BBA - General Subjects (v.1860, #1PA)
Editorial Board (i).
Effects of cytosine methylation on DNA morphology: An atomic force microscopy study by V. Cassina; M. Manghi; D. Salerno; A. Tempestini; V. Iadarola; L. Nardo; S. Brioschi; F. Mantegazza (1-7).
Methylation is one of the most important epigenetic mechanisms in eukaryotes. As a consequence of cytosine methylation, the binding of proteins that are implicated in transcription to gene promoters is severely hindered, which results in gene regulation and, eventually, gene silencing. To date, the mechanisms by which methylation biases the binding affinities of proteins to DNA are not fully understood; however, it has been proposed that changes in double-strand conformations, such as stretching, bending, and over-twisting, as well as local variations in DNA stiffness/flexibility may play a role. The present work investigates, at the single molecule level, the morphological consequences of DNA methylation in vitro. By tracking the atomic force microscopy images of single DNA molecules, we characterize DNA conformations pertaining to two different degrees of methylation. In particular, we observe that methylation induces no relevant variations in DNA contour lengths, but produces measurable incremental changes in persistence lengths. Furthermore, we observe that for the methylated chains, the statistical distribution of angles along the DNA coordinate length is characterized by a double exponential decay, in agreement with what is predicted for polyelectrolytes. The results reported herein support the claim that the biological consequences of the methylation process, specifically difficulties in protein-DNA binding, are at least partially due to DNA conformation modifications.
Keywords: DNA methylation; Atomic force microscopy (AFM); Persistence length;
Cellular response of human neuroblastoma cells to α-synuclein fibrils, the main constituent of Lewy bodies by Laura Pieri; Philippe Chafey; Morgane Le Gall; Guilhem Clary; Ronald Melki; Virginie Redeker (8-19).
α-Synuclein (α-Syn) fibrils are the main constituent of Lewy bodies and a neuropathological hallmark of Parkinson's disease (PD). The propagation of α-Syn assemblies from cell to cell suggests that they are involved in PD progression. We previously showed that α-Syn fibrils are toxic because of their ability to bind and permeabilize cell membranes. Here, we document the cellular response in terms of proteome changes of SH-SY5Y cells exposed to exogenous α-Syn fibrils.We compare the proteomes of cells of neuronal origin exposed or not either to oligomeric or fibrillar α-Syn using two dimensional differential in-gel electrophoresis (2D-DIGE) and mass spectrometry.Only α-Syn fibrils induce significant changes in the proteome of SH-SY5Y cells. In addition to proteins associated to apoptosis and toxicity, or proteins previously linked to neurodegenerative diseases, we report an overexpression of proteins involved in intracellular vesicle trafficking. We also report a remarkable increase in fibrillar α-Syn heterogeneity, mainly due to C-terminal truncations.Our results show that cells of neuronal origin adapt their proteome to exogenous α-Syn fibrils and actively modify those assemblies.Cells of neuronal origin adapt their proteome to exogenous toxic α-Syn fibrils and actively modify those assemblies. Our results bring insights into the cellular response and clearance events the cells implement to face the propagation of α-Syn assemblies associated to pathology.Display Omitted
Keywords: α-Synuclein; Proteomic; 2D-DIGE; Post-translational modifications; Parkinson's Disease;
The mitochondrial carnitine/acylcarnitine carrier is regulated by hydrogen sulfide via interaction with C136 and C155 by Nicola Giangregorio; Annamaria Tonazzi; Lara Console; Imma Lorusso; Annalisa De Palma; Cesare Indiveri (20-27).
