Top PDF Spectroscopic characterization of DNA-mediated charge transfer

Spectroscopic characterization of DNA-mediated charge transfer

Spectroscopic characterization of DNA-mediated charge transfer

My thesis committee is also in need of special recognition. I thank Professor Harry B. Gray for serving as Chairman and for being one of the most personable and entertaining people in the chemistry world. My decision to attend Caltech was based in large part on the two hours Harry took out of his busy schedule to spend with me during my visit to campus as a senior in college. My choice of research topics was greatly influenced by the work of Professor Rudolph A. Marcus. Rudy gave a seminar detailing his work on electron transfer at the University of Illinois when I was a sophomore. Since starting research at Caltech he has been very helpful in shaping our group’s ideas about electron transfer through DNA. Professor Jonas C. Peters was the last faculty member to join my committee. Jonas came on board in time for my fourth-year meeting, as he was appointed to the Caltech faculty after I started graduate school (I remember reading articles he was publishing as a graduate student at M.I.T.). His expertise has helped us overcome several problems we have encountered trying to synthesize new molecules.
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Investigating DNA-Mediated Charge Transport by Time-Resolved Spectroscopy

Investigating DNA-Mediated Charge Transport by Time-Resolved Spectroscopy

conduit for charge, the probe should interact strongly with the DNA base stack. Such an interaction can be difficult to achieve, considering the geometry of DNA. In general, the only access a diffusing molecule has to the base stack is either at the ends of the DNA strand or within the relatively narrow major and minor grooves which run lengthwise along the sides of the DNA molecule. Probes which are too large, or which are strongly negatively charged and therefore are repelled by the phosphate backbone of DNA, do not easily interface with the DNA π-stack. Second, depending on the function of the probe, it must provide a straightforward means of either initiating or reporting on DNA CT, or both. Often, the photophysical or electrochemical properties of a molecule are utilized for these purposes. Some probes may also report CT events through chemical pathways such as degradation. Third, the probe should not degrade or interact chemically with the DNA strand or with other components of the sample unless this is by design. Not only must the probe be stable enough to persist in solution, but the excited state of the molecule must also be stable if photochemical means are used to initiate or report CT, and the various redox states of the molecule must be able to withstand the charge transfer process. Finally, the ideal probe would be synthetically versatile and easy to build or modify in order to control sensitively the parameters of the experiment. Metallointercalators, transition metal complexes which bind DNA primarily by intercalation, are one class of molecules that fulfill all of these requirements.
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Spectroscopic Characterization, DNA Binding and Antibacterial Activity of Cu(II), Co(II) Complexes of Antipyrine Derivatives

Spectroscopic Characterization, DNA Binding and Antibacterial Activity of Cu(II), Co(II) Complexes of Antipyrine Derivatives

the pathogenic bacteria indicated that the complexes show the enhanced activity in comparison to free ligand [8]. Copper(II) chelates have been found to interact with biological systems and to exhibit antineoplastic activity [9–11] and antibacterial, antifungal [12, 13], and anticancer activity [14]. Some copper(II) N,S,O/N,N donor chelators are good anticancer agents due to strong binding ability with DNA base pair[15]. DNA binding metal complexes have been extensively investigated during the past several decades because they can be used as potential anticancer durgs, DNA structural probes, DNA-dependent electron transfer probes, DNA foot printing, sequence-specfic cleaving agants and so on [16-18].
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Fundamental mechanisms and biological applications of DNA mediated charge transport

Fundamental mechanisms and biological applications of DNA mediated charge transport

It is well established that the π-stack of the DNA double helix can serve as an efficient medium for charge transport [1-5]. With reactions spanning distances over 200 Å, this process is acutely sensitive to the intervening bridging bases [6, 7]. Oxidative base damage resulting from DNA-mediated charge transport reaction has particular relevance in the field of aging and in many diseases including cancer and neurodegenerative disorders [8-10]. Guanine, having the lowest oxidation potential of the naturally occurring bases can effectively serve as a hole trap [11]. Upon oxidation, the neutral guanine radical, with a millisecond lifetime, can react irreversibly with water or oxygen to form permanent damage products such as 8-oxo-G, oxazolone, and imidazolone [12]. While biochemical techniques to probe guanine damage yields at long range have been auspicious in underscoring the exquisite sensitivity of charge transport to base stacking and sequence, due to the slow trapping rate of the guanine radical, these studies are inevitably convoluted by processes such as back electron transfer and hence provide information several steps removed from the initial transport event [13].
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Spectroscopic Characterization of the Function and Mechanism of Dehaloperoxidase

