Impact of temperature on the binding interaction between dsDNA and curcumin: An electrochemical study

In this study, we investigated the binding mode between double-stranded deoxyribonucleic acid (dsDNA) and curcumin (CU) using differential pulse voltammetry (DPV), UV-Vis spectroscopy, and molecular docking. By employing these techniques, we predicted the binding within the minor groove region of dsDNA and CU. Significantly, we employed electrochemistry, specifically cyclic voltammetry (CV), to explore the temperature effect on the dsDNA and CU binding. To the best of our knowledge, this is the first study to utilize electrochemical methods for investigating the temperature-dependent behavior of this binding interaction. Our findings revealed temperature-dependent variations in the binding constants: 2.42 × 103 M-1 at 25 °C, 4.26 × 103 M-1 at 30 °C, 5.44 × 103 M-1 at 35 °C, 6.29 × 103 M-1 at 40 °C, and 7.52 × 103 M-1 at 45 °C. Notably, the binding constant exhibited an increasing trend with elevated temperatures, indicating a temperature-dependent enhancement of the binding interaction.

A simple and available measurement of onco-sEV dsDNA to protein ratio as a potential tumor marker

BACKGROUND

Small extracellular vesicles (sEVs) have great potential as new biomarkers in liquid biopsy. However, due to the limitations of sEVs extraction and component analysis procedures, further clinical applications of sEVs are hampered. Carcinoembryonic antigen (CEA) is a commonly used broad-spectrum tumor marker that is strongly expressed in a variety of malignancies.

RESULTS

In this study, CEA⁺ sEVs were directly separated from serum using immunomagnetic beads, and the nucleic acid to protein ultraviolet absorption ratio (NPr) of CEA⁺ sEVs was determined. It was found that the NPr of CEA⁺ sEVs in tumor group was higher than that of healthy group. We further analyzed the sEV-derived nucleic acid components using fluorescent staining and found that the concentration ratio of double-stranded DNA to protein (dsDPr) in CEA⁺ sEVs was also significantly different between the two groups, with a sensitivity of 100% and a specificity of 41.67% for the diagnosis of pan-cancer. The AUC of dsDPr combined with NPr was 0.87 and the ACU of dsDPr combined with CA242 could reach 0.94, showing good diagnostic performance for pan-cancer.

CONCLUSIONS

This study demonstrates that the dsDPr of CEA⁺ sEVs can effectively distinguish sEVs derived from tumor patients and healthy individuals, which can be employed as a simple and cost-effective non-invasive screening technology to assist tumor diagnosis.

Suitability of double-stranded DNA as a molecular standard for the validation of analytical ultracentrifugation instruments

To address the current lack of validated molecular standards for analytical ultracentrifugation (AUC), we investigated the suitability of double-stranded DNA molecules. We compared the hydrodynamic properties of linear and circular DNA as a function of temperature. Negatively supercoiled, nicked, and linearized 333 and 339 bp minicircles were studied. We quantified the hydrodynamic properties of these DNAs at five different temperatures, ranging from 4 to 37 °C. To enhance the precision of our measurements, each sample was globally fitted over triplicates and five rotor speeds. The exceptional stability of DNA allowed each sample to be sedimented repeatedly over the course of several months without aggregation or degradation, and with excellent reproducibility. The sedimentation and diffusion coefficients of linearized and nicked minicircle DNA demonstrated a highly homogeneous sample, and increased with temperature, indicating a decrease in friction. The sedimentation of linearized DNA was the slowest; supercoiled DNA sedimented the fastest. With increasing temperature, the supercoiled samples shifted to slower sedimentation, but sedimented faster than nicked minicircles. These results suggest that negatively supercoiled DNA becomes less compact at higher temperatures. The supercoiled minicircles, as purified from bacteria, displayed heterogeneity. Therefore, supercoiled DNA isolated from bacteria is unsuitable as a molecular standard. Linear and nicked samples are well suited as a molecular standard for AUC and have exceptional colloidal stability in an AUC cell. Even after sixty experiments at different speeds and temperatures, measured over the course of 4 months, all topological states of DNA remained colloidal, and their concentrations remained essentially unchanged.