The carnitine/acylcarnitine carrier (CAC or CACT) mediates transport of acylcarnitines into mitochondria for the β-oxidation. CAC possesses Cys residues which respond to redox changes undergoing to SH/disulfide interconversion.The effect of H2S has been investigated on the [3H]carnitine/carnitine antiport catalyzed by recombinant or native CAC reconstituted in proteoliposomes. Site-directed mutagenesis was employed for identifying Cys reacting with H2S.H2S led to transport inhibition, which was dependent on concentration, pH and time of incubation. Best inhibition with IC50 of 0.70 μM was observed at physiological pH after 30–60 min incubation. At longer times of incubation, inhibition was reversed. After oxidation of the carrier by O2, transport activity was rescued by H2S indicating that the inhibition/activation depends on the initial redox state of the protein. The observed effects were more efficient on the native rat liver transporter than on the recombinant protein. Only the protein containing both C136 and C155 responded to the reagent as the WT. While reduced responses were observed in the mutants containing C136 or C155. Multi-alignment of known mitochondrial carriers, highlighted that only the CAC possesses both Cys residues. This correlates well with the absence of effects of H2S on carriers which does not contain the Cys couple.Altogether, these data demonstrate that H2S regulates the CAC by inhibiting or activating transport on the basis of the redox state of the protein.CAC represents a specific target of H2S among mitochondrial carriers in agreement with the presence of a reactive Cys couple.
Keywords: Redox biology; Carnitine; Cys modification; Membrane transport; Mutagenesis; Beta oxidation;
CdTe quantum dots as fluorescent probes to study transferrin receptors in glioblastoma cells by Paulo E. Cabral Filho; Ana L.C. Cardoso; Maria I.A. Pereira; Ana P.M. Ramos; Fernando Hallwass; M. Margarida C.A. Castro; Carlos F.G.C. Geraldes; Beate S. Santos; Maria C. Pedroso de Lima; Giovannia A.L. Pereira; Adriana Fontes (28-35).
Overexpression of transferrin receptors (TfRs), which are responsible for the intracellular uptake of ferric transferrin (Tf), has been described in various cancers. Although molecular biology methods allow the identification of different types of receptors in cancer cells, they do not provide features about TfRs internalization, quantification and distribution on cell surface. This information can, however, be accessed by fluorescence techniques. In this work, the quantum dots (QDs)' unique properties were explored to strengthen our understanding of TfRs in cancer cells.QDs were conjugated to Tf by covalent coupling and QDs-(Tf) bioconjugates were applied to quantify and evaluate the distribution of TfRs in two human glioblastoma cells lines, U87 and DBTRG-05MG, and also in HeLa cells by using flow cytometry and confocal microscopy.HeLa and DBTRG-05MG cells showed practically the same TfR labeling profile by QDs-(Tf), while U87 cells were less labeled by bioconjugates. Furthermore, inhibition studies demonstrated that QDs-(Tf) were able to label cells with high specificity.HeLa and DBTRG-05MG cells presented a similar and a higher amount of TfR than U87 cells. Moreover, DBTRG-05MG cells are more efficient in recycling the TfR than the other two cells types.This is the first study about TfRs in human glioblastoma cells using QDs. This new fluorescent tool can contribute to our understanding of the cancer cell biology and can help in the development of new therapies targeting these receptors.
Keywords: Nanoparticles; Cancer cells; Transferrin; Receptors; Bioconjugation; Covalent binding;
Alpha-lipoic acid supplementation protects enzymes from damage by nitrosative and oxidative stress by Sylvia Hiller; Robert DeKroon; Eric D. Hamlett; Longquan Xu; Cristina Osorio; Jennifer Robinette; Witold Winnik; Stephen Simington; Nobuyo Maeda; Oscar Alzate; Xianwen Yi (36-45).
