Top PDF Fundamental mechanisms and biological applications of DNA mediated charge transport

Fundamental mechanisms and biological applications of DNA mediated charge transport

Fundamental mechanisms and biological applications of DNA mediated charge transport

is exquisitely sensitive to perturbations in the intervening base pair stack; DNA binding-proteins, intervening mismatches, and base lesions can serve to attenuate charge migration [20]. This sensitivity of DNA CT to stacking perturbations has led to its application in developing novel electrochemical sensors [21, 22]. DNA CT has also been proposed to play a biological role in the detection of base lesions by DNA repair proteins [23]. Moreover, long-range oxidative DNA damage through CT has been demonstrated to occur within nucleosomes and within the cell nucleus [24, 25]. DNA CT can furthermore be harnassed to promote a variety of redox reactions on DNA triggered from a distance. We have shown that thymine dimers in DNA can be repaired at long range through DNA-mediated CT [26]. Most recently, we have determined that DNA CT can be utilized to promote the formation of disulfide bonds from thiols incorporated into the DNA backbone [27]. It is this chemistry, triggered from a distance, that we considered might also be useful in promoting reactions of proteins bound to DNA. Since p53 contains cysteine residues in close proximity within the DNA binding domain, we wondered if we could selectively oxidize the DNA-bound protein and in so doing, alter DNA binding through long-range CT. This chemistry from a distance, mediated by DNA, would then provide a completely new mechanism to globally regulate p53 binding. Figure 4.1 schematically illustrates this general chemistry.
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DNA-Mediated Charge Transport for Long-Range Sensing and Protein Detection

DNA-Mediated Charge Transport for Long-Range Sensing and Protein Detection

DNA-mediated electrochemistry through 100-mer monolayers revealed large signals for well matched duplexes, comparable to those observed with shorter duplexes. This result indicates that CT through DNA is robust in these long DNA films. Nonetheless, attenuation by single base mismatches illustrates the delicacy of this process and strongly argues that the integrity of the base pair π-stack is crucial. That a single mismatch within a 100-mer of otherwise well matched bases causes signal attenuation equal to that seen in mismatched DNA that is ~20% of the length establishes a new point of reference for the sensitivity of DNA CT to minor perturbations. Cutting with the RsaI restriction endonuclease demonstrates the biological integrity of the monolayers and also illustrates the utility of these longer DNA assemblies for sensing DNA-binding protein reactions. The ability to construct these CT-active assemblies using smaller oligonucleotides may be particularly useful for associated nanoelectronics applications. All of these results document that DNA can efficiently facilitate CT over 100 base pairs, or 34 nm, close to the persistence length of duplex DNA in solution. This remarkable distance for CT surpasses those in other reports of long-range transport through conjugated molecular wires (8, 9), and is among the longest distances reported for a molecular monolayer (4, 5, 7, 48).
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DNA Mediated Charge Transport Devices for Protein Detection

DNA Mediated Charge Transport Devices for Protein Detection

Detection of biologically relevant targets, including small molecules, proteins, DNA, and RNA, is vital for fundamental research as well as clinical diagnostics. Sensors with biological elements provide a natural foundation for such devices because of the inherent recognition capabilities of biomolecules. Electrochemical DNA platforms are simple, sensitive, and do not require complex target labeling or expensive instrumentation. Sensitivity and specificity are added to DNA electrochemical platforms when the physical properties of DNA are harnessed. The inherent structure of DNA, with its stacked core of aromatic bases, enables DNA to act as a wire via DNA-mediated charge transport (DNA CT). DNA CT is not only robust over long molecular distances of at least 34 nm, but is also especially sensitive to anything that perturbs proper base stacking, including DNA mismatches, lesions, or DNA-binding proteins that distort the π- stack. Electrochemical sensors based on DNA CT have previously been used for single- nucleotide polymorphism detection, hybridization assays, and DNA-binding protein detection. Here, improvements to (i) the structure of DNA monolayers and (ii) the signal amplification with DNA CT platforms for improved sensitivity and detection are described.
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Investigating DNA-Mediated Charge Transport by Time-Resolved Spectroscopy