Absorption and escape kinetics of spherical biomolecules from fully porous particles utilized in size exclusion chromatography

The increasing demand for the characterization of large biomolecules such as monoclonal antibodies, double-stranded deoxyribonucleic acid (dsDNA), and virus-like particles (VLPs) is raising fundamental questions pertaining to their absorption (ingress) and escape (egress) kinetics from fully porous particles. The exact expression of their concentration profiles is derived as a function of time and radial position across a single sub-3 μm Bridge-Ethylene-Hybrid (BEH^TM) Particle present in size exclusion chromatography (SEC) columns. The boundary condition at the external surface area of the particle is a rectangular concentration profile mimicking the passage of the chromatographic zone. Four different BEH Particles were considered in the calculations depending on the molecular size of the analyte: 2.0 μm 100 Å BEH Particles for small molecules, 2.0 μm 200 Å BEH Particles for monoclonal antibodies, 2.0 μm 300 Å BEH Particles for dsDNA (100 base pairs), and 2.5 μm 900 Å BEH Particles for virus-like particles (VLPs). The calculated concentration profiles of small molecules and monoclonal antibodies confirm that all BEH Particles present in the column reach quasi-instantaneously thermodynamic equilibrium with the bulk mobile phase during the passage of the chromatographic band. This is no longer the case for larger biomolecules such as dsDNA or VLPs, especially when the SEC particle is located near the column inlet and for high velocities. The kinetics of biomolecule egress is slower than its kinetics of ingress leading to pronounced peak tailing. The mean concentration of the largest biomolecules in the SEC particles remains always smaller than the maximum bulk concentration. This persistent and transient intra-particle diffusion regime has direct implications on the theoretical expressions of the observed retention factors and plate heights. Classical theories of chromatography assume uniform spatial distribution of the analyte in the particle volume: this hypothesis is not verified for the largest biomolecules. These results imply that non-porous particles or monolithic structures are the most promising stationary phases for the separation and purification of the largest biomolecules in life science.

Single-Molecule Characterization of Cy3.5 -Cy5.5 Dye Pair for FRET Studies of Nucleic Acids and Nucleosomes

Single molecule FRET (Forster resonance energy transfer) is very powerful method for studying biomolecular binding dynamics and conformational transitions. Only a few donor - acceptor dye pairs have been characterized for use in single-molecule FRET (smFRET) studies. Hence, introducing and characterizing additional FRET dye pairs is important in order to widen the scope of applications of single-molecule FRET in biomolecular studies. Here we characterize the properties of the Cy3.5 and Cy5.5 dye pair under FRET at the single-molecule level using naked double-stranded DNA (dsDNA) and the nucleosome. We show that this pair of dyes is photostable for ~ 5 min under continuous illumination. We also report Cy3.5-Cy5.5 FRET proximity dependence and stability in the presence of several biochemical buffers and photoprotective reagents in the context of double-stranded DNA. Finally, we demonstrate compatibility of the Cy3.5-Cy5.5 pair for smFRET in vitro studies of nucleosomes.

Comparing the Biological Properties of Double-Stranded DNA Extracted from Human and Porcine Placenta and Salmon Sperm

Background

Double-stranded fragmented extracellular DNA is a participant, inducer, and indicator of various processes occurring in the organism. When investigating the properties of extracellular DNA, the question regarding the specificity of exposure to DNA from different sources has always been raised. The aim of this study was to perform comparative assessment of biological properties of double-stranded DNA obtained from the human placenta, porcine placenta and salmon sperm.

Methods

The intensity of leukocyte-stimulating effect of different dsDNA was assessed in mice after cyclophosphamide-induced cytoreduction. The stimulatory effect of different dsDNA on maturation and functions of human dendritic cells and the intensity of cytokine production by human whole blood cells was analyzed ex vivo. The oxidation level of the dsDNA was also compared.

Results

Human placental DNA exhibited the strongest leukocyte-stimulating effect. DNA extracted from human and porcine placenta exhibited similar stimulatory action on maturation of dendritic cells, allostimulatory capacity, and ability of dendritic cells to induce generation of cytotoxic CD8+CD107a+ T cells in the mixed leukocyte reaction. DNA extracted from salmon sperm stimulated the maturation of dendritic cells, while having no effect on their allostimulatory capacity. DNA extracted from human and porcine placenta was shown to exhibit a stimulatory effect on cytokine secretion by human whole blood cells. The observed differences between the DNA preparations can be caused by the total methylation level and are not related to differences in oxidation level of DNA molecules.

Conclusions

Human placental DNA exhibited the maximum combination of all biological effects.