S-nitrosylation of mitochondrial enzymes involved in energy transfer under nitrosative stress may result in ATP deficiency. We investigated whether α-lipoic acid, a powerful antioxidant, could alleviate nitrosative stress by regulating S-nitrosylation, which could result in retaining the mitochondrial enzyme activity.In this study, we have identified the S-nitrosylated forms of subunit 1 of dihydrolipoyllysine succinyltransferase (complex III), and subunit 2 of the α-ketoglutarate dehydrogenase complex by implementing a fluorescence-based differential quantitative proteomics method.We found that the activities of these two mitochondrial enzymes were partially but reversibly inhibited by S-nitrosylation in cultured endothelial cells, and that their activities were partially restored by supplementation of α-lipoic acid. We show that protein S-nitrosylation affects the activity of mitochondrial enzymes that are central to energy supply, and that α-lipoic acid protects mitochondrial enzymes by altering S-nitrosylation levels.Inhibiting protein S-nitrosylation with α-lipoic acid seems to be a protective mechanism against nitrosative stress.Identification and characterization of these new protein targets should contribute to expanding the therapeutic power of α-lipoic acid and to a better understanding of the underlying antioxidant mechanisms.
Keywords: α-Lipoic acid; Antioxidant; Nitric oxide (NO); Nitrosative stress (NS); Reactive oxygen species (ROS); Mitochondria; S-nitrosylation; ATP;
Basic leucine zipper (bZIP) transcription factors involved in abiotic stresses: A molecular model of a wheat bZIP factor and implications of its structure in function by Pradeep Sornaraj; Sukanya Luang; Sergiy Lopato; Maria Hrmova (46-56).
Basic leucine zipper (bZIP) genes encode transcription factors (TFs) that control important biochemical and physiological processes in plants and all other eukaryotic organisms.Here we present (i) the homo-dimeric structural model of bZIP consisting of basic leucine zipper and DNA binding regions, in complex with the synthetic Abscisic Acid-Responsive Element (ABREsyn); (ii) discuss homo- and hetero-dimerisation patterns of bZIP TFs; (iii) summarise the current progress in understanding the molecular mechanisms of function of bZIP TFs, including features determining the specificity of their binding to DNA cis-elements, and (iv) review information on interaction partners of bZIPs during plant development and stress response, as well as on types and roles of post-translational modifications, and regulatory aspects of protein-degradation mediated turn-over. Finally, we (v) recapitulate on the recent advances regarding functional roles of bZIP factors in major agricultural crops, and discuss the potential significance of bZIP-based genetic engineering in improving crop yield and tolerance to abiotic stresses.An accurate analysis and understanding of roles of plant bZIP TFs in different biological processes requires the knowledge of interacting partners, time and location of expression in plant organs, and the information on mechanisms of homo- and hetero-dimerisation of bZIP TFs.Studies on molecular mechanisms of plant bZIP TFs at the atomic levels will provide novel insights into the regulatory processes during plant development, and responses to abiotic and biotic stresses.
Keywords: 14–3-3 proteins; Abiotic stress; DNA binding; Genetic engineering; Homo- and hetero-dimerisation; Kinases; Phytohormones; Plant development; Protein-protein interactions;
Identification of a neuropeptide precursor protein that gives rise to a “cocktail” of peptides that bind Cu(II) and generate metal-linked dimers by Christopher E. Jones; Meet Zandawala; Dean C. Semmens; Sarah Anderson; Graeme R. Hanson; Daniel A. Janies; Maurice R. Elphick (57-66).
