Optical Anisotropy of Chromatin. Flow Linear Dichroism and Electric Dichroism Studies

Abstract

The optical anisotropy of chromatin with different length of the linker DNA isolated from a variety of sources (Frend erythroleukemia cells, calf thymus, hen erythrocytes and sea urchin sperm) has been studied in a large range of mono- and bivalent cations concentraitons by the use of flow linear dichroism (LD) and electric dichroism.

We have found that all chromatins studied displayed negative LD values in the range of 0.25 mM EDTA—2 mM NaCl and close positive values in the range of 2–100 mM NaCl. Mg²⁺ cations, in contrast to Na⁺ cations, induce optically isotropic chromatin fibers. All chromatin samples exhibit positive form effect amounting to 5–10% of LD amplitude observed at 260 nm. This form effect is determined by the anisotropic scattering of polarized light by single chromatin fibers.

The conformational transition at 2 mM NaCl leads to the distortion of chromatin filament structure. The reversibility of this distortion depends on the length of the linker DNA—for chromatins with the linker DNA of 10–30 b.p. it is parially reversible, while for preparations with longer linker DNA it is irreversible.

Relatively low electric field does not affect chromatin structure, while higher electric field (more than 7 kV/cm) distorts the structure of chromatin.

Presented resutls explain the contradictory data obtained by electrooptical and hydrooptical methods.     

Recognition of Double-Stranded Dna by Peptide Nucleic Acid

Abstract

Peptide nucleic acid (PNA) is an oligonucleotide mimic in which the backbone of DNA has been replaced by a pseudopeptide. We here show that there are distinct variations as to how PNA oligomers interact with double-stranded DNA depending on choice of nucleobases. Thymine-rich homopyrimidine PNA oligomers recognise double-stranded polynucleotides by forming PNA₂-DNA triplexes with the DNA purine strand. By contrast, cytosine-rich homopyrimidine PNAs add to double-stranded polynucleotides as Hoogsteen strands, forming PNA-DNA₂ triplexes, while homopurine, or alternating thymine-guanine, PNA oligomers invade DNA to form PNA-DNA duplexes.     

Modelling dendritic spines with the finite element method,investigating the impact of geometry on electric and calcic responses

Understanding the relationship between shape and function of dendritic spines is an elusive topic. Several modelling approaches have been used to investigate the interplay between spine geometry, calcium diffusion and electric signalling. We here use a second order finite element method to solve the Poisson–Nernst–Planck equations and describe electrodiffusion in dendritic spines. With this, we obtain relationships between dendritic geometry and calcic as well as electric responses to synaptic events. Our findings support the hypothesis that spine geometry plays a role shaping the electrical responses to synaptic events. Our method was also able to reveal the fine scale distribution of calcium in spines with irregular shapes.

     

Mode Controlling of Surface Plasmon Polaritons by Geometric Phases

Metasurfaces are made of two-dimensional arrays of subwavelength nanostructures that form a spatially varying optical response, to control the wave fronts of optical waves. As the feature size of its constituent materials is nanoscale, investigation of the light-nanostructure interactions in the near field is critical for understanding the novel properties of metasurfaces. Here, we used a scanning near-field optical microscope (SNOM) to observe the near-field distribution of surface plasmon polaritons (SPPs) from a ring-shaped metasurface under illumination of circularly polarized light. It was found that with an additional degree of freedom of the geometric phase provided by the regularly arranged metamolecules, control over the near-field interference of the SPPs can be achieved, which is governed by the metasurface geometric symmetry that can be tuned by its topological charge. Meanwhile, the planar chiral character of the metamolecules exerts a deep influence on the near-field interference patterns. Our results can pave the way for active control of SPP propagation in near fields and have potential applications in highly integrated optical communication systems.

     

Incorporation of reporter molecule-labeled nucleotides by DNA polymerases. II. High-density labeling of natural DNA

The modification of nucleic acids using nucleotides linked to detectable reporter or functional groups is an important experimental tool in modern molecular biology. This enhances DNA or RNA detection as well as expanding the catalytic repertoire of nucleic acids. Here we present the evaluation of a broad range of modified deoxyribonucleoside 5′-triphosphates (dNTPs) covering all four naturally occurring nucleobases for potential use in DNA modification. A total of 30 modified dNTPs with either fluorescent or non-fluorescent reporter group attachments were systematically evaluated individually and in combinations for high-density incorporation using different model and natural DNA templates. Furthermore, we show a side-by-side comparison of the incorporation efficiencies of a family A (Taq) and B (Vent_R exo^–) type DNA polymerase using the differently modified dNTP substrates. Our results show superior performance by a family B-type DNA polymerase, Vent_R exo^–, which is able to fully synthesize a 300 bp DNA product when all natural dNTPs are completely replaced by their biotin-labeled dNTP analogs. Moreover, we present systematic testing of various combinations of fluorescent dye-modified dNTPs enabling the simultaneous labeling of DNA with up to four differently modified dNTPs.     

