DNA Loading Research Articles

Excellent properties of NaF and NaBr induced DNA/gold nanoparticle conjugation system: Better stability, shorter modified time, and higher loading capacity

The functionalization of gold nanoparticle (AuNP) is the key procedure for the biochemical and biomedical application. The conventional salt-aging method requires the stepwise additions of NaCl and excessive thiolated DNA, mainly due to the poor tolerance of the DNA/AuNP mixture toward NaCl. Herein, we found that NaF is capable of improving the stability for the modification of AuNP with different bases of DNA sequences (poly A/T/C/G), and allows for adding up with a high concentration of 200 mM at one time, which greatly reduces the total modification time to 0.5–1 h. Intriguingly, the introduction of NaBr effectively increases the DNA loading capacity. Besides the advantages of NaF and NaBr, the modification performance is improved via the introduction of the oligo A/T spacer for the G-rich DNA sequences. Furthermore, this method shows the superiority to another two methods (pH 3-based and salt-aging) in terms of the loading capacity or sequence components.

Histone variant macroH2A1 regulates synchronous firing of replication origins in the inactive X chromosome.

MacroH2A has been linked to transcriptional silencing, cell identity, and is a hallmark of the inactive X chromosome (Xi). However, it remains unclear whether macroH2A plays a role in DNA replication. Using knockdown/knockout cells for each macroH2A isoform, we show that macroH2A-containing nucleosomes slow down replication progression rate in the Xi reflecting the higher nucleosome stability. Moreover, macroH2A1, but not macroH2A2, regulates the number of nano replication foci in the Xi, and macroH2A1 downregulation increases DNA loop sizes corresponding to replicons. This relates to macroH2A1 regulating replicative helicase loading during G1 by interacting with it. We mapped this interaction to a phenylalanine in macroH2A1 that is not conserved in macroH2A2 and the C-terminus of Mcm3 helicase subunit. We propose that macroH2A1 enhances the licensing of pre-replication complexes via DNA helicase interaction and loading onto the Xi.

Hybridization-driven synchronous regeneration of biosensing interfaces for Listeria monocytogenes based on recognition of fullerol to single- and double-stranded DNA

A novel sensitive and reusable electrochemical biosensor for Listeria monocytegenes DNA has been constructed based on the recognition of water-soluble hydroxylated fullerene (fullerol) to single- and double-stranded DNA. First, the fullerol was electrodeposited on glassy carbon electrode (GCE), acting as a matrix for non-covalent adsorption of single-stranded probe DNA. Upon hybridization with the target DNA, the double helix structure was formed and desorbed from the electrode surface, driving synchronous regeneration of the biosensing interfaces. The biosensor showed a probe DNA loading density of 144 pmol∙cm−2 with the hybridization efficiency of 72.2%. The biosensor is applicable for the analysis of target DNA in actual milk samples with recoveries between 101.0% and 104.0%. This sensing platform provides a simple method for the construction of sensitive and reusable biosensor to monitor Listeria monocytogenes-related food pollution.

Scalable isolation of surface-engineered extracellular vesicles and separation of free proteins via tangential flow filtration and size exclusion chromatography (TFF-SEC)

BackgroundExtracellular vesicles (EVs) represent small lipid bilayer structures pivotal in mediating intercellular communication via biomolecular transfer. Their inherent characteristics, including packaging, non-immunogenicity, and biofluid stability, position EVs as promising drug delivery vectors. However, developing clinical quality EVs requires multifaceted technological advancement.MethodsIn this study, a method is introduced for engineering extracellular vesicles (eEVs) from cultured cells and their subsequent isolation using lab-scale tangential flow filtration (TFF). This is the first study to evaluate DNA loading efficacy into EVs isolated by TFF, marking a significant milestone in the field of targeted drug delivery. Initially, cells are transfected with EV-display constructs to facilitate the secretion of eEVs bearing the desired coding molecules. Following brief centrifugation, the cell culture media undergoes filtration using hollow fiber filters. TFF, by applying a constant flow, effectively segregates molecules based on designated molecular weight cut-off (MWCO), enriching particles between 50 and 650 nm.ResultsCompared to conventional methods like ultracentrifugation, TFF demonstrates higher efficiency in removing undesired molecules/aggregates while exerting less stress on EVs. Characterization of eEVs through various assays confirms TFF’s superiority in isolating pure EV populations. Additionally, the necessity of size-exclusion chromatography (SEC) after tangential flow filtration (TFF) becomes evident for effectively removing unbound protein contaminants.ConclusionIn conclusion, TFF-SEC emerges as a scalable and superior approach for eEV isolation, promising significant advancements in clinical applications.

