Blowing DNA bubbles

Time-Lapse Single-Biomolecule Atomic Force Microscopy Investigation on Modified Graphite in Solution

Atomic force microscopy (AFM) of biomolecular processes at the single-molecule level can provide unique information for understanding molecular function. In AFM studies of biomolecular processes in solution, mica surfaces are predominantly used as substrates. However, owing to its high surface charge, mica may induce high local ionic strength in the vicinity of its surface, which may shift the equilibrium of studied biomolecular processes such as biopolymer adsorption or protein-DNA interaction. In the search for alternative substrates, we have investigated the behavior of adsorbed biomolecules, such as plasmid DNA and E. coli RNA polymerase σ⁷⁰ subunit holoenzyme (RNAP), on highly oriented pyrolytic graphite (HOPG) surfaces modified with stearylamine and oligoglycine-hydrocarbon derivative (GM) monolayers using AFM in solution. We have demonstrated ionic-strength-dependent DNA mobility on GM HOPG and nativelike dimensions of RNAP molecules adsorbed on modified HOPG surfaces. We propose an approach to the real-time AFM investigation of transcription on stearylamine monolayers on graphite. We conclude that modified graphite allows us to study biomolecules and biomolecular processes on its surface at controlled ionic strength and may be used as a complement to mica in AFM investigations.

Nanotemplate-directed DNA segmental thermal motion

Nanotemplate directed DNA segmental thermal motion on molecular nanotemplates on graphite was directly observed and characterized using AFM in a liquid.

Statistical analysis of molecular nanotemplate driven DNA adsorption on graphite

In this work, we have studied the conformation of DNA molecules aligned on the nanotemplates of octadecylamine, stearyl alcohol, and stearic acid on highly oriented pyrolytic graphite (HOPG). For this purpose, fluctuations of contours of adsorbed biopolymers obtained from atomic force microscopy (AFM) images were analyzed using the wormlike chain model. Moreover, the conformations of adsorbed biopolymer molecules were characterized by the analysis of the scaling exponent ν, which relates the mean squared end-to-end distance and contour length of the polymer. During adsorption on octadecylamine and stearyl alcohol nanotemplates, DNA forms straight segments, which order along crystallographic axes of graphite. In this case, the conformation of DNA molecules can be described using two different length scales. On a large length scale (at contour lengths l > 200-400 nm), aligned DNA molecules have either 2D compact globule or partially relaxed 2D conformation, whereas on a short length scale (at l ≤ 200-400 nm) their conformation is close to that of rigid rods. The latter type of conformation can be also assigned to DNA adsorbed on a stearic acid nanotemplate. The different conformation of DNA molecules observed on the studied monolayers is connected with the different DNA-nanotemplate interactions associated with the nature of the functional group of the alkane derivative in the nanotemplate (amine, alcohol, or acid). The persistence length of λ-DNA adsorbed on octadecylamine nanotemplates is 31 ± 2 nm indicating the loss of DNA rigidity in comparison with its native state. Similar values of the persistence length (34 ± 2 nm) obtained for 24-times shorter DNA molecules adsorbed on an octadecylamine nanotemplate demonstrate that this rigidity change does not depend on biopolymer length. Possible reasons for the reduction of DNA persistence length are discussed in view of the internal DNA structure and DNA-surface interaction.

Statistics of time-dependent rupture of single ds-DNA

Double-stranded (ds-) DNA molecules were stretched and ruptured on molecularly modified graphite surfaces with a scanning force microscope (SFM) exerting a force parallel to the surface. The stretching force was either large enough to break the molecule immediately or compensated by the elastic restoring force of the DNA backbone, which stabilized the molecular length. However, the size-stabilized molecules broke gradually from longer molecules to shorter ones with time. The breakage of different lengths of stabilized molecules was recorded in order to study time-dependent mechanical properties of the molecules under constant forces. From these data, a relatively high rate constant, k0 = (2.2 ± 0.1) × 10(-7) s(-1), was calculated. Moreover, we found a nonlinear stress-strain dependence of DNA on the surface which we attributed to DNA conformational transition. Assuming that the structural transition on the surface is similar to that in solution we estimated the forces needed to stretch the molecules and thereby verify the estimation of the activation energy barrier.