Spectroscopic Characterization of the Function and Mechanism of Dehaloperoxidase

On the distal side peroxidases and globins both have a prominent histidine, known as the distal histidine. However, peroxidases also have a highly conserved arginine that is thought to stabilize proton transfer essential to rapid activation of bound peroxide to form compound. 13, 18, 19, 30, 36-38 However, bound hydroxide presents an especially interesting situation since there are both hydrogen bond donor and acceptor interactions. Depending upon the nature of the hydrogen bonding groups in the distal pocket, the Fe-OH bond can either be strengthened or weakened by interactions in the distal pocket. A hydrogen bond donor interaction with a σ-bonding distal ligand acts as a charge relay in reverse and reduces the ligation strength of the bound ligand. The situation for π-bonding ligands such as CO is more complex due to the competition between σ-donation and π- backbonding. 39 The proximal and distal charge relays are illustrated in scheme 1.
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Exploring DNA Mediated Charge Transport with Fast Radical Traps

Exploring DNA Mediated Charge Transport with Fast Radical Traps

Importantly, Ap * fluorescence quenching is insensitive to processes that occur after the CT event, including radical trapping, incoherent hopping or back electron transfer (BET). For hole acceptors in DNA, product yields for different photooxidants scale inversely to the propensity for BET, 13 and attenuating BET, both between the hole donor and the oxidized bridge and between the hole donor and oxidized acceptor, extends the lifetime of the charge separated state. 14 While other spectroscopic investigations of CT across adenine tracts have not revealed a similar periodicity, these other studies have been performed on systems for which BET is known to be substantial 15,16 or where slow trapping allows charge equilibration after the initial CT step. 17,18 We have recently shown that for both hole and electron transport, CT efficiency is dictated in the same manner by the dynamics and structure of the intervening DNA bases. 19 If the periodicity is the result of CT-active states that serve as more efficient pathways for forward CT, then they will also mediate more efficient BET. Hence, we propose that conformations that promote forward CT also promote BET, and this BET will serve to suppress the apparent periodicity.
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DNA-mediated Charge Transport in a Biological Context: Cooperation among Metalloproteins to Find Lesions in the Genome

DNA-mediated Charge Transport in a Biological Context: Cooperation among Metalloproteins to Find Lesions in the Genome

exploit DNA CT to recognize their lesions. We have thus proposed a mechanism that may be activated within cells for repair utilizing DNA CT. Importantly, binding to DNA shifts the potential of the EndoIII [4Fe4S] cluster toward oxidation, which could activate it when repair is required (37). The BER proteins all have similar DNA-bound redox potentials and contain a reduced [4Fe4S] 2+ in solution in the absence of oxidative stress (38). Guanine radicals, forming endogenously under conditions of oxidative stress, could initiate binding of protein to DNA, oxidizing the [4Fe4S] cluster from 2+ to 3+, increasing protein affinity for the duplex. As this occurs, an electron is transferred through the DNA to a distally bound BER protein. This distant protein is then reduced, loses its affinity for DNA, and is free to relocate onto another site. The process continues as a scan of the region of DNA between the proteins as long as CT occurs. In the presence of a lesion such as a mismatch or oxidized base, however, known to attenuate charge transfer, DNA CT does not proceed between bound proteins and thus the proteins remain in the vicinity of the damage, and slowly proceed to the site of damage (Figure 1.6). In this model, proteins are expected to redistribute onto regions of DNA that contain lesions. Additionally, the rate of this process depends on the distance over which CT can occur (hundreds of base pairs) and the percentage of oxidized protein (39). Assuming only facilitated diffusion and instantaneous interrogation, the amount of time required for a protein that is in low copy number to search for damage within the cell is reduced by at least an order of magnitude when it is able to cooperate with other proteins (39).
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Synthesis and characterization of charge transfer complex of  αααα Naphthol and p Chloranil

Synthesis and characterization of charge transfer complex of αααα Naphthol and p Chloranil

The electronic absorption spectra of p-chloranil complex contain a charge transfer band (CTB), apart from the absorption bands of donor and acceptor. The appearance of CTB is a characteristics feature of the formation of complex and gives spectroscopic evidence for the formation of a charge transfer complex between α-naphthol and p-chloranil.