Investigating DNA-Mediated Charge Transport by Time-Resolved Spectroscopy

One especially useful tool for the study of oxidative damage in DNA is DNA-mediated charge transport (CT). Due to orbital overlap between the π systems of neighboring nucle- obases, DNA can serve as a bridge in long-range electron transfer (ET) reactions. Unlike photocleavage mechanisms, many of which result in the formation of nonspecific damage by reactive oxygen species, 8–10 or photoligation mechanisms, which lead to the formation of unnatural adducts between metal complexes and DNA, 11 DNA-mediated CT results in preferential damage at sites of low oxidation potential. Oxidative events at low potential guanine sites (E ◦ [G •+ /G] = 1.29 V vs. NHE) 12 can be initiated by many different DNA- bound oxidants, including organic molecules, transition metal complexes, and DNA base analogues, 13–18 allowing for the study of DNA oxidation in a wide variety of environments and sequence contexts. Additionally, oxidative probes are capable of inducing damage in regions far from the site of charge injection. In solution studies, damage at guanine sites was observed almost 200 ˚ A away from a DNA-bound oxidant. 19 Recently, our laboratory observed the propagation of robust redox signals over a distance of 100 base pairs, or 340 ˚ A, in DNA monolayers on gold electrodes. 20 DNA CT may fulfill biological roles as well. The observed funneling of oxidative damage to regions of mitochondrial DNA that contain genes necessary for replication may serve as a check against the propagation of damaged genetic material in situations of high oxidative stress. 21 DNA CT also may be involved in other capacities within the cell, 22 for example, to activate transcription 23,24 and to perform long- range signaling. 25
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Evolution Subject to an Energy Driven Fundamental Time Arrow

Evolution Subject to an Energy Driven Fundamental Time Arrow

rite was reasonably protected against radiation damage. Here the “living” or- ganic layer could have started first taking advantage from a photovoltaic effect, which has been demonstrated for natural pyrite. It would have been like replac- ing dark electron transfer by photo-induced electron transfer in the Belou- sov-Zhabotinsky reaction when introducing a dye. In such self-organized thin organic layers on pyritemineral surfaces in tidal areas of the ocean Chloro- phyll-like dye molecules may have appeared. They started interacting photo-chemically, contributing radiation energy into the “energy-hungry” self-organized early living system, which then gradually separated from pyrite and continued increasing local order at the expense of solar energy. The entropy law identified for self-organized systems explains the feedback-driven “pressure” towards maximum energy turnover and towards mechanisms facilitating it. All available energy for the self-organized system is turned over in direction of dis- sipation and entropy formation (of course within the restraints of the system). A higher energy through-flux will shift the system further away from equilibrium. This can facilitate additional build-up of order. Early evolution of photosynthe- sis, as analysed in detail in the literature (Blankenship, 2010), could proceed its way. But somewhere during the early stage of life genetic mechanisms must have been integrated to take control over reproduction and evolution including life’s sometimes critical and destructive exposure to maximum entropy (energy) turnover (see later). Formation of self-similar copies is a characteristic property of self-organization and self-organization of chemical DNA information (as to be explained below) will provide the necessary mechanism.
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Magnetic Field Effects and Biophysical Studies on DNA Charge Transport and Repair

Magnetic Field Effects and Biophysical Studies on DNA Charge Transport and Repair

Recently DinG, a DNA damage response helicase from E. coli, was shown to contain a 4Fe-4S cluster (30). DinG is part of the SOS response, which is activated by DNA damaging agents and cellular stressors. DinG shares homology with the nucleotide excision repair protein XPD as well as with a host of Superfamily 2 helicases from archaea and eukaryotes that are linked to human disease and share a conserved 4Fe-4S domain (5). DinG unwinds DNA that has single-stranded overhangs with a 5′ to 3′ polarity (31). DNA-RNA hybrid duplexes that form within a DNA bubble, termed R- loops, represent a unique substrate that DinG has been shown to unwind in vitro (32). Importantly, DinG is required to unwind R-loops in vivo in order to resolve stalled replication forks and thus to maintain the integrity of the genome (33). Here we examine the DNA-bound redox properties of DinG and explore more generally crosstalk among redox-active DNA-processing enzymes in E. coli via 4Fe-4S clusters.
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A Review on Total and Paired Domination of
Cartesian product Graphs