PEGylation improves nanoparticle formation and transfection efficiency of messenger RNA

PURPOSE

Cationic polymers have been intensively investigated for plasmid-DNA (pDNA), but few studies addressed their use for messenger-RNA (mRNA) delivery. We analyzed two types of polymers, linear polyethylenimine (l-PEI) and poly-N,N-dimethylaminoethylmethacrylate P(DMAEMA), to highlight specific requirements for the design of mRNA delivery reagents. The effect of PEGylation was investigated using P(DMAEMA-co-OEGMA) copolymer.

METHODS

The influence of polymer structure on mRNA binding and particle formation was assessed in a side-by-side comparison with pDNA by methods such as agarose-retardation assay and scanning probe microscopy. Transfection studies were performed on bronchial epithelial cells.

RESULTS

Binding of cationic polymers inversely correlated with type of nucleic acid. Whereas P(DMAEMA) bound strongly to pDNA, only weak mRNA binding was observed, which was vice versa for l-PEI. Both polymers resulted in self-assembled nanoparticles forming pDNA complexes of irregular round shape; mRNA particles were significantly smaller and more distinct. Surprisingly, PEGylation improved mRNA binding and transfection efficiency contrary to observations made with pDNA. Co-transfections with free polymer improved mRNA transfection.

CONCLUSIONS

Gene delivery requires tailor-made design for each type of nucleic acid. PEGylation influenced mRNA-polymer binding efficiency and transfection and may provide a method of further improving mRNA delivery.

Generation of multiblock copolymers by PCR: synthesis, visualization and nanomechanical properties

PCR was successfully implemented into polymer chemistry to produce linear multiblock structures up to pentablock architectures. Salient features of the generated DNA polymer hybrids were the ultrahigh molecular weights and their structural accuracy. Besides pushing the limits in block copolymer synthesis. a highly sophisticated characterization of the DNA/synthetic polymer hybrids was carried out by scanning force microscopy (SFM). Direct visualization revealed single polymer chains with the expected contour lengths for the DNA blocks and a characteristic kink at the central organic polymer unit bridging them. Furthermore, DNA triblock copolymers were manipulated by SFM, which so far has only been demonstrated for neat DNA and dendronized polymers. Upon blowing circular topologies, the DNA and the organic polymer chain have been extended and the contours of the three blocks could thereby be imaged separately.

Temperature-controlled assembly of high ordered/disordered dodecylamine layers on HOPG: consequences for DNA patterning

It is shown that temperature-controlled ordered layers of dodecylamine, self-assembled on highly oriented pyrolytic graphite (HOPG), are an appropriate substrate for aligning individual DNA molecules. High resolution atomic force microscopy (AFM) permits visualization of the lamellar structure of dodecylamine on HOPG. The DNA adsorbed on ordered dodecylamine layers is stretched and oriented along the lamellae, while DNA on disordered dodecylamine layers is found to be in a random conformation. Small DNA bubbles appear in the case of partially denaturated linear double stranded DNA (dsDNA) adsorbed on ordered layers of dodecylamine.

Scaling of the rupture dynamics of polymer chains pulled at one end at a constant rate

We consider the rupture dynamics of a homopolymer chain pulled at one end at a constant loading rate r . Compared to single bond breaking, the existence of the chain introduces two aspects into rupture dynamics: The non-Markovian aspect in the barrier crossing and the slow down of the force propagation to the breakable bond. The relative impact of both these processes is investigated, and the second one was found to be the most important at moderate loading rates. The most probable rupture force is found to decrease with the number of bonds as f{max} proportional, variant-[ln(const N/r)]2/3 and finally to approach a saturation value independent on N . All of our analytical findings are confirmed by extensive numerical simulations.

Micromechanical properties of tobacco mosaic viruses

A tobacco mosaic virus (TMV) subject to local forces can be viewed as an uniform beam with local loads. We used a custom built Atomic Force Microscope (AFM) to determine the curvature induced in the TMV by concentrated load or by distributed forces. Local forces were created by the AFM tip. Distributed forces were applied to the virus via the surface tension of receding droplets. The experimental results of both methods can be described when we attribute a Young modulus of 6 +/- 3 GPa to the virus. Our value is about five times larger than published data. We compare our results to the literature and work out possible error sources in our experiment and in published one.