STING/NF-κB/IL-6-Mediated Inflammation in Microglia Contributes to Spared Nerve Injury (SNI)-Induced Pain Initiation

Innate immune response acts as the first line of host defense against damage and is initiated following the recognition of pathogen-associated molecular patterns (PAMPs). For double-stranded DNA (dsDNA) sensing, interferon gene stimulator (STING) was discovered to be an integral sensor and could mediate the immune and inflammatory response. Selective STING antagonist C-176 was administered and pain behaviors were assessed following spared nerve injury (SNI)-induced neuropathic pain. The level of serum dsDNA following neuropathic pain was assessed using Elisa analysis. STING signaling pathway, microglia activation, and proinflammatory cytokines were assessed by qPCR, western blots, Elisa, and immunofluorescence staining. STING agonist DMXAA was introduced into BV-2 cells to assess the inflammatory response in microglial cells. dsDNA was significantly increased following SNI and STING/TANK-binding kinase 1 (TBK1)/nuclear factor-kappa B (NF-κB) pathway was activated in vivo and vitro. Early but not the late intrathecal injection of C-176 attenuated SNI-induced pain hypersensitivity, microglia activation, proinflammatory factors, and phosphorylated JAK2/STAT3 in the spinal cord dorsal horn, and the analgesic effect of C-176 was greatly abolished by recombinant IL-6 following SNI. We provided evidence clarifying dsDNA mediated activation of microglia STING signaling pathway, after which promoting expression of proinflammatory cytokines that are required for hyperalgesia initiation in the spinal cord dorsal horn of SNI model. Further analysis showed that microglial STING/TBK1/NF-κB may contribute to pain initiation via IL-6 signaling. Pharmacological blockade of STING may be a promising target in the treatment of initiation of neuropathic pain.

Observations of three "re-entrant" twisted structures in double-stranded DNA dispersion particles

In this work we report on observations of new twisted (cholesteric-like) structures in liquid-crystalline dispersion particles with a hexagonal packing of double-stranded (ds) DNA molecules. Heating up to 80 °C of the DNA dispersion formed in a aqueous-salt solution with a high osmotic pressure (concentration) of poly(ethylene glycol) induces the formation of a new, optically active, spirally twisted structure of these molecules ("re-entrant" cholesteric structure (rest-A structure)). Cooling of this dispersion up to 22 °C is accompanied by the formation of an additional "re-entrant" cholesteric structure (rest-B). Modification of particles of the ds DNA dispersion (with rest-B structure) by replacing Na⁺ cations by multi-charged Gd³⁺ cations results in the third " re-entrant" structure (rest-C) despite a high density packing of ds nucleic acid molecules.

Hairpin-Bisulfite PCR

Ligation of a hairpin oligonucleotide to genomic DNA prior to bisulfite conversion and PCR amplification physically links the two complementary DNA strands. This additional step in the conversion procedure overcomes the limitations of conventional bisulfite sequencing where information of the cytosine methylation status is only obtained from one of the two strands of an individual DNA molecule. Sequences derived from hairpin bisulfite PCR products reveal the dynamics of this epigenetic memory system on both strands of individual DNA molecules. The chapter describes a reliable step-by-step procedure to generate hairpin-linked DNA. It also provides a guide for efficient bisulfite conversion that is suitable for both conventional and hairpin bisulfite sequencing approaches.

Sensitive detection of transcription factor by coupled fluorescence-encoded microsphere with exonuclease protection

Aberrant transcription factors (TFs) activities are closely related to the occurrence and development of various diseases. Herein, we presented a fluorescence-encoded microsphere-based approach for TFs detection coupling with common DNA footprinting assay. Target TFs specifically bound the binding sites of double-stranded DNA (dsDNA) probes which were conjugated to microspheres. Thus, the probes were protected from being hydrolyzed by exonuclease III (Exo III). Afterwards, biotins labeled on the probes reacted with streptavidin-phycoerythrin (SA-PE) to produce fluorescent signal; however, in the absence of target TFs, the dsDNA probes would be hydrolyzed by Exo III resulting in biotins falling off and thus fluorescence signal was not generated. This strategy can be used to detect nuclear factor-kappa B p50 (NF-κB p50) with a detection limit of 0.2 nM. The steric hindrance of microspheres overcome the disadvantage of Exo III that can nibble into the protein-bound DNA region. Meanwhile, the fluorescent label of microsphere was specific to each TF, enabling multiplex detection could be achieved by changing specific protein binding site of corresponding dsDNA probe. This method has been successfully applied for simultaneous detection of NF-κB p50, AP-1 and CREB in nuclear extract isolated from HeLa cells stimulated or unstimulated by TNF-α, showing great potential for biomedical researches and precise disease diagnosis.