Neuropeptides with an Amino Terminal Cu(II), Ni(II) Binding (ATCUN) motif (H2N-xxH) bind Cu(II)/Ni(II) ions. Here we report the novel discovery of a neuropeptide precursor that gives rise to a “cocktail” of peptides that bind Cu(II)/Ni(II) and form ternary complexes — the L-type SALMFamide precursor in the starfish Asterias rubens.Echinoderm transcriptome sequence data were analysed to identify transcripts encoding precursors of SALMFamide-type neuropeptides. The sequence of the L-type SALMFamide precursor in the starfish Asterias rubens was confirmed by cDNA sequencing and peptides derived from this precursor (e.g. AYHSALPF-NH2, GYHSGLPF-NH2 and LHSALPF-NH2) were synthesized. The ability of these peptides to bind metals was investigated using UV/Vis, NMR, circular dichroism and EPR spectroscopy.AYHSALPF-NH2 and GYHSGLPF-NH2 bind Cu(II) and Ni(II) and generate metal-linked dimers to form ternary complexes with LHSALPF-NH2. Investigation of the evolutionary history of the histidine residue that confers these properties revealed that it can be traced to the common ancestor of echinoderms, which is estimated to have lived ~ 500 million years ago. However, L-type precursors comprising multiple SALMFamides with the histidine residue forming an ATCUN motif appears to be a feature that has evolved uniquely in starfish (Asteroidea).The discovery of a SALMFamide-type neuropeptide precursor protein that gives rise to a “cocktail” of peptides that bind metal ions and generate metal-linked dimers provides a new insight on ATCUN motif-containing neuropeptides. This property of L-type SALMFamides in the Asteroidea may be associated with a role in regulation of the unusual extra-oral feeding behaviour of starfish.Display Omitted
Keywords: ATCUN; SALMFamide; Copper; Neuropeptide; Starfish; Echinoderm;
Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design by Xiaofeng Yu; Prajwal Nandekar; Ghulam Mustafa; Vlad Cojocaru; Galina I. Lepesheva; Rebecca C. Wade (67-78).
Cytochrome P450 sterol 14α-demethylase (CYP51) is an essential enzyme for sterol biosynthesis and a target for anti-parasitic drug design. However, the design of parasite-specific drugs that inhibit parasitic CYP51 without severe side effects remains challenging. The active site of CYP51 is situated in the interior of the protein. Here, we characterize the potential ligand egress routes and mechanisms in Trypanosoma brucei and human CYP51 enzymes.We performed Random Acceleration Molecular Dynamics simulations of the egress of four different ligands from the active site of models of soluble and membrane-bound T. brucei CYP51 and of soluble human CYP51.In the simulations, tunnel 2 f, which leads to the membrane, was found to be the predominant ligand egress tunnel for all the ligands studied. Tunnels S, 1 and W, which lead to the cytosol, were also used in T. brucei CYP51, whereas tunnel 1 was the only other tunnel used significantly in human CYP51. The common tunnels found previously in other CYPs were barely used. The ligand egress times were shorter for human than T. brucei CYP51, suggesting lower barriers to ligand passage. Two gating residues, F105 and M460, in T. brucei CYP51 that modulate the opening of tunnels 2 f and S were identified.Although the main egress tunnel was the same, differences in the tunnel-lining residues, ligand passage and tunnel usage were found between T. brucei and human CYP51s.The results provide a basis for the design of selective anti-parasitic agents targeting the ligand tunnels.Display Omitted
Keywords: Sterol 14α-demethylase; CYP51; Cytochrome P450; Random acceleration molecular dynamics; Membrane-bound protein; Ligand access and egress;
CacyBP/SIP — Structure and variety of functions by Agnieszka M. Topolska-Woś; Walter J. Chazin; Anna Filipek (79-85).
CacyBP/SIP (Calcyclin-Binding Protein and Siah-1 Interacting Protein) is a small modular protein implicated in a wide range of cellular processes. It is expressed in different tissues of mammals but homologs are also found in some lower organisms. In mammals, a high level of CacyBP/SIP is present in tumor cells and in neurons. CacyBP/SIP binds several target proteins such as members of the S100 family, components of a ubiquitin ligase complex, and cytoskeletal proteins.CacyBP/SIP has been shown to be involved in protein de-phosphorylation, ubiquitination, cytoskeletal dynamics, regulation of gene expression, cell proliferation, differentiation, and tumorigenesis. This review focuses on very recent reports on CacyBP/SIP structure and function in these important cellular processes.CacyBP/SIP is a multi-domain and multi-functional protein. Altered levels of CacyBP/SIP in several cancers implicate its involvement in the maintenance of cell homeostasis. Changes in CacyBP/SIP subcellular localization in neurons of AD brains suggest that this protein is strongly linked to neurodegenerative diseases. Elucidation of CacyBP/SIP structure and cellular function is leading to greater understanding of its role in normal physiology and disease pathologies.The available results suggest that CacyBP/SIP is a key player in multiple biological processes. Detailed characterization of the physical, biochemical and biological properties of CacyBP/SIP will provide better insight into the regulation of its diverse functions in vivo, and given the association with specific diseases, will help clarify the potential of therapeutic targeting of this protein.
