampered by limitations regarding mechanical, biological, and functional performance when compared to traditional materials. Therefore, a common strategy to tune and broaden the final properties of biopolymers is through the effect of different reinforcing agents. This research work focused on the fabrication and characterization of a bio-based and bioresorbable composite material obtained by compounding a poly(3-hydroxybutyrate--3-hydroxyhexanoate) (PHBH) matrix with acetylated cellulose nanocrystals (CNCs). The developed biocomposite was further processed to obtain three-dimensional scaffolds by additive manufacturing (AM). The 3D printability of the PHBH-CNC biocomposites was demonstrated by realizing different scaffold geometries, and the results of in vitro cell viability studies provided a clear indication of the cytocompatibility of the biocomposites. Moreover, the CNC content proved to be an important parameter in tuning the different functional properties of the scaffolds. It was demonstrated that the water affinity, surface roughness, and in vitro degradability rate of biocomposites increase with increasing CNC content. Therefore, this tailoring effect of CNC can expand the potential field of use of the PHBH biopolymer, making it an attractive candidate for a variety of tissue engineering applications.
Topics: Humans; Cellulose; Poly A; Hydroxybutyrates; Printing, Three-Dimensional
PubMed: 37589321
DOI: 10.1021/acs.biomac.3c00263 -
Cancer Science Sep 2023Vasohihibin-2 (VASH2) is a homolog of vasohibin-1 (VASH1) and is overexpressed in various cancers. Vasohihibin-2 acts on both cancer cells and cancer microenvironmental...
Vasohihibin-2 (VASH2) is a homolog of vasohibin-1 (VASH1) and is overexpressed in various cancers. Vasohihibin-2 acts on both cancer cells and cancer microenvironmental cells. Previous analyses have shown that VASH2 promotes cancer progression and abrogation of VASH2 results in significant anticancer effects. We therefore propose VASH2 to be a practical molecular target for cancer treatment. Modifications of antisense oligonucleotide (ASO) such as bridged nucleic acids (BNA)-based modification increases the specificity and stability of ASO, and are now applied to the development of a number of oligonucleotide-based drugs. Here we designed human VASH2-ASOs, selected an optimal one, and developed 2',4'-BNA-based VASH2-ASO. When systemically administered, naked 2',4'-BNA-based VASH2-ASO accumulated in the liver and showed its gene-silencing activity. We then examined the effect of 2',4'-BNA-based VASH2-ASO in liver cancers. Intraperitoneal injection of naked 2',4'-BNA-based VASH2-ASO exerted a potent antitumor effect on orthotopically inoculated human hepatocellular carcinoma cells. The same manipulation also showed potent antitumor activity on the splenic inoculation of human colon cancer cells for liver metastasis. These results provide a novel strategy for the treatment of primary as well as metastatic liver cancers by using modified ASOs targeting VASH2.
Topics: Humans; Oligonucleotides, Antisense; Liver Neoplasms; Cell Line; Transcription Factors; Oligonucleotides; Cell Cycle Proteins; Angiogenic Proteins
PubMed: 37430466
DOI: 10.1111/cas.15897 -
Nature Communications Aug 2023Conformational cooperativity is a universal molecular effect mechanism and plays a critical role in signaling pathways. However, it remains a challenge to develop...
Conformational cooperativity is a universal molecular effect mechanism and plays a critical role in signaling pathways. However, it remains a challenge to develop artificial molecular networks regulated by conformational cooperativity, due to the difficulties in programming and controlling multiple structural interactions. Herein, we develop a cooperative strategy by programming multiple conformational signals, rather than chemical signals, to regulate protein-oligonucleotide signal transduction, taking advantage of the programmability of allosteric DNA constructs. We generate a cooperative regulation mechanism, by which increasing the loop lengths at two different structural modules induced the opposite effects manifesting as down- and up-regulation. We implement allosteric logic operations by using two different proteins. Further, in cell culture we demonstrate the feasibility of this strategy to cooperatively regulate gene expression of PLK1 to inhibit tumor cell proliferation, responding to orthogonal protein-signal stimulation. This programmable conformational cooperativity paradigm has potential applications in the related fields.
Topics: Oligonucleotides; Allosteric Regulation; Molecular Conformation; Signal Transduction
PubMed: 37580346
DOI: 10.1038/s41467-023-40589-z -
Frontiers in Endocrinology 2023Preeclampsia (PE), a hypertensive pregnancy disorder, can originate from varied etiology. Placenta malperfusion has long been considered the primary cause of PE....