Detection of phospholipase A2 in serum based on LRET mechanism between upconversion nanoparticles and SYBR green I

Phospholipase A₂ (PLA₂) may be a vital biomarker for the prediction and diagnosis of some diseases. Consequently, it is of great significance to quantitatively detect PLA₂ in biologic samples. Herein, on the basis of the principle of luminescence resonance energy transfer (LRET) between upconversion nanoparticles (UCNPs) and SYBR Green I (SG), we proposed a technology for the highly sensitive detection of PLA₂ amount. Therein, as an energy receptor, SG will be quantitatively loaded into liposomes firstly. Then, due to the hydrolysis of liposomes under the catalysis of PLA₂, SG will be released and inserted into the double-stranded DNA (dsDNA) on the surface of UCNPs, which triggers the LRET because of the shortening of effective spatial distance between UCNPs and SG. Under exciting of NIR light, UCNPs emit luminescence at 476 nm, which makes SG emit fluorescence at 522 nm through LRET. Under optimal conditions, the emission intensity ratio (I_{522 nm}/I_{476 nm}) increased linearly with the PLA₂ amount in the range of 20 U/L to 400 U/L, and the limit of detection (LOD) reached 15 U/L. Here, after comparing with the clinical standard method, it is found that the biosensor is expected to provide a convenient and sensitive assay for the detection of PLA₂ in actual serum samples. Furthermore, such biosensor can also be used to test the inhibitor of PLA₂.

Total and double-stranded DNA-specific immunoglobulin E in bronchoalveolar lavage fluid of children with human adenovirus pneumonia

BACKGROUND

Some antibodies and autoreactive antibodies are associated with the severity of infectious diseases. The roles of humoral responses to lung inflammation in children with human adenovirus (HAdVs) pneumonia remain unknown.

PATIENTS AND METHODS

A retrospective study was done to compare plasma immunoglobulin E (IgE) levels between HAdVs pneumonia patients and healthy children by searching the electronic medical record system of Guangzhou Women and Children's Medical Center. Then, a prospective study was performed for children with HAdVs pneumonia who needed flexible bronchoscopy for examination and treatment purposes during July 2017 to July 2019. We examined the IgE and autoreactive IgE levels in plasma and bronchoalveolar lavage fluid (BALF) of these children to explore their role in HAdVs pneumonia.

RESULTS

A significantly higher level of IgE was found in plasma from children hospitalized with HAdVs pneumonia compared with that from healthy children in the same age range. Furthermore, the levels of IgE, double-stranded DNA (dsDNA), and double-stranded DNA-specific immunoglobulin E (dsDNA-IgE) in BALF were increased compared to plasma in children with HAdVs pneumonia. The levels of IgE, dsDNA, and dsDNA-IgE in BALF were significantly higher in the severe group compared to the non-severe group. The ability of IgE in BALF to recognize dsDNA was verified by the ELISPOT test.

CONCLUSIONS

Our findings indicate that IgE and dsDNA-IgE in BALF may contribute to lung injury caused by HAdVs, especially in severe cases. Elevated dsDNA-IgE may serve as an indicator of severity in children with HAdVs pneumonia.

Imbalance between plasma double-stranded DNA and deoxyribonuclease activity predicts mortality after out-of-hospital cardiac arrest

AIM

Despite an increased rate of return of spontaneous circulation (ROSC) in out-of-hospital cardiac arrest (OHCA) patients, almost half of patients do not survive up to hospital discharge. Understanding pathophysiological mechanisms of post-cardiac arrest syndrome is essential for developing novel therapeutic strategies. During systemic inflammatory responses and concomitant cell death, double-stranded (ds) DNA is released into circulation, exerting pro-inflammatory effects. Deoxyribonuclease (DNase) degrades dsDNA. The role of DNase activity in OHCA survivors and impact on clinical outcome has not been analyzed yet.

METHODS

In a prospective, single-center study, dsDNA and DNase activity were determined at hospital admission (acute phase) and 24 h (subacute phase) after ROSC. The ratio between dsDNA levels and DNase activity was calculated to determine the extent of dsDNA release in relation to the patients' capacity of degradation. Thirty-day mortality was defined as study end point.

RESULTS

We enrolled 64 OHCA survivors, of whom 26.6% (n = 17) died within 30 days. A peak of circulating dsDNA was observed at admission which decreased within 24 h. DNase activity did not differ between acute and subacute phase, while dsDNA load per DNase activity significantly decreased. The ratio between dsDNA levels and DNase activity in the subacute phase was the strongest predictor of 30-day mortality with an adjusted HR per 1 SD of 3.59 (95% CI, 1.80-7.18, p < 0.001).

CONCLUSION

Disproportionally increased dsDNA levels uncompensated by DNase activity are a strong predictor of mortality in OHCA survivors. This pilot study points to a potentially protective effect of DNase activity in patients undergoing cardiac arrest.