A rapid and ultrasensitive cardiac troponin I aptasensor based on an ion-sensitive field-effect transistor with extended gate

Acute myocardial infarction (AMI) is a life-threatening disease with a short course and a high mortality rate. However, it is still a great challenge to achieve the on-site diagnosis of this disease within minutes, meaning there is an urgent need to develop an efficient technology for realizing the rapid diagnosis and early warning of AMI in clinical emergencies. In this study, an ultrasensitive electrochemical aptasensor based on an extended-gate ion-sensitive field-effect transistor (EGISFET) was designed to achieve the quantitative assay of cardiac troponin I (cTnI), which is a highly sensitive and specific biomarker of AMI, within only 5 min. The EGISFET exhibits extremely high detection sensitivity due to its separated structure with a large sensing area and the surface-modified Prussian blue-gold nanoparticles (PB-AuNPs) composite, which serves as a signal magnifier and DNA loading platform for good electrocatalytic ability with a large specific area. Additionally, a target-induced strand-release strategy is proposed to shorten the recognition time of cTnI using a particular DNA strand. Under optimal conditions, the as-prepared aptasensor exhibits a wide linear range of 1–1000 pg/mL, an ultralow detection limit of 0.3 pg/mL, and reliable detection results in real serum samples. It is highly anticipated that this EGISFET-based aptasensor will have broad applications in the early warning and rapid diagnosis of AMI and other acute diseases in emergency treatment.

Hollow Polyethyleneimine Nanoparticles with Drug Loaded DNA for Chemotherapeutic Applications.

The next generation of anticancer agents are emerging from rationally designed nanostructured materials. This work involved the synthesis and characterization of novel hollow DNA-conjugated gold nanoparticles (DNA-AuNPs) for controlled drug delivery. Polyethyleneimine (PEI) was bound to AuNPs, forming polymer-shell nanoparticles. Dissolution of the gold core via iodine formed hollow core polymeric nanoparticles (HCPNPs) and a high density (85 molecules/particle) of DNA intercalated with daunorubicin was conjugated. Particles were spherical with an average diameter of 105.7±17.3 nm and zeta potential of 20.4±3.54 mV. We hypothesize the DNA backbone electrostatically condensed to the primary amines on the surface of the particle toroidally, weaving itself within the polymer shell. During the DNA intercalation process, increasing the ionic concentration and decreasing the amine/phosphate ratio 10-fold increased drug intercalation 64 % and 61 %, respectively, allowing us to determine the optimal method of particle synthesis. As intercalation sites increased with increasing DNA strand length, drug loading increased. An average of 874±40.1 daunorubicin molecules were loaded per HCPNP. HCPNPs with drug intercalated DNA have strong potential to be clinically efficacious drug delivery vehicles due to the versatility of DNA and high drug loading capacities.

Unwinding of a eukaryotic origin of replication visualized by cryo-EM

To prevent detrimental chromosome re-replication, DNA loading of a double hexamer of the minichromosome maintenance (MCM) replicative helicase is temporally separated from DNA unwinding. Upon S-phase transition in yeast, DNA unwinding is achieved in two steps: limited opening of the double helix and topological separation of the two DNA strands. First, Cdc45, GINS and Polε engage MCM to assemble a double CMGE with two partially separated hexamers that nucleate DNA melting. In the second step, triggered by Mcm10, two CMGEs separate completely, eject the lagging-strand template and cross paths. To understand Mcm10 during helicase activation, we used biochemical reconstitution with cryogenic electron microscopy. We found that Mcm10 splits the double CMGE by engaging the N-terminal homo-dimerization face of MCM. To eject the lagging strand, DNA unwinding is started from the N-terminal side of MCM while the hexamer channel becomes too narrow to harbor duplex DNA.

Structural homology-based identification of BEN domain proteins in Poxviruses

BEND family transcription factors directly interact with DNA through BEN domains and have been found across metazoan species. Interestingly, certain insect and mammalian viruses have also hijacked Bend genes into their genome. However, the phylogenetic classification and evolution of these viral BEN domains remain unclear. Building on our previous finding that in silico method accurately determine the 3D model of BEN domains, we used AlphaFold2 to predict the tertiary structures of poxviral BEN domains for comprehensive homologous comparison.We revealed that the majority of poxviral BEN modules exhibit characteristics of type II BEN. Additionally, electrostatic surface potential analysis found various poxviral BEN domains, including the first BEN of OPG067 in Orthopoxvirus, the third BEN of OPG067 in Yatapoxvirus and the third BEN of MC036R in MCV, have positively charged protein surfaces, indicating a structural basis for DNA loading. Notably, MC036R shares structural resemblance with human BEND3, as they both contain four BEN domains and an intrinsically disordered region. In summary, our discoveries provide deeper insights into the functional roles of BEN proteins within poxviruses.