A Review on Total and Paired Domination of Cartesian product Graphs

Using graph theory as a modeling tool in biological networks allows the utilization of the most graphical invariants in such a way that it is possible to identify secondary RNA (Ribonucleic acid) motifs numerically. Those graphical invariants are variations of the domination number of a graph. The results of the research carried out in show that the variations of the domination number can be used for correctly distinguishing among the trees that represent native structures and those that are not likely candidates to represent RNA.
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Preparation and Characterization of Cationic PLA PEG Nanoparticles for Delivery of Plasmid DNA

Preparation and Characterization of Cationic PLA PEG Nanoparticles for Delivery of Plasmid DNA

gene transport. Although PLA-PEG nanoparticles has several good qualities, such as good biodegradability, biocompatibility, and nonimmunogenicity, it takes on negative surface charges because of the carboxylic end groups of PLA. To prepare PLA-PEG mediated DNA complex, the cationic surface-active agent CTAB was used to modify the surface of PLA-PEG nanoparticles to make the surface take on positive charges. However, it was found that nanoparticles prepared with sole CTAB as surfactant (CTAB-NPs) revealed highly aggregated structures and heterogeneous size in TEM imaging (Fig. 1a), which was in accord with the other report [29]. In contrast, nanopar- ticles formulated with the popular non-ionic surfactant, Tween 80 (Tween 80-NPs) exhibited a uniform and smaller particle size without aggregation (Fig. 1b), which might be due to the superior emulsifying capacity of Tween 80. Moreover, it has some interesting characteristics useful for gene therapy because of the presence of poly(ethylene- glycol) (PEG) chains in its structure. It has been hypothe- sized that Tween 80 may have a similar fusogenic property with DOPE (Dioleylphosphatidylethanolamine) [30]. When a comparable concentration of Tween 80 is added to the formulation of nanoparticles, their transfection capacity will be improved significantly [31]. Besides, Tween 80 has another important characteristic for the transfection of these systems in vivo. It creates a steric barrier [32] which shields the excess of positive charges of the systems and reduces the interaction with blood components, such as serum proteins, which could limit the arrival of the gene therapy system to the cell surface. Taking these into con- sideration, Tween 80 was applied as a cosurfactant together with the cationic surfactant CTAB to formulate PLA-PEG nanoparticles in the present study.
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Biological effects of lithium – fundamental and medical aspects

Biological effects of lithium – fundamental and medical aspects

Inhibiting another phosphatase, namely phos- phoadenylate 3'­nucleotidase (PAPase), lithium af- fects processes of sulfation, DNA repair and apo- ptosis. It was demonstrated that lithium inhibits Golgi­resident PAPase [74]. Inactivation of this phosphatase by molecular and biological methods led to neonatal lethality, abnormal lung development (similar to atelectasis), and dwarfism, associa ted with changes in cartilage [74]. PAPase inhibition was reported to cause accumulation of 3′­phosphoade­ nosine 5′­phosphate in cells [75]. It is formed from 3′­phosphoadenosine 5′­phosphosulfate ­ a universal donor of sulfate groups. The further transfer of sul- fur to various acceptors is catalyzed by sulfotrans- ferase and is very important. Generated 3′­phos- phoadenosine 5′­phosphate is a potent inhibitor of PARP­1. In vitro, in micromolar range, it inhibited PARP­1 and reduced both PARP­1 automodification and heteromodification of histones.
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Application of metabolic engineering approaches in enhancing biological hydrogen production

Application of metabolic engineering approaches in enhancing biological hydrogen production

Besides glucose, other sugars and carbon sources have been explored as substrates for biological hydrogen production such as in dark or mixed acids fermentation. 9 For example, glycerol could be fermented by Escherichia coli into hydrogen with a theoretical yield of 7 mol of hydrogen per mole of glycerol. 1 An initial concentration of glycerol of 10 g/L has been found to be optimal for E. coli cell growth and hydrogen production. 1 Higher concentrations of glycerol have been found to depress hydrogen production. 1 Both crude and pure glycerol have been found to improve hydrogen production. 1 Specifically, in crude glycerol fermentation,
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Charge transport mechanisms and memory effects in amorphous TaNx
               thin films