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Activation of Transcription from a Distance: Investigations on the Oxidation of SoxR by DNA Mediated Charge Transport

Activation of Transcription from a Distance: Investigations on the Oxidation of SoxR by DNA Mediated Charge Transport

Examination of guanine oxidation at this 180-mer duplex reveals that damage occurs preferentially at sites which consist of guanine multiplets, and in particular, a 4-guanine site 20 base pairs away from the site of SoxR binding. The overall yield of damage is low, given the short-lived excited state of the Rh photooxidant and its low quantum yield of damage, which is due to rapid back-electron transfer to the long-lived guanine radical (12). Nevertheless, some damage is seen and is not localized near the site of Rh binding, suggesting that the hole equilibrates along the entire length of this DNA. Thus, DNA-mediated CT can occur along a distance long enough to effect SoxR oxidation. In a biological sense, these results highlight the competency of DNA to act as an antenna for oxidative damage in the cell, as the precursor species, oxidative radicals, are able to migrate along the base stack and localize at low potential hot spots that are proximal to the SoxR binding site. Indeed, previous studies have demonstrated that holes formed in DNA are able to be filled oxidation of reduced SoxR (Chapter 3).
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DNA-Mediated Charge Transfer Between [4Fe-4S] Cluster Glycosylases

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

Later in graduate school, I joined Prufrock Group, a cooking group that also became a community of treasured friends. They provided many free meals and the opportunity to transfer my scientific frustrations into culinary endeavors. There's a reason I'm good at chopping potatoes! More importantly, though, most members of Prufrock were close to my year in graduate school and, as we grew up together, they also provided me with encouragement and perspective as I navigated its difficult moments. Many thanks to Zuli Kurji, Theresa Emery, Matt Kelley, Heather McCaig, and Michael Mendenhall for keeping my stomach full and your ears open. In addition to maintaining the Prufrock club's backyard garden, Heather McCaig was an outstanding roommate for the better part of five years. Heather is a fellow tea fanatic, an outstanding cook of often unusual cuisines, and a willing participant in late-night social gatherings. I am still amazed that she and I have managed to remain such good friends after living in the same apartment for so long. She has remained upbeat and undeniably quirky through all the difficulties of her Ph.D. project, and I admire her spirit. I am also constantly amazed when I watch her dance ballet. I wish Heather all the best in her post-Caltech endeavors.
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Charge Transfer Complexes of the Donor Acriflavine and the Acceptors Quinol, Picric acid, TCNQ and DDQ: Synthesis, Spectroscopic Characterizations and Antimicrobial Studies

Charge Transfer Complexes of the Donor Acriflavine and the Acceptors Quinol, Picric acid, TCNQ and DDQ: Synthesis, Spectroscopic Characterizations and Antimicrobial Studies

Scanning electron microscopy (SEM) provides general information about the microstructure, the surface morphology, the particle size, the microscopic aspects of the physical behavior and the chemical composition of the respective Acf charge-transfer complexes and demonstrates the porous structures of the surface of these complexes. In addition, the chemical compositions of the complexes were determined using energy-dispersive X-ray diffraction (EDX). SEM surface images of the Acf CT complexes along with their EDX spectra are shown in Fig. 7. Analysis of the SEM images of the Acf complexes shows that the sizes of the particles are quite different with different acceptors. Furthermore, the uniformity and similarity between the particles of the synthesized Acf complexes indicate that the morphological phases of these complexes have a homogeneous matrix. Based on these observations, the [(Acf)(QL) 2 ], [(Acf)(TCNQ)] and [(Acf)(DDQ) complexes particles
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The investigation of novel charge transfer systems

The investigation of novel charge transfer systems

1. The most conductive complexes are associated with only partial charge transfer due to the Banner in which electrons move through, the acceptor stacks, (in for exaaple the TCNQ system). In fully ionized complexes every acceptor molecule carries a negative charge and movement of electrons through the stack would involve placing two electrons on one acceptor site. The large amount of energy required to achieve this inhibits electron mobility. However, if charge transfer is only partial then there is a proportion of uncharged sites to which electrons can hop, allowing electrons to move between adjacent acceptor sites49.
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MULLIKEN’S THEORY IN CHARGE-TRANSFER COMPLEXATION