A few-minute, simple, and affordable route to functionalized electrodes with DNA

A key challenge in developing DNA-based electrochemical sensors is the rapid and easy immobilization of DNA on different electrode surfaces. The current methods are often laborious and time-consuming. Here, we present a cost-effective and easy-to-perform method for efficiently functionalizing electrode surfaces with DNA in just a few minutes. Our strategy operates in two simple and rapid steps, regardless of the type of electrode, and avoids complicated and time-consuming procedures. The method uses phosphorothioate (PS) modification as an anchoring agent, which is a more cost-effective alternative to thiol (SH) modification, and eliminates the need for complex pretreatment processes. Additionally, a low-pH DNA loading method was used to quickly bind PS DNA to the gold surface without the need for surface-covering agents. We attributed the effect of low pH to the protonation of adenine (A), which leads to the formation of a parallel poly-A duplex (A motif) and facilitates vertical PS-DNA attachment to the electrode surface. Electrochemical techniques were used to confirm the vertical attachment of DNA to the electrode surface, and evaluation of the adsorption stability and hybridization efficiency confirmed the effectiveness of the method. The simplicity and efficiency of this method make it an ideal solution for researchers who require a fast and reliable method for DNA functionalization of electrode surfaces.

Enhancing the safety and effectiveness of polyethylenimine gene delivery through cell membrane encapsulation

Due to the powerful DNA loading capacity and excellent proton sponge effect, the cationic polymer polyethyleneimine (PEI) has been demonstrated as a versatile, efficient DNA delivery tool both in vitro and in vivo. However, the excess surface positive charge of PEI and the common capture/clearance of PEI/DNA complex by the immune system limit its further clinical applications. To reduce the cytotoxicity resulting from surface charge and avoid the clearance of nanoparticles interacting with proteins and circulating immune cells in the blood, a bionic gene delivery system was developed by coating PEI/DNA complexes with natural cell membranes. The obtained RAW Cell membrane-coated PEI/DNA capsules (RAWm-PDc) and Red blood Cell membrane-coated PEI/DNA capsules (RBCm-PDc) complex showed excellent dispersibility and stability with an average particle size of 200–300 nm. Moreover, the RAWm-PDc/RBCm-PDc complex had great DNA loading capacity and protected the bound DNA effectively from nuclease hydrolysis. Most importantly, the RAWm-PDc/RBCm-PDc complex exhibited low protein adsorption, reduced cytotoxicity and high gene delivery efficiency. All the results demonstrated the potential of RAWm-PDc/RBCm-PDc as a promising non-viral gene delivery vector.

Dual stimuli-responsive upconversion nanoparticle-poly-N-isopropylacrylamide/DNA core-shell microgels.

Stimuli-responsive upconversion nanoparticle (UCNP)-poly-N-isopropylacrylamide (pNIPAM)/DNA core-shell microgels with tunable sizes and programmable functions have been prepared. Thanks to the near-infrared (NIR)-responsive UCNP cores and thermosensitive polymeric shells, functional DNA-incorporated microgels with high DNA activity and loading efficiency are obtained, and the activity of the loaded DNA structures can be smartly regulated by NIR illumination and temperature simultaneously.

Development of a Novel H-Shaped Electrochemical Aptasensor for Detection of Hg2+ Based on Graphene Aerogels-Au Nanoparticles Composite.

Hg2+, a highly toxic heavy metal, poses significant environmental and health risks, necessitating rapid detection methods. In this study, we employed an electrochemical aptasensor for rapid and sensitive detection of Hg2+ based on DNA strands (H2 and H3) immobilized graphene aerogels-Au nanoparticles (GAs-AuNPs) hybrid recognition interface and exonuclease III (Exo III)-mediated cyclic amplification. Firstly, Gas-AuNPs were modified on the surface of the ITO electrode to form a sensing interface to increase DNA loading and accelerate electron transfer. Then, DNA helper was generated with the addition of Hg2+ via Exo III-mediated cycling. Finally, the hairpin structures of H2 and H3 were opened with the DNA helper, and then the methylene blue (MB) functionalized DNA (A1 and A2) combined with the H2 and H3 to form an H-shaped structure. The current response of MB as an electrochemical probe was proportional to the concentration of Hg2+. Under optimal conditions, the aptasensor showed excellent performance for Hg2+, achieving a linear range from 1 fM to 10 nM and a detection limit of 0.16 fM. Furthermore, the aptasensor was used to detect Hg2+ in spiked milk samples, achieving a high recovery rate and demonstrating promising application prospects.