Charge transport mechanisms and memory effects in amorphous TaNx thin films

the space charge and surface current. The conduction of the devices is also expected to be greatly influenced by the eventual presence of Ta nanoparticles embedded in the amorphous matrix and the choice of the metal elec- trodes, as it is shown in the case of the a-TaN x films deposited on Si. Large variations between neighboring nanodomains on the same film are found. These varia- tions in conductivity between nanodomains of the same film establish the importance of C-AFM technique as a diagnostic tool in nanoelectronics. Finally, significant current hysteresis effects are demonstrated, indicating the possible use of a-TaN x in memory applications, espe- cially for a-TaN x deposited on Au where bipolar memory effects are observed.
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Reactivity and structural studies of metal complexes bound to DNA

Reactivity and structural studies of metal complexes bound to DNA

Interestingly, in the case of the GT mismatch, the electrochemical data clearly differ from the guanine oxidation data. GT shows a very high distal/proximal oxidation ratio, while the integrated cathodic charge is very small as compared to that for the fully matched sequence. We reconcile this difference on the basis of the difference in time scale for the two experiments. The GT mismatch is known to exist as a wobble pair, well stacked in the helix and stabilized by hydrogen bonding (34). On the fast time scale for long-range oxidative damage (<10 -7 s) (35), the mismatched bases are fully stacked in one of the two hydrogen-bonded structures. If, however, the time scale for the wobble is comparable to that for the electrochemical measurement (10 -2 s), an attenuation in electrochemical signal should be observed. The dynamics of the wobble pair, therefore, appears to modulate charge transport through this mismatched duplex.
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Organic anion transporter 3- and organic anion transporting polypeptides 1B1- and 1B3-mediated transport of catalposide

Organic anion transporter 3- and organic anion transporting polypeptides 1B1- and 1B3-mediated transport of catalposide

OAT3, OATP1B1, and OATP1B3 transporters mediated renal and hepatic uptake of catalposide, which would be excreted via renal and biliary routes with or without coupling non-CYP mediated metabolism. Therefore, we first explored the involvement of P-gp and BCRP. From the results of Table 2, we concluded that these transporters were not involved in the excretion of catalposide. In spite of the lack of involvement of P-gp and BCRP in the transport of catalposide (Table 2), we should note the limitation of the use of specific inhibitors. We used CsA (25 μ M) and FTC (100 μ M) as P-gp and BCRP inhibitors, respectively. CsA inhibits not only P-gp but also other transporters such as OATP family transporters, multidrug resistance-associated protein 2 (MRP2), bile salt efflux pump, and Na + -taurocholate cotransporting polypeptide. 8 Therefore,
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The Simulation of Ionic Charge Transport in Biological Ion Channels: an Introduction to Numerical Methods

The Simulation of Ionic Charge Transport in Biological Ion Channels: an Introduction to Numerical Methods

ening, angular deformations, bond rotational barriers, etc. that are included in the potential energy functions used to describe the molecules under study. Force field parametrization is usually performed in a way that accounts for the average effects of the atomic polarization field, and involves a redistribution of the electric charge. In other words, the simulated particles (ions and atoms or groups of atoms in the protein and in the membrane) are assigned effective properties such as charge, size, and hardness, which normally depend on their position within the system. These force field parameters [165] are optimized in such a way that the simulation reproduces some of the desired bulk properties of the solution. The idea of the parameterization is to include the effects of the true many-body polar interactions in a simple pairwise additive fashion, so that the many-body effects can be embedded implicitly in the equations for the short range force. This approach is efficient from a computational viewpoint, but it involves a few problems. First the parametrization is not unique [138]. Second, the effects of the real polarization fields are assumed to be fixed rather than consistently evolving with the charge distribution. Finally, the effects of polar- ization on the molecular flexibility are necessarily neglected. It is safe to assume that in narrow pores the polarization field plays some role in the structural prop- erties of the protein, and plays a crucial role in the ion-water and ion-protein interactions. One can try to address the problem by treating the polarization field macroscopically, i.e. by computing an effective position-dependent dielec- tric tensor at equilibrium [143], and then use this dielectric tensor in Brownian dynamics or in an appropriately modified parametrization of molecular dynam- ics. This approach, however, neglects the transient dynamics of the polarization fields that may assist permeation and selectivity in ultra-narrow channels.
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The role of BRCA1 in homologous recombination repair in response to replication stress: significance in tumorigenesis and cancer therapy

