Effective and reversible DNA condensation induced by a simple cyclic/rigid polyamine containing carbonyl moiety

New Insights into the Role of Ligand-Binding Modes in GC-DNA Condensation through Thermodynamic and Spectroscopic Studies

In biological systems, the unprompted assembly of DNA molecules by cationic ligands into condensed structures is ubiquitous. The ability of ligands to provoke DNA packaging is crucial to the molecular organization and functional control of DNA, yet their underlined physical roles have remained elusive. Here, we have examined the DNA condensation mechanism of four cationic ligands, including their primary DNA-binding modes through extensive biophysical studies. We observed contrasting changes for these ligands binding to poly[dGdC]:poly[dGdC] (GC-DNA) and poly[dAdT]:poly[dAdT] (AT-DNA). Based on a CD spectroscopic study, it was confirmed that only GC-DNA undergoes B- to Ψ-type DNA transformation in the presence of ligands. In the fluorescence displacement assay (FDA), the ability of ligands to displace GC-DNA-bound EtBr follows the order: protamine²¹⁺ > cohex³⁺ > Ni²⁺ > spermine⁴⁺, which indicates that there is no direct correlation between the ligand charge and its ability to displace the drug from the DNA, indicating that GC-DNA condensation is not just influenced by electrostatic interaction but ligand-specific interactions may also have played a crucial role. Furthermore, the detailed ITC-binding studies suggested that DNA-ligand interactions are generally driven by unfavorable enthalpy and favorable entropy. The correlations from various studies insinuate that cationic ligands show major groove binding as one of the preferred binding modes during GC-DNA condensation.

The effect of spermidine on guanine decomposition via photoinduced electron transfer in DNA

The addition of spermidine caused the attenuation of guanine decomposition via photoinduced electron transfer in pyrene-modified DNA, and higher added concentrations of spermidine resulted in the promotion of decomposition in condensed DNA.

Biodegradable Polymers for Gene Delivery

The cellular transport process of DNA is hampered by cell membrane barriers, and hence, a delivery vehicle is essential for realizing the potential benefits of gene therapy to combat a variety of genetic diseases. Virus-based vehicles are effective, although immunogenicity, toxicity and cancer formation are among the major limitations of this approach. Cationic polymers, such as polyethyleneimine are capable of condensing DNA to nanoparticles and facilitate gene delivery. Lack of biodegradation of polymeric gene delivery vehicles poses significant toxicity because of the accumulation of polymers in the tissue. Many attempts have been made to develop biodegradable polymers for gene delivery by modifying existing polymers and/or using natural biodegradable polymers. This review summarizes mechanistic aspects of gene delivery and the development of biodegradable polymers for gene delivery.

A Comprehensive Biophysical Analysis of the Effect of DNA Binding Drugs on Protamine-induced DNA Condensation

DNA condensation is a ubiquitous phenomenon in biology, yet the physical basis for it has remained elusive. Here, we have explored the mechanism of DNA condensation through the protamine-DNA interaction, and by examining on it the influence of DNA binding drugs. We observed that the DNA condensation is accompanied by B to Ψ-DNA transition as a result of DNA base pair distortions due to protamine binding, bringing about the formation of toroidal structure through coil-globule transition. The binding energetics suggested that electrostatic energy, bending energy and hydration energy must play crucial roles in DNA condensation. EtBr intercalation interferes with the protamine-DNA interaction, challenging the distortion of the DNA helix and separation of DNA base pairs by protamine. Thus, EtBr, by competing directly with protamine, resists the phenomenon of DNA condensation. On the contrary, netropsin impedes the DNA condensation by an allosteric mechanism, by resisting the probable DNA major groove bending by protamine. In summary, we demonstrate that drugs with distinct binding modes use different mechanism to interfere with DNA condensation.

Hyperbranched poly(ethylenimine-co-oxazoline) by thiol–yne chemistry for non-viral gene delivery: investigating the role of polymer architecture

Synthesis of long-chain hyperbranched poly(ethylenimine-co-oxazoline)s by AB₂ thiol–yne chemistry is reported, and their application as pDNA transfection agents studied.

The Mixing Counterion Effect on DNA Compaction and Charge Neutralization at Low Ionic Strength

DNA compaction and charge neutralization in a mixing counterion solution involves competitive and cooperative electrostatic binding, and sometimes counterion complexation. At normal ionic strength, it has been found that the charge neutralization of DNA by the multivalent counterion is suppressed when being added extra mono- and di-valent counterions. Here, we explore the effect mixing counterion on DNA compaction and charge neutralization under the condition of low ionic strength. Being quite different from normal ionic strength, the electrophoretic mobility of DNA in multivalent counterion solution (octalysine, spermine) increases the presence of mono- and di-valent cations, such as sodium and magnesium ions. It means that the charge neutralization of DNA by the multivalent counterion is promoted rather than suppressed when introducing extra mono- and di-valent counterions into solution. This conclusion is also supported by the measurement of condensing and unraveling forces of DNA condensates under the same condition by single molecular magnetic tweezers. This mixing effect can be attributed to the cooperative electrostatic binding of counterions to DNA when the concentration of counterions in solution is below a critical concentration.