Exosomal double-stranded DNA as a biomarker for the diagnosis and preoperative assessment of pheochromocytoma and paraganglioma

Pheochromocytomas (PCCs) and paragangliomas (PGLs) are the most heritable endocrine tumors. Genetic testing for 12 driver susceptibility genes is recommended in all PCC and PGL cases. However, detection of somatic mutations in PCC and PGL remains unrealizable for genetic diagnosis and preoperative assessment. We compared the serum exosomal DNA and tumor tissue DNA from patients or mice with PCC or PGL and found double-stranded DNA (dsDNA) fragments in the circulating exosomes of patients with PCC or PGL. Exosomal dsDNA shared the same mutations in the susceptibility genes with that of the parent tumor cells. Moreover, our research showed that serum-derived exosomal dsDNA in PCC and PGL was highly consistent with the paired tumor genome. Our findings provide the first definitive evidence of the presence of exosomal dsDNA that can be used as a noninvasive genetic marker in one of the most effective somatic mutation screens for the diagnosis and preoperative assessment of PCCs and PGLs.

Nuclear factor kappa B in patients with a history of unstable angina: case re-opened

This study aims at assessing NF-kB activity in unstable angina (UA) patients free of symptoms after a 1 year follow-up (1YFU). Plasma oxidized low-density lipoproteins (oxLDL), circulating NF-kB, Interleukin 6 (IL-6) and Interleukin 1β (IL-1β), high-sensitivity C-reactive protein (hs-CRP), as markers of oxidative stress and inflammation and plasma double-stranded DNA (ds-DNA), as marker of Neutrophil Extracellular Traps (NETs), were measured in 23 of the previously enrolled 27 UA patients. These measurements were compared to the UA data at baseline, and then compared to the data derived from the stable angina (SA) and controls (C) enrolled in our previous study (we demonstrated that UA had higher levels of NF-kB compared to SA and C). After a 1YFU, UA patients show a significant decrease in NF-kB, IL-6, hs-CRP, oxLDL, and ds-DNA plasma levels (p < 0.001) and in IL-1β and White Blood Cells (WBC) (p < 0.005), without differences in lipid and glucose assessment. If compared to SA and C, UA after a 1YFU have higher levels of NF-kB, IL-6, ds-DNA, WBC, and oxLDL compared to C (p < 0.001), but only IL-6 is higher than SA (p < 0.001). No differences are found in lipid and glucose assessment. After a 1YFU, patients with a history of UA improve their oxidative and inflammatory status, such as the levels of circulating ds-DNA, without achieving the status of C. They become comparable to SA subjects. This study provides new insight on the multiple and apparently contradictory facets of NF-kB in UA and on its possible role as mediator in NETs' formation.

A label-free fluorescent aptasensor for detection of kanamycin based on dsDNA-capped mesoporous silica nanoparticles and Rhodamine B

Kanamycin is an aminoglycoside antibiotic that can be useful against both gram negative and positive bacteria. However, if its serum levels are not controlled properly, it can cause serious side effects like ototoxicity and nephrotoxicity. The aim of this study was to design a simple and rapid fluorescent aptasensor for detection of kanamycin, based on Aptamer/Complementary strand (dsDNA)-capped mesoporous silica nanoparticles (MSNs) and Rhodamine B as a fluorescent probe. The MSNs pores were filled with Rhodamine B and then gated with dsDNA. In the presence of kanamycin, the aptamer sequence was separated from its complementary strand (CS), so that, uncovered the pores and leading to leakage of Rhodamine B. Thus, a significant increase in the fluorescence intensity was observed. The relative fluorescence intensity showed a linearity range from 24.75 nM to 137.15 nM of kanamycin with a detection limit of 7.5 nM. The aptasensor also showed to be useful for detection of kanamycin in serum samples and was able to distinguish kanamycin from other antibiotics, resulting in a sensitive, rapid and inexpensive method for kanamycin detection.

Suppressive oligodeoxynucleotides containing TTAGGG motifs inhibit cGAS activation in human monocytes

Type I interferon (IFN) is a critical mediator of autoimmune diseases such as systemic lupus erythematosus (SLE) and Aicardi-Goutières Syndrome (AGS). The recently discovered cyclic-GMP-AMP (cGAMP) synthase (cGAS) induces the production of type I IFN in response to cytosolic DNA and is potentially linked to SLE and AGS. Suppressive oligodeoxynucleotides (ODN) containing repetitive TTAGGG motifs present in mammalian telomeres have proven useful in the treatment of autoimmune diseases including SLE. In this study, we demonstrate that the suppressive ODN A151 effectively inhibits activation of cGAS in response to cytosolic DNA, thereby inhibiting type I IFN production by human monocytes. In addition, A151 abrogated cGAS activation in response to endogenous accumulation of DNA using TREX1-deficient monocytes. We demonstrate that A151 prevents cGAS activation in a manner that is competitive with DNA. This suppressive activity of A151 was dependent on both telomeric sequence and phosphorothioate backbone. To our knowledge this report presents the first cGAS inhibitor capable of blocking self-DNA. Collectively, these findings might lead to the development of new therapeutics against IFN-driven pathologies due to cGAS activation.

