Proton concentration (pH) switches the higher-order structure of DNA in the presence of spermine

Photoinduced conformational changes in DNA by poly(vinyl alcohol) carrying a malachite green moiety for protecting DNA against attack by nuclease

Light is a highly advantageous means of specific cell targeting. Though targeted gene delivery is an important characteristic of an ideal delivery vehicle, there has been little effort to develop a photoresponsive vector. Among nonviral vectors, cationic substances interact effectively with negatively charged DNA. With this property in mind, we designed copolymers of poly(vinyl alcohol) carrying a malachite green moiety (PVAMG) with different molecular weights. Though PVAMG has no affinity for DNA in the absence of light, it undergoes photoionization in the presence of light to afford cationic DNA binding sites. The DNA-PVAMG complex was investigated with respect to DNA conformational changes and its protective nature, which are important properties for nonviral vectors. PVAMG irradiation promoted DNA conformational transitions from coils to partial globules to compacted globules. The complex had a protective effect against DNase I after PVAMG irradiation, while DNA was degraded under dark conditions. The effect on DNA transition and the protective nature were sensitive to the molecular weight of PVAMG. The data regarding binding constants and binding mode provided insight into the structure of the DNA-PVAMG complex. To withstand DNase I attacks, complexation results in the compaction of DNA, which is further covered with PVAMG.

Small cyclen-imidazolium-containing molecules and their interactions with DNA

Three small organic molecules containing different numbers of cyclen and imidazolium units were synthesized. Their interactions with plasmid DNA and their potential for gene delivery vectors were investigated. Agarose gel retardation and ethidium bromide exclusion assays revealed that these molecules can effectively condense DNA, and compounds with higher molecular weights are needed to lower w/w ratio for full condensation. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) indicated that these compounds may form nanosized spherical particles with DNA. Furthermore, the complex formed from 10, i.e., 10/DNA, can partially release DNA from compact state at a relatively higher concentration of NaCl (200 mM). In the presence of the lipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), 10 could transfer plasmid DNA into BEL-7402 cells. In addition, these compounds exhibited much lower cytotoxicity than PEI 25 kDa.

Equilibrium dynamics of spermine-induced plasmid DNA condensation revealed by fluorescence lifetime correlation spectroscopy

The spermine-induced DNA condensation is a first-order phase transition. Here, we apply a novel technique fluorescence lifetime correlation spectroscopy to analyze this transition in a greater detail. We show that the method allows for the observation of the condensed and uncondensed molecules simultaneously based solely on different fluorescence lifetimes of the intercalating fluorophore PicoGreen in the folded und unfolded domains of DNA. The auto- and cross-correlation functions reveal that a small fraction of the DNA molecules is involved in the dynamic intramolecular equilibrium. Careful inspection of the cross-correlation curves suggests that folding occurs gradually within milliseconds.

Weak Interaction Induces an ON/OFF Switch, whereas Strong Interaction Causes Gradual Change: Folding Transition of a Long Duplex DNA Chain by Poly-l-lysine

A large-scale conformational change in genomic DNA is an essential feature of gene activation in living cells. Considerable effort has been applied to explain the mechanism in terms of key-lock interaction between sequence-specific regulatory proteins and DNA, in addition to the modification of DNA and histones such as methylation and acetylation. However, it is still unclear whether these mechanisms can explain the ON/OFF switching of a large number of genes that accompanies differentiation, carcinogenesis, etc. In this study, using single-molecule observation of DNA molecules by fluorescence microscopy with the addition of poly-L-lysine with different numbers of monomer units (n = 3, 5, 9, and 92), we found that an ON/OFF discrete transition in the higher-order structure of long duplex DNA is induced by short poly-L-lysine, whereas a continuous gradual change is induced by long poly-L-lysine. On the other hand, polycations with a lower positive charge have less potential to induce DNA compaction. Such a drastic difference in the conformational transition of a giant DNA between short and large oligomers is discussed in relation to the mechanisms of gene regulation in a living cell.