Preeclampsia (PE), a hypertensive pregnancy disorder, can originate from varied etiology. Placenta malperfusion has long been considered the primary cause of PE. However, we and others have showed that this disorder can also result from heightened inflammation at the maternal-fetal interface. To advance our understanding of this understudied PE subtype, it is important to establish validated rodent models to study the pathophysiology and test therapies. We evaluated three previously described approaches to induce inflammation-mediated PE-like features in pregnant rats: 1) Tumor necrosis factor-α (TNF-α) infusion via osmotic pump from gestational day (GD) 14-19 at 50ng/day/animal; 2) Polyinosinic:polycytidylic acid (Poly I:C) intraperitoneal (IP) injections from GD 10-18 (alternate days) at 10mg/kg/day/animal; and, 3) Lipopolysaccharide (LPS) IP injections from GD 13-18 at 20ug-70ug/kg/day per animal. Maternal blood pressure was measured by tail-cuff. Upon sacrifice, fetal and placenta weights were recorded. Placenta histomorphology was assessed using H&E sections. Placenta inflammation was determined by quantifying TNF-α levels and inflammatory gene expression. Placenta metabolic and mitochondrial health were determined by measuring mitochondrial respiration rates and placenta NAD/NADH content. Of the three rodent models tested, we found that Poly I:C and LPS decreased both fetal weight and survival; and correlated with a reduction in region specific placenta growth. As the least effective model characterized, TNF-α treatment resulted in a subtle decrease in fetal/placenta weight and placenta mitochondrial respiration. Only the LPS model was able to induce maternal hypertension and exhibited pronounced placenta metabolic and mitochondrial dysfunction, common features of PE. Thus, the rat LPS model was most effective for recapitulating features observed in cases of human inflammatory PE. Future mechanistic and/or therapeutic intervention studies focuses on this distinct PE patient population may benefit from the employment of this rodent model of PE.
Topics: Pregnancy; Female; Humans; Rats; Animals; Pre-Eclampsia; Tumor Necrosis Factor-alpha; Lipopolysaccharides; Hypertension; Inflammation; Poly I
PubMed: 37842294
DOI: 10.3389/fendo.2023.1219205 -
Biosensors Jun 2023DNA-mediated nanotechnology has become a research hot spot in recent decades and is widely used in the field of biosensing analysis due to its distinctive properties of... (Review)
Review
DNA-mediated nanotechnology has become a research hot spot in recent decades and is widely used in the field of biosensing analysis due to its distinctive properties of precise programmability, easy synthesis and high stability. Multi-mode analytical methods can provide sensitive, accurate and complementary analytical information by merging two or more detection techniques with higher analytical throughput and efficiency. Currently, the development of DNA-mediated multi-mode analytical methods by integrating DNA-mediated nanotechnology with multi-mode analytical methods has been proved to be an effective assay for greatly enhancing the selectivity, sensitivity and accuracy, as well as detection throughput, for complex biological analysis. In this paper, the recent progress in the preparation of typical DNA-mediated multi-mode probes is reviewed from the aspect of deoxyribozyme, aptamer, templated-DNA and G-quadruplex-mediated strategies. Then, the advances in DNA-mediated multi-mode analytical methods for biological samples are summarized in detail. Moreover, the corresponding current applications for biomarker analysis, bioimaging analysis and biological monitoring are introduced. Finally, a proper summary is given and future prospective trends are discussed, hopefully providing useful information to the readers in this research field.
Topics: Biosensing Techniques; DNA; Nanotechnology; DNA Probes; Oligonucleotides
PubMed: 37504092
DOI: 10.3390/bios13070693 -
Biosensors Aug 2023Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from... (Review)
Review
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
Topics: Humans; Aptamers, Nucleotide; Nanotechnology; Nanostructures; DNA
PubMed: 37622908
DOI: 10.3390/bios13080822 -
Proceedings of the National Academy of... Oct 2023The emergence of functional oligonucleotides on early Earth required a molecular selection mechanism to screen for specific sequences with prebiotic functions. Cyclic...
The emergence of functional oligonucleotides on early Earth required a molecular selection mechanism to screen for specific sequences with prebiotic functions. Cyclic processes such as daily temperature oscillations were ubiquitous in this environment and could trigger oligonucleotide phase separation. Here, we propose sequence selection based on phase separation cycles realized through sedimentation in a system subjected to the feeding of oligonucleotides. Using theory and experiments with DNA, we show sequence-specific enrichment in the sedimented dense phase, in particular of short 22-mer DNA sequences. The underlying mechanism selects for complementarity, as it enriches sequences that tightly interact in the dense phase through base-pairing. Our mechanism also enables initially weakly biased pools to enhance their sequence bias or to replace the previously most abundant sequences as the cycles progress. Our findings provide an example of a selection mechanism that may have eased screening for auto-catalytic self-replicating oligonucleotides.
Topics: Oligonucleotides; DNA; Temperature; Base Pairing
PubMed: 37847736
DOI: 10.1073/pnas.2218876120