Electrochemically mediated in situ growth of electroactive polymers for highly sensitive detection of double-stranded DNA without sequence-preference

The ability to directly detect double-stranded DNA (dsDNA) without sequence-preference continues to be a major challenge. Herein, we report an electrochemical method for the direct, highly sensitive detection of dsDNA based on the strand replacement of dsDNA by peptide nucleic acid (PNA) and the in situ growth of electroactive polymers through the surface-initiated electrochemically mediated atom transfer radical polymerization (SI-eATRP). Thiolated PNA molecules are firstly self-assembled onto gold electrode surface for the specific recognition of target dsDNA (dsDNA-T), which in turn leads to the formation of a high density of PNA/DNA heteroduplexes on the electrode surface for the subsequent attachment of ATRP initiators via the phosphate-Zr⁴⁺-carboxylate chemistry. By applying a negative potential to the electrode, the air-stable Cu^II deactivators can be reduced into the Cu^I activators so as to trigger the surface-initiated polymerization for the in situ growth of electroactive polymers. Due to the strand replacement of dsDNA by PNA, dsDNA can be directly detected without sequence-preference. Besides, the growth of polymers enables the modification of numerous electroactive probes, thereby greatly improving the electrochemical signal. Under optimal conditions, a good linearity between the electrochemical signal and the logarithm of dsDNA-T concentration over the range from 1.0 fM to 1.0nM, with a detection limit of 0.47 fM, can be obtained. Results indicate that it is highly selective, and holds high anti-interference capability in the presence of human serum samples. Therefore, this method offers great promises in providing a universal and efficient solution for the direct detection of dsDNA.

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

Background

Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a.k.a phages) due to the challenges of obtaining appropriately scaled genomic datasets.

Results

Here we explore the role of recombination in both maintaining and differentiating whole genomes of 142 wild double-stranded DNA marine cyanophages. Phylogenomic analysis across the 51 core genes revealed ten lineages, six of which were well represented. These phylogenomic lineages represent discrete genotypic populations based on comparisons of intra- and inter- lineage shared gene content, genome-wide average nucleotide identity, as well as detected gaps in the distribution of pairwise differences between genomes. McDonald-Kreitman selection tests identified putative niche-differentiating genes under positive selection that differed across the six well-represented genotypic populations and that may have driven initial divergence. Concurrent with patterns of recombination of discrete populations, recombination analyses of both genic and intergenic regions largely revealed decreased genetic exchange across individual genomes between relative to within populations.

Conclusions

These findings suggest that discrete double-stranded DNA marine cyanophage populations occur in nature and are maintained by patterns of recombination akin to those observed in bacteria, archaea and in sexual eukaryotes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3286-x) contains supplementary material, which is available to authorized users.

A label-free electrochemical aptasensor based on graphene oxide/double-stranded DNA nanocomposite

A novel label-free electrochemical impedance aptasensor based on a gold nanoparticles/double-stranded DNA-graphene (AuNPs/dsDNA-GO) nanocomposite modified glassy carbon electrode was presented for quantitative determination of thrombin. GO was covalently functionalized with dsDNA via a facile amidation process, and then AuNPs were electrodeposited onto the surface of dsDNA-GO. The morphology, conductivity and interaction of the as-prepared nanocomposites were characterized by scanning electron microscopy, cyclic voltammetry, electrochemical impedance spectroscopy (EIS), Raman and Fourier transform infrared spectroscopy. The thrombin-binding aptamer (TBA) was conjugated to AuNPs via gold-thiol chemistry to construct electrochemical aptasensing platform, and the specific recognition between TBA and thrombin was monitored by EIS. Under optimum conditions, thrombin could be quantified in a wide range of 0.1-100nM (R(2)=0.9960) with low detection limit of 0.06nM (S/N=3).

Comparative analysis of pathologic processes developing in mice housed in SPF vs non-SPF conditions and treated with cyclophosphamide and dsDNA preparation

In our earlier studies, we observed that when mice are treated with cyclophosphamide and fragmented exogenous dsDNA (18-30 h post cytostatic treatment), they develop a very characteristic set of symptoms and 80-90% of such animals succumb within 6-25 days. This was called "delayed death" phenomenon, and the gap between cyclophosphamide and DNA injections required for such phenotype to develop was termed "death window". We established that mice succumbed to multi-organ failure, which was caused by systemic inflammation and sepsis. These processes unfolded along with accidental involution of lymphoid organs, which resulted from the failure of CD34(+) hematopoietic stem cells to differentiate into lymphoid lineage progenitors. Here we compare SPF and non-SPF animals, and demonstrate that the major cause of systemic inflammation and sepsis observed upon such treatments is activation of an opportunistic infection. Mice of the same strain (CBA) housed under SPF conditions do not develop the characteristic symptoms, nor do they become moribund. Yet, regardless of the breeding conditions, upon synergistic action of cyclophosphamide and dsDNA, CD34(+) hematopoietic stem cells consistently fail to give rise to lymphoid lineage progenitors. We demonstrate that this differentiation defect is reversible and that population of lymphoid progenitors is restored by day 29 after cyclophosphamide injection.