Keywords: CacyBP/SIP; Cytoskeletal reorganization; Proliferation and tumorigenesis; Differentiation; Post-translational modifications; Protein structure;
De novo lipogenesis in Atlantic salmon adipocytes by Marta Bou; Marijana Todorčević; Jacob Torgersen; Stanko Škugor; Isabel Navarro; Bente Ruyter (86-96).
Carnivorous teleost fish utilize glucose poorly, and the reason for this is not known. It is possible that the capacity of adipocytes to synthesize lipids from carbohydrate precursors through a process known as “de novo lipogenesis” (DNL) is one of the factors that contributes to glucose intolerance in Atlantic salmon.Primary adipocytes from Atlantic salmon differentiated in vitro were incubated with radiolabelled glucose in order to explore the capacity of salmon adipocytes to synthesize and deposit lipids from glucose through DNL. The lipid-storage capacity of adipocytes incubated with glucose was compared with that of cells incubated with the fatty acid palmitic acid. Quantitative PCR and immunohistochemistry were used to assess changes of genes and proteins involved in glucose and lipid transport and metabolism.Less than 0.1% of the radiolabelled glucose was metabolized to the fatty acids 16:0 and the stearoyl-CoA desaturase products 16:1 and 18:1 by DNL, whereas approximately 40% was converted to glycerol to form the triacylglycerol backbone of lipids. Transcriptional analysis indicated that adipocytes ensure the availability of necessary cofactors and other substrates for lipid synthesis and storage from glycolysis, the pentose phosphate pathway and glyceroneogenesis.We have shown for the first time that the DNL pathway is active in fish adipocytes. The capacity of the pathway to convert glucose into cellular lipids for storage is relatively low.The limited capacity of adipocytes to utilize glucose as a substrate for lipid deposition may contribute to glucose intolerance in salmonids.
Keywords: Glucose metabolism; Differentiation; Palmitic acid; Teleost; Adipose tissue;
Proton pump inhibitors drastically modify triosephosphate isomerase from Giardia lamblia at functional and structural levels, providing molecular leads in the design of new antigiardiasic drugs by Itzhel García-Torres; Ignacio de la Mora-de la Mora; Jaime Marcial-Quino; Saúl Gómez-Manzo; América Vanoye-Carlo; Gabriel Navarrete-Vázquez; Blanca Colín-Lozano; Pedro Gutiérrez-Castrellón; Edgar Sierra-Palacios; Gabriel López-Velázquez; Sergio Enríquez-Flores (97-107).
Proton pump inhibitors (PPIs) are extensively used in clinical practice because of their effectiveness and safety. Omeprazole is one of the best-selling drugs worldwide and, with other PPIs, has been proposed to be potential drugs for the treatment of several diseases. We demonstrated that omeprazole shows cytotoxic effects in Giardia and concomitantly inactivates giardial triosephosphate isomerase (GlTIM). Therefore, we evaluated the efficiency of commercially available PPIs to inactivate this enzyme.We assayed the effect of PPIs on the GlTIM WT, single Cys mutants, and the human counterpart, following enzyme activity, thermal stability, exposure of hydrophobic regions, and susceptibility to limited proteolysis.PPIs efficiently inactivated GlTIM; however, rabeprazole was the best inactivating drug and was nearly ten times more effective. The mechanism of inactivation by PPIs was through the modification of the Cys 222 residue. Moreover, there are important changes at the structural level, the thermal stability of inactivated-GlTIM was drastically diminished and the structural rigidity was lost, as observed by the exposure of hydrophobic regions and their susceptibility to limited proteolysis.Our results demonstrate that rabeprazole is the most potent PPI for GlTIM inactivation and that all PPIs tested have substantial abilities to alter GITIM at the structural level, causing serious damage.General significance.This is the first report demonstrating the effectiveness of commercial PPIs on a glycolytic parasitic enzyme, with structural features well known. This study is a step forward in the use and understanding the implicated mechanisms of new antigiardiasic drugs safe in humans.