The role of BRCA1 in homologous recombination repair in response to replication stress: significance in tumorigenesis and cancer therapy

Germ line mutations in breast cancer gene 1 (BRCA1) predispose women to breast and ovarian cancers. Although BRCA1 is involved in many important biological processes, the function of BRCA1 in homologous recombination (HR) mediated repair is considered one of the major mechanisms contributing to its tumor suppression activity, and the cause of hypersensitivity to poly(ADP-ribose) polymerase (PARP) inhibitors when BRCA1 is defective. Mounting evidence suggests that the mechanism of repairing DNA double strand breaks (DSBs) by HR is different than the mechanism operating when DNA replication is blocked. Although BRCA1 has been recognized as a central component in HR, the precise role of BRCA1 in HR, particularly under replication stress, has remained largely unknown. Given the fact that DNA lesions caused by replication blockages are the primary substrates for HR in mitotic cells, functional analysis of BRCA1 in HR repair in the context of replication stress should benefit our understanding of the molecular mechanisms underlying tumorigenesis associated with BRCA1 deficiencies, as well as the development of therapeutic approaches for cancer patients carrying BRCA1 mutations or reduced BRCA1 expression. This review focuses on the current advances in this setting and also discusses the significance in tumorigenesis and cancer therapy.
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Investigations of the mechanisms of receptor-mediated immunoglobulin transport in mammals and birds

Investigations of the mechanisms of receptor-mediated immunoglobulin transport in mammals and birds

wtFc transport in the rFcRn-GFP-MDCK cells (Figure 4A). The most likely explanation is that the addition of GFP to the C-terminus of the rFcRn cytoplasmic tail interferes with the binding of downstream effectors responsible for mediating intracellular trafficking processes. This is sur- prising, as a C-terminal GFP fusion of hFcRn has been shown to function in recycling of IgG ligands in the human endothelial cell line HMEC-1.CDC (35,37). Whether this discrepancy is due to differences in the interactions required for transcytosis versus recycling, differences in the behavior of the receptors when expressed in HMEC-1.CDC versus MDCK cells or fundamental differences between the hFcRn and rFcRn proteins is not clear. However, the fact that rFcRn-GFP-MDCK cells function in specific uptake of Fc ligands (Figure 2) suggests that signals responsible for endocytosis are intact, implying different signaling mech- anisms for endocytosis versus transcytosis, or that rFcRn can internalize bound ligand via non-specific membrane flow after binding to ligand molecules at the cell surface. Having demonstrated that rFcRn expressed in MDCK cells functions in binding, endocytosis and transcytosis of Fc and IgG ligands, both of which are naturally bivalent, we sought to study the interaction of rFcRn with RSA, a mono- valent ligand that binds to rFcRn with the same pH dependency as the FcRn–IgG interaction and for which FcRn acts as a protection receptor in vivo (14,34). Despite using high ligand concentrations (10 mM) and low pH (pH 5) to facilitate binding (14,27), we were not able to detect specific binding of radiolabeled RSA to rFcRn (Figure 5A). We note, however, that although the experiments were performed at concentrations near or above the K D of
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DNA-Mediated Charge Transfer Between [4Fe-4S] Cluster Glycosylases

DNA-Mediated Charge Transfer Between [4Fe-4S] Cluster Glycosylases

In our model for DNA damage detection, a bound enzyme transmits an electron to another protein bound to a distal location on the DNA. Upon reduction, this “distal” protein loses some of its DNA affinity, dissociates, and re-binds to a different region of the genome. However, if a lesion is present in the DNA sequence between the two bound proteins, CT will not proceed efficiently, both proteins remain oxidized and DNA-bound, and then localize to find and repair the damage between them. This model is supported by the fact that DNA-mediated charge-transfer (CT) can occur efficiently over long distances [13, 14], but is attenuated by mismatches and damage sites in the DNA helix [14, 15]. We have also shown that the affinity of certain BER enzymes for DNA is stronger in their oxidized 3 + form than in their reduced 2 + form [16]. Because CT would provide a means of DNA damage detection that is much faster than a processive search [17], perhaps the presence of a [4Fe-4S] cluster enables UDGs from thermophilic organisms to detect DNA damage more efficiently and thus cope with excess, temperature-induced DNA damage.
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MicroRNA-mediated drug resistance in breast cancer