Thermodynamics and kinetic studies in the binding interaction of cyclic naphthalene diimide derivatives with double stranded DNAs

Previously, we reported our investigations of the interaction between a cyclic naphthalene diimide derivative (cNDI 1) and double stranded DNA (dsDNA) (Bioorg. Med. Chem.2014, 22, 2593). Here, we report the synthesis of the novel cNDI 2, which has shorter linker chains than cNDI 1. We performed comparative investigations of the interactions of both cNDI 1 and cNDI 2 with different types of dsDNA, including analysis of their thermodynamics and kinetics. Interactions between the cNDIs and calf thymus DNA (CT-DNA), poly[d(A-T)]2, or poly[d(G-C)]2 were explored by physicochemical and biochemical methods, including UV-Vis spectroscopy, circular dichroism (CD) spectroscopy, stopped-flow kinetics, and a topoisomerase I assay. Upon addition of cNDIs to CT-DNA, the existence of an induced CD signal at approximately the wavelength of the naphthalene diimide chromophore and unwinding of the DNA duplex, as detected by the topoisomerase I assay, revealed that cNDIs bound to the DNA duplex. As indicated by the steric constraint in the formation of the complex, bis-threading intercalation was the more favorable binding mode. UV-Vis spectroscopic titration of the cNDIs with DNA duplexes showed affinities on the order of 10(5)-10(6)M(-1), with a stoichiometry of one cNDI molecule per four DNA base pairs. Thermodynamic parameters (ΔG, ΔH, and ΔS) based on the van't Hoff equation indicated that exothermic and entropy-dependent hydrophobic interactions played a major role in the reaction. Stopped-flow association and dissociation analysis showed that cNDI interactions with poly[d(G-C)]2 were more stable and had a slower dissociation rate than their interactions with poly[d(A-T)]2 and CT-DNA. Measurement of ionic strength indicated that electrostatic attraction is also an important component of the interaction between cNDIs and CT-DNA. Because of its longer linker chain, cNDI 1 showed higher binding selectivity, a more entropically favorable interaction, and much slower dissociation from dsDNA than cNDI 2.

Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq(®))

Sequence-independent methods for viral discovery have been widely used for whole genome sequencing of viruses. Different protocols for viral enrichment, library preparation and sequencing have increasingly been more available and at lower costs. However, no study to date has focused on optimization of viral sample preparation for commercial deep sequencing. Accordingly, the aim of the present study was to evaluate an In-House enzymatic protocol for double-stranded DNA (dsDNA) synthesis and also compare the use of a commercially available kit protocol (Nextera XT, Illumina Inc, San Diego, CA, USA) and its combination with a library quantitation kit (Kapa, Kapa Biosystems, Wilmington, MA, USA) for deep sequencing (Illumina Miseq). Two RNA viruses (canine distemper virus and dengue virus) and one ssDNA virus (porcine circovirus type 2) were tested with the optimized protocols. The tested method for dsDNA synthesis has shown satisfactory results and may be used in laboratory setting, particularly when enzymes are already available. Library preparation combining commercial kits (Nextera XT and Kapa) has yielded more reads and genome coverage, probably due to a lack of small fragment recovering at the normalization step of Nextera XT. In addition, libraries may be diluted or concentrated to provide increase on genome coverage with Kapa quantitation.

Combination of cyclophosphamide and double-stranded DNA demonstrates synergistic toxicity against established xenografts

BACKGROUND

Extracellular double-stranded DNA participates in various processes in an organism. Here we report the suppressive effects of fragmented human double-stranded DNA along or in combination with cyclophosphamide on solid and ascites grafts of mouse Krebs-2 tumor cells and DNA preparation on human breast adenocarcinoma cell line MCF-7.

METHODS

Apoptosis and necrosis were assayed by electrophoretic analysis (DNA nucleosomal fragmentation) and by measurements of LDH levels in ascitic fluid, respectively. DNA internalization into MCF-7 was analyzed by flow cytometry and fluorescence microscopy.