Keywords: Proton pump inhibitors; Giardia lamblia; Triosephosphate isomerase; Structural perturbation; Sulfenamide;
Using solution X-ray scattering to determine the high-resolution structure and morphology of PEGylated liposomal doxorubicin nanodrugs by Y. Schilt; T. Berman; X. Wei; Y. Barenholz; U. Raviv (108-119).
Among nanodrugs, PEGylated nanoliposomes loaded with an active agent are of major importance. In this paper we studied the structures and morphology of PEGylated nanoliposomes before and after remote loading with doxorubicin.High-resolution structures were obtained by solution X-ray scattering combined with our advanced analysis tools. We studied the PEGylated liposomal doxorubicin (PLD) product Doxil®, and its generics, where remote doxorubicin loading is performed by a gradient of ammonium sulfate, and LC100, a novel PLD under development, where remote loading was done by a gradient of ammonium methanesulfonate. The PLD structures were compared with drug-free nanoliposomes having identical composition.We determined the membrane electron density profiles of the empty and loaded PLDs, the thickness and density of the PEG layers, and the structure of the drug inside the liposomes.The liposomal membranes had the same structure for both ammonium salts. We found that the drug formed crystals inside PLDs loaded by ammonium sulfate, whereas it had an amorphous morphology in the PLD loaded by ammonium methanesulfonate. The variations of the drug's structural parameters between the generics of Doxil® are similar to the variations between batches of the same product, suggesting that all these products were structurally similar.This paper demonstrates that solution X-ray scattering, when combined with our powerful analysis tools, can determine the high-resolution structure of complex non-crystallized nanoparticle dispersions used in nanomedicine, thereby providing useful physical insights into their functions.Display Omitted
Keywords: Liposomal doxorubicin; SAXS; WAXS; Drug delivery; PEGylated liposomes; Generic drugs;
Ankyrin exposure induced by activated protein kinase C plays a potential role in erythrophagocytosis by Fuzhou Tang; Yang Ren; Ruofeng Wang; Xiaofeng Lei; Xueru Deng; Yajin Zhao; Dong Chen; Xiang Wang (120-128).
In physiological and pathological conditions activated protein kinace C (PKC) has been observed in the erythrocytes. Externalization of ankyrin followed by Arg–Gly–Asp (RGD)/integrin recognition also triggers erythrophagocytosis. In the present study, to test whether activated PKC is associated with ankyrin exposure in erythrophagocytosis.Phorbol 12-myristate-13-acetate (PMA)-induced PKC activation and ankyrin phosphorylation were tested, and under different treatment conditions the subpopulation of erythrocytes with ankyrin exposure and the levels of intracellular calcium were analyzed by flow cytometry.Results showed that treatment of erythrocytes with PMA in a calcium-containing buffer led to ankyrin exposure. In the absence of extracellular calcium, no ankyrin exposure was observed. PKC inhibition with calphostin C, a blocker of the PMA binding site, completely prevented the calcium entry, protein phosphorylation and ankyrin exposure. PKC inhibition with chelerythrine chloride, an inhibitor of the active site, diminished the level of ankyrin-exposing cells and ankyrin phosphorylation; however it even led to a higher percentage of cells with increased levels of calcium than with PMA treatment alone. Although PKC was activated and ankyrin phosphorylation occurred, no ankyrin exposure was observed in the absence of extracellular calcium.Analyses of results suggested that PMA induces calcium influx into the erythrocytes, leading to the activation of calcium-dependent enzymes and the phosphorylation of membrane proteins, ultimately inducing ankyrin exposure and erythrophagocytosis. This study may provide insights into the molecular mechanisms of removing aged or diseased erythrocytes.