Development of a biomimetic DNA delivery system by encapsulating polyethyleneimine functionalized silicon quantum dots with cell membranes.

Quantum dots (QDs) are renowned for their remarkable optoelectronic properties, making them suitable for applications such as bioimaging and optoelectronics. However, their use in gene delivery has been restricted due to the low DNA loading capacity. This study aimed to develop a biomimetic DNA delivery system by encapsulating polyethyleneimine (PEI) functionalized silicon QDs (SiQDs) with cell membranes and evaluate its potential as a gene vector in vitro. To achieve this, hydrophilic dispersed silicon QDs (PQDs) were prepared through a one-pot hydrothermal reaction of PEI and 3-Aminopropyltrimethoxysilane (APTMS). Subsequently, red blood cell membrane (RBCM) encapsulated biomimetic QDs (CM-PQDs) was obtained through the extrusion method. The CM-PQDs exhibited higher DNA loading capacity and better stability than naked SiQDs. The CM-PQDs/DNA complex was effectively taken up by cells, as observed through the fluorescence characteristics of QDs themselves. Both CM-P10QDs (prepared with PEI10k) and CM-P25QDs (prepared with PEI25k) could deliver DNA into cells and express the reporter protein successfully. CM-P25QDs showed a higher transfection efficiency of 77.32% in 293T cells and 47.11% in HeLa cells than SiQDs and CM-P10QDs. The results also indicated that cell membrane encapsulation could effectively reduce the cytotoxicity of SiQDs further. Therefore, the study concludes that CM-PQDs have the potential to serve as a safe and traceable biomimetic gene delivery system.

Smaller Gold Nanoparticles Release DNA More Efficiently During fs Laser Pulsed Optical Heating.

This work investigates the effect of plasmonic gold nanoparticle (AuNP) size on the rate of thermal release of single-stranded oligonucleotides under femtosecond (fs)-pulsed laser irradiation sources. Contrary to the theoretical predictions that larger AuNPs (50-60nm diameter) would produce the most solution heating and fastest DNA release, it is found that smaller AuNP diameters (25nm) lead to faster dsDNA denaturation rates. Controlling for the pulse energy fluence, AuNP concentration, DNA loading density, and the distance from the AuNP surface finds the same result. These results imply that the solution temperature increases around the AuNP during fs laser pulse optical heating may not be the only significant influence on dsDNA denaturation, suggesting that direct energy transfer from the AuNP to the DNA (phonon-phonon coupling), which is increased as AuNPs decrease in size, may play a significant role.

Label-free genosensing of dengue serotypes with an electrodeposited reduced graphene oxide-tris(bipyridine)ruthenium(II)

Constructing a label-free electrochemical transducer platform without compromising inherent biocompatibility against specific bioreceptor remains challenging, particularly probing nucleic acid hybridization at electrode interface without external redox-mediator. Here, we show that electrochemically reduced graphene oxide-tris(bipyridine)ruthenium(II) (ErGO-TBR) nanosheets electrodeposited on carbon screen printed electrode can quantify hybridization of clinically important target sequences specific to serotypes of dengue virus (DENV) non-structural 1 (NS1) protein. Different variables including deposition potential, time, and electrolytic composition were optimized for fabrication of label-free transducer platform. Structural and electrochemical properties of ErGO-TBR/SPE were comprehensively elucidated using microscopic and spectroscopic techniques. Electrochemical quartz crystal microbalance (EQCM) analysis reveals the growth of electrodeposited redox-active species on the electrode interface. Surface functional group investigations suggested that TBR deposited on the basal and edges of ErGO substrate via electrostatic and π-π interactions. Functionalization of bio-affinity layer (B) on ErGO-TBR/SPE enables better loading of probe DNA (PDNA) toward specific detection of DENV target DNA (TDNA) with an ultralow detection limit promising for clinical diagnosis. Scalable chronoamperometry-based redox-active surface growth, customizable bioactivation strategy and external mediator-less probing of nucleic acid hybridization make the present system suitable for other translational application in healthcare diagnosis.