Aromatic residues in RNase T stack with nucleobases to guide the sequence‐specific recognition and cleavage of nucleic acids

RNase T is a classical member of the DEDDh family of exonucleases with a unique sequence preference in that its 3′‐to‐5′ exonuclease activity is blocked by a 3′‐terminal dinucleotide CC in digesting both single‐stranded RNA and DNA. Our previous crystal structure analysis of RNase T‐DNA complexes show that four phenylalanine residues, F29, F77, F124, and F146, stack with the two 3′‐terminal nucleobases. To elucidate if the π–π stacking interactions between aromatic residues and nucleobases play a critical role in sequence‐specific protein–nucleic acid recognition, here we mutated two to four of the phenylalanine residues in RNase T to tryptophan (W mutants) and tyrosine (Y mutants). The Escherichia coli strains expressing either the W mutants or the Y mutants had slow growth phenotypes, suggesting that all of these mutants could not fully substitute the function of the wild‐type RNase T in vivo. DNA digestion assays revealed W mutants shared similar sequence specificity with wild‐type RNase T. However, the Y mutants exhibited altered sequence‐dependent activity, digesting ssDNA with both 3′‐end CC and GG sequences. Moreover, the W and Y mutants had reduced DNA‐binding activity and lower thermal stability as compared to wild‐type RNase T. Taken together, our results suggest that the four phenylalanine residues in RNase T not only play critical roles in sequence‐specific recognition, but also in overall protein stability. Our results provide the first evidence showing that the π−π stacking interactions between nucleobases and protein aromatic residues may guide the sequence‐specific activity for DNA and RNA enzymes.     

The Potential Around Electrode Tips: Model Considerations

SUMMARY

As a new approach we considered the time and frequency depending electrical properties of biological material. Our model shows that in the near field around an electrode tip (distance < 15 μm) the spread of potential differs significantly from a model which denies time and frequency dependence of the biological material. On the other hand this effect decreases in the far-field (distance > 20 μm) due to the low-pass filtering characteristic of biological material. Furthermore it can be seen that the distortion of the signal in the near-field of an electrode tip depends on the inner resistance of the stimulus generator: current sources distort much more than voltage sources.     

Sexual and seasonal plasticity in the emission of social electric signals. Behavioral approach and neural bases

Behavior in electric fish includes modulations of a stereotyped electric organ discharge (EOD) in addition to locomotor displays. Gymnotiformes can modulate the EOD rate to produce signals that participate in different behaviors. We studied the reproductive behavior of Brachyhypopomus pinnicaudatus both in the wild and laboratory settings. During the breeding season, fish produce sexually dimorphic social electric signals (SES): males emit three types of chirps (distinguished by their duration and internal structure), and accelerations, whereas females interrupt their EOD. Since these SES imply EOD frequency modulations, the pacemaker nucleus (PN) is involved in their generation and constitutes the main target organ to explore seasonal and sexual plasticity of the CNS. The PN has two types of neurons, pacemakers and relays, which receive modulatory inputs from pre-pacemaker structures. These neurons show an anisotropic rostro-caudal and dorso-ventral distribution that is paralleled by different field potential waveforms in distinct portions of the PN. In vivo glutamate injections in different areas of the PN provoke different kinds of EOD rate modulations. Ventral injections produce chirp-like responses in breeding males and EOD interruptions in breeding females, whereas dorsal injections provoke EOD frequency rises in both sexes. In the non-breeding season, males and females respond with interruptions when stimulated ventrally and frequency rises when injected dorsally. Our results show that changes of glutamate effects in the PN could explain the seasonal and sexual differences in the generation of SES. By means of behavioral recordings both in the wild and in laboratory settings, and by electrophysiological and pharmacological experiments, we have identified sexual and seasonal plasticity of the CNS and explored its underlying mechanisms.     

Dynamics and Conformational Changes in Human NEIL2 DNA Glycosylase Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry

Base excision DNA repair (BER) is necessary for removal of damaged nucleobases from the genome and their replacement with normal nucleobases. BER is initiated by DNA glycosylases, the enzymes that cleave the N-glycosidic bonds of damaged deoxynucleotides. Human endonuclease VIII-like protein 2 (hNEIL2), belonging to the helix–two-turn–helix structural superfamily of DNA glycosylases, is an enzyme uniquely specific for oxidized pyrimidines in non-canonical DNA substrates such as bubbles and loops. The structure of hNEIL2 has not been solved; its closest homologs with known structures are NEIL2 from opossum and from giant mimivirus. Here we analyze the conformational dynamics of free hNEIL2 using a combination of hydrogen/deuterium exchange mass spectrometry, homology modeling and molecular dynamics simulations. We show that a prominent feature of vertebrate NEIL2 – a large insert in its N-terminal domain absent from other DNA glycosylases – is unstructured in solution. It was suggested that helix–two-turn–helix DNA glycosylases undergo open–close transition upon DNA binding, with the large movement of their N- and C-terminal domains, but the open conformation has been elusive to capture. Our data point to the open conformation as favorable for free hNEIL2 in solution. Overall, our results are consistent with the view of hNEIL2 as a conformationally flexible protein, which may be due to its participation in the repair of non-canonical DNA structures and/or to the involvement in functional and regulatory protein–protein interactions.     