Exploitation of the coil-globule plasmid DNA transition induced by small changes in temperature, pH salt, and poly(ethylene glycol) compositions for directed partitioning in aqueous two-phase systems

In this study, the interplay of two linked equilibria is examined, one concerning an aqueous two-phase system (ATPS) composed of poly(ethylene glycol) (PEG) and salt employed to partition plasmid DNA (pDNA), and the other a potential structural transition of pDNA depending on PEG and salt concentration and other system parameters. The boundary conditions for pDNA partitioning are set by PEG and salt concentrations, PEG molecular weight, pH, and temperature. While investigating these parameters, it was found that a small increase/decrease of the respective values led to a drastic and significant change in pDNA behavior. This behavior could be attributed to a coil-globule transition of the pDNA triggered by the respective phase conditions. The combination of this structural change, aggregation effects linked to the transition process, and the electrostatic potential difference found in PEG-salt systems thus offers a sensitive way to separate nucleic acid forms on the basis of their unique property to undergo coil-globule transitions under distinct system properties.

Folding transition into a loosely collapsed state in plasmid DNA as revealed by single-molecule observation

The conformational transition of a plasmid DNA, pGEG.GL3 (12.5 kbp, circular), induced by spermine(4+) was studied through the observation of individual DNA by fluorescence microscopy. We deduced the change in the hydrodynamic radius R(H) from an analysis of the Brownian motion of single DNA molecules. R(H) decreases in a continuous manner with an increase in spermine(4+), in contrast to the large discrete on/off change for long linear DNA. Just after the transition to the collapsed state, a small number of DNA molecules tend to form an assembly, which disperses in the bulk solution without precipitation.

Coil−Globule Transition of DNA Molecules Induced by Cationic Surfactants: A Dynamic Light Scattering Study

The compaction and aggregation of DNA induced by cationic surfactants was studied by dynamic light scattering (DLS). Furthermore, the effect on surfactant-compacted DNA of the addition of nonionic amphiphiles and salt was studied. When using sufficiently low amounts of DNA and cetyltrimethylammonium bromide (CTAB), compacted DNA molecules could be monitored by the appearance of a band characterized by lower hydrodynamic radius and by the decrease in the intensity of the peak corresponding to extended DNA molecules. Notably, we observed a region where compacted molecules coexist with extended ones; these two populations were found to be stable with time. For higher concentrations of CTAB, only compacted molecules were observed and the size of the particles increased with time indicating aggregation. The number of globules present in the coexistence region increased linearly with the surfactant concentrations, as given by the area of the band corresponding to this population, which indicates a double-cooperativity of the binding. The DLS experiments were in good agreement with previous fluorescence microscopy studies, with certain advantages over this technique since there is no need to add fluorescence dyes and antioxidants. Furthermore, it allows the study of molecules which are too small to be visualized by fluorescence microscopy.

Giant DNA molecules exhibit on/off switching of transcriptional activity through conformational transition

We found that the transcriptional activity of large DNAs (40 kbp) can be completely inhibited by adding condensing agents, spermine and poly(ethylene glycol), whereas under the same conditions short fragments (140 bp) still show active transcription. Fluorescence microscopic observations of large DNAs revealed clear correlation between the higher-order structure of templates and their transcriptional activity. The steep decrease in transcriptional activity leading to complete inhibition, or on/off switching, is interpreted in terms of conformational transition of the ensemble of DNA molecules.

Compaction and multiple chain assembly of DNA with the cationic polymer poly(aluminum chloride) (PAC)

Assembly of DNA molecules by the addition of poly(aluminum chloride) (PAC) was studied. In the absence of PAC, electron microscopy indicated the formation of elongated coiled DNA molecules. In the presence of PAC, multiple doughnut-like structures, 8-15 nm thick, formed and fused together. When salt was added, the doughnut-like structures tended to be thinner and the morphology of the fused doughnuts became irregular. We obtained a view of a single DNA structure by fluorescent microscopy, which revealed that individual DNA molecules undergo a discrete transition from an elongated to compacted state with an increase in PAC concentration. Electron microscopic observation showed that a regular doughnut is the typical structure seen under low salt conditions. At high salt concentrations, the doughnut shape deformed, yielding results similar to those produced by the salt effect on DNA assembly at high DNA concentrations.