MULLIKEN’S THEORY IN CHARGE-TRANSFER COMPLEXATION

Fig. 1.1 shows the change that occurs in the spectrum of iodine when it is dissolved in n-heptane and then when ethanol is added (Ethanol is transparent upto 220 nm). Iodine is well known for its electron-accepting properties, which may be deduced from molecular orbital consideration. It has been used in the past as a model acceptor to investigate the electron-donating properties of organic molecules [45] and during the past few decades the charge-transfer complexation of iodine with a wide variety of drugs molecule has been the subject of extensive research [46-49].
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Preparation, spectroscopic and thermal investigations on charge transfer complexes formed in the reaction of ribavirin drug and various acceptors

Preparation, spectroscopic and thermal investigations on charge transfer complexes formed in the reaction of ribavirin drug and various acceptors

For acid–base interaction, a proton transfer from the acceptor (acid) to the donor (base) is expected to occur. This seems to be liable to occur in the case of RV interaction with picric and chloranilic acids. Such assumption is strongly supported as follow; the spectrum of free donor reveals to absorption peaks at 3448 and 3349 cm −1 which is characteristic to the presence of an –NH 2 and –OH groups are slightly shifted toward lower frequencies. This small

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Engineered DNA-Mediated Antibody Gene Transfer for Prophylaxis Against Infectious Diseases

Engineered DNA-Mediated Antibody Gene Transfer for Prophylaxis Against Infectious Diseases

Monoclonal antibodies (mAbs) have become important therapeutic and prophylactic agents for a number of indications, including infectious diseases. However, due to many issues, particularly the high cost of antibody production, mAb therapies are limited to the world’s richest populations. Furthermore, lengthy product development programs mean only a small number of mAb products can be produced at any one time. Engineering novel, low-cost, and simple methods of developing and delivering mAbs would be highly advantageous, potentially expanding the utility of antibody approaches into a wider array of applications. Here, we describe an approach to deliver human IgG neutralizing mAbs in vivo using DNA plasmid-mediated antibody gene transfer. This approach, which we term DNA mAb (DMAb) delivery, generates biologically relevant levels of mAbs after a single intramuscular injection of antibody-encoding DNA followed by in vivo electroporation (EP). First, we developed antibody-encoding DNA plasmids that could reproducibly deliver human mAbs to mouse serum. We show that these plasmid-encoded antibodies have similar binding capacity and functionality to in vitro-produced purified antibodies. Then, we use a mouse model to show that
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Characterization of magnesium requirement of human 5' tyrosyl DNA phosphodiesterase mediated reaction

Characterization of magnesium requirement of human 5' tyrosyl DNA phosphodiesterase mediated reaction

(hTDP2) has been identified for the excision of TopII- DNA adducts [9,10]. Previously, TDP2 was known as TTRAP (TRAF and TNF receptor-associated protein), a protein of unknown function and a putative member of the Mg 2+ /Mn 2+ -dependent phosphodiesterase superfam- ily, with the DNA repair protein apurinic/apyrimidinic (AP) endonuclease-1 (APE-1, also known as APEX1) being its closest relative. hTDP2 possesses both 3 ’ phos- photyrosyl and 5 ’ phosphotyrosyl activity. Knockdown/ knockout of TDP2 in A549 and DT40 cells increased sensitivity to the TopII targeting agent etoposide but not to the TopI targeting agent camptothecin (CPT). The 5’-tyrosyl DNA phosphodiesterase activity of hTDP2 can enable the repair of TopII-induced double strand breaks (DSBs) without the need for nuclease activity, because it creates a “clean” DSB with 5’-phos- phate termini and a 3 ’ -hydroxyl group. These “ clean ” DSBs are religatable by DNA ligase, providing an oppor- tunity for error free repair [9,10]. hTDP2 may thus pro- vide an “ error-free ” mechanism for direct end-joining of TopII-induced DSBs. This is different from currently
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Two dimensional core–shell donor–acceptor assemblies at metal–organic interfaces promoted by surface mediated charge transfer

Two dimensional core–shell donor–acceptor assemblies at metal–organic interfaces promoted by surface mediated charge transfer