RESULTS

Direct cytotoxic activity of double-stranded DNA (along or in combination with cyclophosphamide) on a solid transplant was demonstrated. This resulted in delayed solid tumor proliferation and partial tumor lysis due to necrosis of the tumor and adjacent tissues. In the case of ascites form of tumor, extensive apoptosis and secondary necrosis were observed. Similarly, MCF-7 cells showed induction of massive apoptosis (up to 45%) as a result of treatments with double-stranded DNA preparation.

CONCLUSIONS

Double-stranded DNA (along or in combination with cyclophosphamide) induces massive apoptosis of Krebs-2 ascite cells and MCF-7 cell line (DNA only). In treated mice it reduces the integrity of gut wall cells and contributes to the development of systemic inflammatory reaction.

Electrochemical determination of the anticancer drug taxol at a ds-DNA modified pencil-graphite electrode and its application as a label-free electrochemical biosensor

In this study a novel biosensor for determination of taxol is described. The interaction of taxol with salmon-sperm double-stranded DNA (ds-DNA) based on the decreasing of the oxidation signals of guanine and adenine bases was studied electrochemically with a pencil-graphite electrode (PGE) using a differential pulse voltammetry (DPV) method. The decreases in the intensity of the guanine and adenine oxidation signals after interaction with taxol were used as indicator signals for the sensitive determination of taxol. DPV exhibits a linear dynamic range of 2.0×10(-7)-1.0×10(-5) M for taxol with a detection limit of 8.0×10(-8) M. Finally, this modified electrode was used for determination of taxol in some real samples.

Real-time single-molecule observations of T7 Exonuclease activity in a microflow channel

T7 Exonuclease (T7 Exo) DNA digestion reactions were studied using direct single-molecule observations in microflow channels. DNA digestion reactions were directly observed by staining template DNA double-stranded regions with SYTOX Orange and staining single-stranded (digested) regions with a fluorescently labeled ssDNA-recognizing peptide (ssBP-488). Sequentially acquired photographs demonstrated that a double-stranded region monotonously shortened as a single-stranded region monotonously increased from the free end during a DNA digestion reaction. Furthermore, DNA digestion reactions were directly observed both under pulse-chase conditions and under continuous buffer flow conditions with T7 Exo. Under pulse-chase conditions, the double-stranded regions of λDNA monotonously shortened by a DNA digestion reaction with a single T7 Exo molecule, with an estimated average DNA digestion rate of 5.7 bases/s and a processivity of 6692 bases. Under continuous buffer flow conditions with T7 Exo, some pauses were observed during a DNA digestion reaction and double-stranded regions shortened linearly except during these pauses. The average DNA digestion rate was estimated to be 5.3 bases/s with a processivity of 5072 bases. Thus, the use of our direct single-molecule observations using a fluorescently labeled ssDNA-recognizing peptide (ssBP-488) was an effective analytic method for investigating DNA metabolic processes.

Interactions of cyclic and non-cyclic naphthalene diimide derivatives with different nucleic acids

Recently, strategy based on stabilization of G-quadruplex telomeric DNA by small organic molecule has been realized by naphthalene diimide derivatives (NDIs). At the same time NDIs bind to DNA duplex as threading intercalators. Here we present cyclic derivative of naphthalene diimide (ligand 1) as DNA-binding ligand with ability to recognition of different structures of telomeric G-quadruplexes and ability to bis-intercalate to double-stranded helixes. The results have been compared to non-cyclic derivative (ligand 2) and revealed that preferential binding of ligands to nucleic acids strongly depends on their topology and structural features of ligands.

Electrochemical molecular beacon biosensor for sequence-specific recognition of double-stranded DNA

Direct recognition of double-stranded DNA (dsDNA) was crucial to disease diagnosis and gene therapy, because DNA in its natural state is double stranded. Here, a novel sensor for the sequence-specific recognition of dsDNA was developed based on the structure change of ferrocene (Fc) redox probe modified molecular beacon (MB). For constructing such a sensor, gold nanoparticles (AuNPs) were initially electrochemical-deposited onto glass carbon electrode (GCE) surface to immobilize thiolated MB in their folded states with Au-S bond. Hybridization of MB with target dsDNA induced the formation of parallel triplex DNA and opened the stem-loop structure of it, which resulted in the redox probe (Fc) away from the electrode and triggered the decrease of current signals. Under optimal conditions, dsDNA detection could be realized in the range from 350 pM to 25 nM, with a detection limit of 275 pM. Moreover, the proposed method has good sequence-specificity for target dsDNA compared with single base pair mismatch and two base pairs mismatches.

Polishing the craft of genetic diversity creation in directed evolution

Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant library preparation were summarised. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outline of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and a study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field.