Thermo-reversible capture and release of DNA by zwitterionic surfactants

The thermo-reversible capture and release of DNA were studied by the protonation and deprotonation of alkyldimethylamine oxide (CnDMAO, n = 10, 12 and 14) in Tris-HCl buffer solution. DNA/C14DMAO in Tris-HCl buffer solution with pH = 7.2 is transparent at 25 °C, indicating that DNA molecules exist mainly in individuals and the binding of C14DMAO is weak. With the increase of temperature, the pH of the buffer solution continuously decreases, which leads to protonation of C14DMAO (C14DMAO + H(+)→ C14DMAOH(+)) and an obvious increase of the turbidity of the samples. This indicates a stronger binding of the protonated C14DMAOH(+) to DNA. Further investigations demonstrated the formation of DNA/C14DMAOH(+) complexes, in which the stretched DNA molecules are effectively compacted as evidenced from UV-vis absorptions, circular dichroism (CD) measurements, atomic force microscopy (AFM) observations, dynamic light scattering (DLS) measurements and agarose gel electrophoresis (AGE). Interestingly, when the temperature is turned back to 25 °C, the compacted DNA molecules can fully recover to the stretched conformation. This cycle can be repeated several times without obvious loss of efficiency. The effect of the chain length of CnDMAO has also been investigated. When C14DMAO was replaced by C12DMAO, similar phenomena can be observed with a slightly higher critical surfactant concentration for DNA compaction and a slightly lower pH of Tris-HCl buffer solution with pH = 6.8. For the DNA/C10DMAO system, however, no DNA compaction was observed even in Tris-HCl buffer solution with a much lower pH and a much higher C10DMAO concentration. The negative charges of DNA molecules can easily be neutralized by positive charges of cationic CnDMAOH(+) (n = 12 and 14) micelles. DNA was compacted and then insoluble DNA/CnDMAOH(+) complexes were formed. Because of the much higher critical micelle concentration (cmc) of the shorter chain length C10DMAOH(+), cationic C10DMAOH(+) micelles cannot form under the studied condition to compact DNA. The strategy may provide an efficient and alternative approach for stimuli-responsive gene therapy and drug release.

DNA Cleavage and Condensation Activities of Mono- and Binuclear Hybrid Complexes and Regulation by Graphene Oxide

Hybrid complexes with N,N'-bis(2-benzimidazolylmethyl)amine and cyclen moieties are novel enzyme mimics and controlled DNA release materials, which could interact with DNA through three models under different conditions. In this paper, the interactions between plasmid DNA and seven different complexes were investigated, and the methods to change the interaction patterns by graphene oxide (GO) or concentrations were also investigated. The cleavage of pUC19 DNA promoted by target complexes were via hydrolytic or oxidative mechanisms at low concentrations ranging from 3.13 × 10(-7) to 6.25 × 10(-5) mol/L. Dinuclear complexes 2a and 2b can promote the cleavage of plasmid pUC19 DNA to a linear form at pH values below 7.0. Furthermore, binuclear hybrid complexes could condense DNA as nanoparticles above 3.13 × 10(-5) mol/L and partly release DNA by graphene oxide with π-π stacking. Meanwhile, the results also reflected that graphene oxide could prevent DNA from breaking down. Cell viability assays showed dinuclear complexes were safe to normal human hepatic cells at relative high concentrations. The present work might help to develop novel strategies for the design and synthesis of DNA controllable releasing agents, which may be applied to gene delivery and also to exploit the new application for GO.

Potentiometric sensing of aqueous phosphate by competition assays using ion-exchanger doped-polymeric membrane electrodes as transducers

Using Zn(2+)-BPMP or Cu(2+)-BPMP as a receptor and o-mercaptophenol as an indicator, potentiometric sensing of aqueous phosphate by competition assays was achieved. With attractive features of portability, low cost and resistance to interference from turbidity and color, this sensor was successfully used for phosphate detection in biological and water samples.

On the correction of calculated vibrational frequencies for the effects of the counterions - α,ω-diamine dihydrochlorides

The present work provides sets of correction factors to adjust the calculated vibrational frequencies of a series of α,ω-diamines hydrochloride salts to account for the intermolecular interactions with the counterion. The study was performed using different theory levels for predicting the vibrational data of isolated dicationic α,ω-diamines and their hydrochloride forms, with and without the explicit account of the interactions with the chloride counterions. Different sets of correction factors were determined for each theory level considering the four smallest elements for the α,ω-diamines series, while their transferability and reliability was evaluated considering the larger elements of the series. The theory level simplification was also evaluated and was found to neither compromise the vibrational frequencies estimates nor the magnitude and accuracy of the pre-defined scaling factors. This suggests that transferability of the correction factors is possible not only for different diamines but also between different levels of theory with the averaged group correction factor, ζ g (a) , being the best choice to account for the effects of the N-H · · · Cl interactions. The possibility of simplifying the theory level without compromising efficiency and accuracy is additionally of utmost importance. This computational approach can constitute a valuable tool in the future for studying the hydrochloride forms of larger and more complex diamine systems. Graphical Abstract A computational approach that may constitute a valuable tool for studying the hydrochloride forms of large and complex diamine systems. Correction factors to adjust the vibrational frequencies calculated for isolated dicationic primary diamines for the effects of the interactions with chloride counterions, without their explicit account in the calculations, are presented and evaluated for eficiency.