Repurposing the atypical type I-G CRISPR system for bacterial genome engineering.

The CRISPR-Cas system functions as a prokaryotic immune system and is highly diverse, with six major types and numerous sub-types. The most abundant are type I CRISPR systems, which utilize a multi-subunit effector, Cascade, and a CRISPR RNA (crRNA) to detect invading DNA species. Detection leads to DNA loading of the Cas3 helicase-nuclease, leading to long-range deletions in the targeted DNA, thus providing immunity against mobile genetic elements (MGE). Here, we focus on the type I-G system, a streamlined, 4-subunit complex with an atypical Cas3 enzyme. We demonstrate that Cas3 helicase activity is not essential for immunity against MGE in vivo and explore applications of the Thioalkalivibrio sulfidiphilus Cascade effector for genome engineering in Escherichia coli. Long-range, bidirectional deletions were observed when the lacZ gene was targeted. Deactivation of the Cas3 helicase activity dramatically altered the types of deletions observed, with small deletions flanked by direct repeats that are suggestive of microhomology mediated end joining. When donor DNA templates were present, both the wild-type and helicase-deficient systems promoted homology-directed repair (HDR), with the latter system providing improvements in editing efficiency, suggesting that a single nick in the target site may promote HDR in E. coli using the type I-G system. These findings open the way for further application of the type I-G CRISPR systems in genome engineering.

DNA Loading Dye (6×)

DNA Loading Dye (6×)

Self-Assembly and In Situ Quaternization of Triblock Bottlebrush Block Copolymers via Organized Spontaneous Emulsification for Effective Loading of DNA.

Microspheres bearing large pores are useful in the capture and separation of biomolecules. However, pore size is typically poorly controlled, leading to disordered porous structures with limited performances. Herein, ordered porous spheres with a layer of cations on the internal surface of the nanopores are facilely fabricated in a single step for effective loading of DNA bearing negative charges. Triblock bottlebrush copolymers (BBCPs), (polynorbornene-g-polystyrene)-b-(polynorbornene-g-polyethylene oxide)-b-(polynorbornene-g-bromoethane) (PNPS-b-PNPEO-b-PNBr), are designed and synthesized for fabrication of the positively charged porous spheres through self-assembly and in situ quaternization during an organized spontaneous emulsification (OSE) process. Pore diameter as well as charge density increase with the increase of PNBr content, resulting in a significant increase of loading density from 4.79 to 22.5ngµg-1 within the spheres. This work provides a general strategy for efficient loading and encapsulation of DNA, which may be extended to a variety of different areas for different real applications.

Toward highly effective loading of DNA in hydrogels for high-density and long-term information storage

Digital information, when converted into a DNA sequence, provides dense, stable, energy-efficient, and sustainable data storage. The most stable method for encapsulating DNA has been in an inorganic matrix of silica, iron oxide, or both, but are limited by low DNA uptake and complex recovery techniques. This study investigated a rationally designed thermally responsive functionally graded (TRFG) hydrogel as a simple and cost-effective method for storing DNA. The TRFG hydrogel shows high DNA uptake, long-term protection, and reusability due to nondestructive DNA extraction. The high loading capacity was achieved by directly absorbing DNA from the solution, which is then retained because of its interaction with a hyperbranched cationic polymer loaded into a negatively charged hydrogel matrix used as a support and because of its thermoresponsive nature, which allows DNA concentration within the hydrogel through multiple swelling/deswelling cycles. We were able to achieve a high DNA data density of 7.0 × 109 gigabytes per gram using a hydrogel-based system.

DNA segment capture by Smc5/6 holocomplexes

Three distinct structural maintenance of chromosomes (SMC) complexes facilitate chromosome folding and segregation in eukaryotes, presumably by DNA loop extrusion. How SMCs interact with DNA to extrude loops is not well understood. Among the SMC complexes, Smc5/6 has dedicated roles in DNA repair and preventing a buildup of aberrant DNA junctions. In the present study, we describe the reconstitution of ATP-dependent DNA loading by yeast Smc5/6 rings. Loading strictly requires the Nse5/6 subcomplex which opens the kleisin neck gate. We show that plasmid molecules are topologically entrapped in the kleisin and two SMC subcompartments, but not in the full SMC compartment. This is explained by the SMC compartment holding a looped DNA segment and by kleisin locking it in place when passing between the two flanks of the loop for neck-gate closure. Related segment capture events may provide the power stroke in subsequent DNA extrusion steps, possibly also in other SMC complexes, thus providing a unifying principle for DNA loading and extrusion.