DFT calculations were employed to rationalize the mechan- ism behind the CT phenomena and the formation of the Au- TCNQ metal–organic structures. To this aim we considered a full monolayer of β-arranged TCNQ molecules (see ESI, section 2.2†) and incorporated one additional Au adatom for each TCNQ molecule, located in a hollow site of the unrecon- structed Au(111) substrate. A stable metal–organic structure formed, as shown in Fig. 6(a) (see ESI, section 2.2,† for details). The presence of the Au adatoms stabilizes the β-assembly, otherwise forbidden due to the proximity of the electronegative N atoms, which are instead mutually screened by the adatoms. Only two N atoms coordinate to each Au adatom bending downwards with respect to the molecular core (≈ 0.7 Å) (Fig. 6(a)). A similar distortion was previously reported for TCNQ and similar acceptor molecules 31,32,58,59 and was correlated with a re-aromatization of the molecular core induced by charge rearrangement at the metal–organic interface. Hence, the bent adsorption configuration of β-TCNQ molecules provides a first element of theoretical confirmation that these molecules are charged. Moreover, the occurrence of CT can be directly investigated by examining the TCNQ pro- jected density of states ( pDOS, see ESI, section 2.3†). Calculations reveal that the electron state corresponding to the Fig. 5 d I /d V spectroscopy on (a) α -TCNQ and (b) β -TCNQ molecules. The positions where the measurements were acquired are identi fi ed by fi lled circles in the STM images (shown as insets), with the same color of the corresponding spectra. A spectrum on clean Au(111) is shown as reference in (a) (black curve). The onset of the Au(111) surface state is indicated by dotted lines in (a).
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Charge transfer induced osmylation of aromatic compounds

Charge transfer induced osmylation of aromatic compounds

Yields for this stoichiometric CT osmylation were of the order of 10% (based on osmium), although no attempt to optimise the reaction was made. The mechanism for the reaction was shown to go via an arene cation radical resulting from the complete transfer of the CT electrons from benzene to osmium tetroxide upon UV irradiation. The radical ion pair formed upon irradiation can, as shown in scheme 2.3, decay in two ways. The primary route for this decay is back to the CT complex and accounts for the fate of 99% of the radical ion pairs formed. The secondary route of decay is one of chemical reaction in the form of cycloaddition (henceforth termed 'primary osmylation') to yield the diene diol osmate ester 67. With concurrent loss of aromaticity, the nascent diene diol osmate ester 67 is prone to further thermal anti osmylation ('secondary osmylation') to the bis-anri-osmate ester 68, scheme 2.4. All attempts to stop the CT osmylation after the primary osmylation through changes in reagent ratios were unsuccessful. The coordinatively unsaturated osmium(VI) centres in species of type 67 and 68 are prone to 'mutual association'^^ which leads to the polymeric osmate ester 65.
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Charge Transfer Complexes as a Semiconductor Models: Outline of Spectroscopic Studies on Electron Donor-Acceptor Complexes of Hexane-1,6-diol with Different p-Acceptors

Charge Transfer Complexes as a Semiconductor Models: Outline of Spectroscopic Studies on Electron Donor-Acceptor Complexes of Hexane-1,6-diol with Different p-Acceptors

Charge transfer complexation is currently achieve the great importance in biochemical, bioelectrochemical energy transfer process [6], biological systems [7], and drug-receptor binding mechanism, for examples, drug action, enzyme catalysis, ion transfers through lipophilic membranes [8], and certain -acceptors have successfully been utilized in pharmaceutical analysis of some drugs in pure form or in pharmaceutical preparations [9-15]. Recently, many studies have been widely reported about the rapid interactions between different kinds of drugs and related compounds as donors like morpholine, norfloxacin, ciprofloxacin, and sulfadoxine, with several types of  and -electron acceptors [16-30]. On the other hand, electron donor-acceptor (EDA) interaction has a worth attention for chemical reactions like addition, substitution and condensation [31,32]. It shows a great important in many application topics and fields, like in non-liner optical materials and electrical conductivities [33-36], second order non-liner optical activity [37], micro emulsion [38], surface chemistry [38], photo catalysts [39], dendrimers [40], solar energy storage [41], organic semiconductors [42], as well as in studying redox processes [43]. Charge transfer complexes using organic species are intensively studied because of their special type of interaction, which is accompanied by the transfer of an electron from the donor to the acceptor [44,45]. In addition, protonation of the donor from acidic acceptors is generally a route for the formation of ion pair adducts [46-48].
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