MicroRNA-mediated drug resistance in breast cancer

Aberrant DNA methylation patterns are a prominent hallmark of cancer cells (Hanahan and Weinberg 2011). The global loss of genomic methylation, as well as regional hyper- and hypomethylation of genes involved in cell signaling, proliferation, and apoptosis, is thought to favor cell survival and tumor progression (Hanahan and Weinberg 2011; Pogribny and Beland 2009). There are three DNA methyltransferases (DNMTs) that have been shown to play a prominent role in cancer-specific DNA methylation, including maintenance DNMT1 and de novo DNA methyltransferases DNMT3A and DNMT3B. Although the mechanisms underlying elevated levels of DNMT remain unclear, recent reports suggest a role of miR-29, miR-148, miR-152, and miR-194 in mediating DNMT expression (Duursma et al. 2008; Fabbri et al. 2007; Meng et al. 2010; Pan et al. 2010) in drug-resistant breast cancer cell lines (Kutanzi et al., unpublished data; Pogribny et al. 2010). Importantly, the down-regulation of miR-148 has been shown to correlate with tumor stage in human breast cancer patients (Kutanzi, unpublished data), suggesting that the loss of this miRNA may contribute to methylation-specific patterns of tumor progression. Hypermethylation of miR-148 by DNMTs in the early stages of tumor development was shown to repress miR-148 gene expression (Lujambio et al. 2008), possibly indicating that a positive feedback loop exists to reinforce the over- expression of DNMTs in breast cancer. Furthermore, reactivation of miR-148 upon treatment with a DNA demethylating agent was associated with reduced tumor growth and inhibition of metastasis (Lujambio et al. 2008).
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DNA-Mediated Hole and Electron Transport

DNA-Mediated Hole and Electron Transport

characterized by scanning tunneling and scanning probe microscopy. 45 A variety of redox-active species, such as MB and DM, intercalate in the base stack of individual DNA helices at a defined distance from the electrodes and act as electrochemical reporters for ET through the intervening DNA bridge. 46-48 The reduction of the probes monitored by cyclic voltammetry or chronocoulometry should provide a measure of the efficiency of ET through DNA. The first observation of ET through a densely packed DNA film used covalently crosslinked daunomycin as a redox probe. 44 Remarkably, efficient reduction of DM exhibited an distance independence on the position of DM up to 100 Å. 48b Electron tunneling through the alkyl linker between the electrode and DNA monolayer is the rate-limiting step in ET through DNA films. 47 The sensitivity of ET through DNA-modified films was further explored using electrocatalysis of noncovalent intercalator MB. 46,49 In this study, the reduction signal of MB was significantly enhanced when coupled to the reduction of a freely diffusive ferricyanide as shown in figure 1.7. With electrocatalysis, all the single base mismatches, including the thermodynamically stable GT and GA mismatches, were detected by both cyclic voltammetry and
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Semiflexible polymers: fundamental theory and applications in DNA packaging

Semiflexible polymers: fundamental theory and applications in DNA packaging

Novel materials such as anionic hydrogels respond to changes in pH and salt concentra- tion by reversibly swelling to many times their original volume [26]; filaments composed of such materials have potential application as mechanical levers in nanoscale devices [27]. In Chap. 5, we study the dynamics of an initially straight elastic filament undergoing expan- sion after a sudden change in the solvent conditions using computer simulation [28]. The expansion proceeds by buckling in the transverse direction with a characteristic wavelength that we predict using linear stability analysis. The wavelike buckles locally adopt helical structures with domains of common handedness; these domains grow in time until the con- formation tends to a pure helix in the late stages in the relaxation process. The coarsening dynamics exhibited in the simulations are analyzed using nonlinear scaling arguments that provide insight into the fundamental nature of the relaxation processes.
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