Keywords: Human erythrocytes; Protein kinase C; Calcium influx; Phosphorylation of membrane proteins; Ankyrin exposure; Erythrophagocytosis;
Synthetic stigmastanes with dual antiherpetic and immunomodulating activities inhibit ERK and Akt signaling pathways without binding to glucocorticoid receptors by Flavia M. Michelini; Carlos A. Bueno; Alejandro M. Molinari; Mario D. Galigniana; Lydia R. Galagovsky; Laura E. Alché; Javier A. Ramírez (129-139).
We have previously shown that some synthetic hydroxylated stigmastanes derived from plant sterols inhibit in vitro HSV-1 replication in ocular cell lines and decrease cytokine production in stimulated macrophages, suggesting that these steroids might combine antiviral and immunomodulating properties. In this paper we report the synthesis of some analogs fluorinated at C-6 in order to study the effect of this modification on bioactivity.The following methods were used: organic synthesis of fluorinated analogs, cytotoxicity determination with MTT assays, cytokine production quantification with ELISAs, glucocorticoid activity determination by displacement assays, immunofluorescence and transcriptional activity assays, studies of the activation of signaling pathways by Western blot, antiviral activity evaluation through virus yield reduction assays.We report the chemical synthesis of new fluorinated stigmastanes and show that this family of steroidal compounds exerts its immunomodulating activity by inhibiting ERK and Akt signaling pathways, but do not act as glucocorticoids. We also demonstrate that fluorination enhances the antiviral activity.Fluorination on C-6 did not enhance the anti-inflammatory effect, however, an increase in the in vitro antiviral activity was observed. Thus, our results suggest that it is possible to introduce chemical modifications on the parent steroids in order to selectively modulate one of the effects.This family of steroids could allow the development of an alternative treatment for ocular immunopathologies triggered by HSV-1, without the undesirable side effects of the currently used drugs.
Keywords: Synthetic steroids; Fluorinated steroids; Antiherpetic; Cytokines; Signaling pathways;
Ab initio electron propagator calculations of transverse conduction through DNA nucleotide bases in 1-nm nanopore corroborate third generation sequencing by Aleksey A. Kletsov; Evgeny G. Glukhovskoy; Aleksey S. Chumakov; Joseph V. Ortiz (140-145).
The conduction properties of DNA molecule, particularly its transverse conductance (electron transfer through nucleotide bridges), represent a point of interest for DNA chemistry community, especially for DNA sequencing. However, there is no fully developed first-principles theory for molecular conductance and current that allows one to analyze the transverse flow of electrical charge through a nucleotide base.We theoretically investigate the transverse electron transport through all four DNA nucleotide bases by implementing an unbiased ab initio theoretical approach, namely, the electron propagator theory.The electrical conductance and current through DNA nucleobases (guanine [G], cytosine [C], adenine [A] and thymine [T]) inserted into a model 1-nm Ag–Ag nanogap are calculated. The magnitudes of the calculated conductance and current are ordered in the following hierarchies: g A > g G > g C > g T and I G > I A > I T > I C correspondingly. The new distinguishing parameter for the nucleobase identification is proposed, namely, the onset bias magnitude. Nucleobases exhibit the following hierarchy with respect to this parameter: V onset (A) < V onset (T) < V onset (G) < V onset (C).The difference in current magnitudes and onset voltages implies the possibility of nucleobases electrical identification by virtue of DNA translocation through an electrode-equipped nanopore.The results represent interest for the theorists and practitioners in the field of third generation sequencing techniques as well as in the field of DNA chemistry.Display Omitted
Keywords: Nucleobase conductance; DNA transverse conduction; Electron propagator theory; Third generation sequencing; Nucleotide identification; Onset voltage;