Differential production of chirping behavior evoked by electrical stimulation of the weakly electric fish, Apteronotus leptorhynchus

Aperonotus leptorhynchus (Gymnotiformes) produces wave-like electric organ discharges distinguished by a high degree of constancy. Transient frequency and amplitude modulations of these discharges occur both spontaneously and during social interactions, which can be mimicked by external electrical stimulation. The so-called chirps can be divided into four different types. Independent of the type of chirp produced under spontaneous conditions, the fish generate only significant numbers of type-2 chirps under evoked conditions. The rate of production of chirps of this type is largely determined by the frequency relative to the fish's frequency and signal intensity. Frequencies of + 10 Hz of the fish's own discharge frequency most effectively elicit chirps. Type-2 chirps can also be evoked through stimulation at or near the higher harmonic frequencies of the fish's frequency, but the chirp rate decreases with increasing number of the higher harmonic component. Over a certain range, the rate of production of type-2 chirps increases with increasing stimulus intensity. At very high intensities the generation of type-2 chirps is accompanied by the production of a novel type of electrical signal ("abrupt frequency rise") characterized by a frequency increase of approximately 20 Hz and high repetition rates of roughly 10 s(-1). We hypothesize that the different types of electric modulations subserve different behavioral functions.     

EOD modulations of brown ghost electric fish: JARs, chirps, rises, and dips.

Weakly electric "wave" fish make highly regular electric organ discharges (EODs) for precise electrolocation. Yet, they modulate the ongoing rhythmicity of their EOD during social interactions. These modulations may last from a few milliseconds to tens of minutes. In this paper we describe the different types of EOD modulations, what they may signal to recipient fish, and how they are generated on a neural level. Our main conclusions, based on a species called the brown ghost (Apteronotus leptorhynchus) are that fish: (1) show sexual dimorphism in the signals that they generate; (2) make different signals depending on Whether they are interacting with a fish of the opposite sex or, within their own sex, to a fish of that which is dominant or subordinate to it; (3) are able to assess relative dominance from electrical cues; (4) have a type of plasticity in the pacemaker nucleus, the control center for the EOD, that occurs after stimulation of NMDA receptors that causes a long-lasting (tens of minutes to hours) change in EOD frequency; (5) that this NMDA receptor-dependent change may occur in reflexive responses, like the jamming avoidance response (JAR), as well as after certain long-lasting social signals. We propose that NMDA-receptor dependent increases in EOD frequency during the JAR adaptively shift the EOD frequency to a new value to avoid jamming by another fish and that such increases in EOD frequency during social encounters may be advantageous since social dominance seems to be positively correlated with EOD frequency in both sexes.     

Characterization and modeling of P-type electrosensory afferent responses to amplitude modulations in a wave-type electric fish

The first stage of information processing in the electrosensory system involves the encoding of local changes in transdermal potential into trains of action potentials in primary electrosensory afferent nerve fibers. To develop a quantitative model of this encoding process for P-type (probability-coding) afferent fibers in the weakly electric fish Apteronotus leptorhynchus, we recorded single unit activity from electrosensory afferent axons in the posterior branch of the anterior lateral line nerve and analyzed responses to electronically generated sinusoidal amplitude modulations of the local transdermal potential. Over a range of AM frequencies from 0.1 to 200 Hz, the modulation transfer function of P-type afferents is high-pass in character, with a gain that increases monotonically up to AM frequencies of 100 Hz where it begins to roll off, and a phase advance with a range of 15–60 degrees. Based on quantitative analysis of the observed gain and phase characteristics, we present a computationally efficient model of P-type afferent response dynamics which accurately characterizes changes in afferent firing rate in response to amplitude modulations of the fish's own electric organ discharge over a wide range of AM frequencies relevant to active electrolocation. Accepted: 14 June 1997     

Synthesis of Dinucleoside Boranophosphates by a Boranophosphotriester Approach

Abstract

Dinucleoside boranophosphates including four kinds of nucleobases were synthesized by a boranophosphotriester method in good yields. In the present boranophosphotriester method, side-reactions at the nucleobases, which caused by a borane reagent, were completely avoided.     

Different Binding Modes of Spermine to A-T and G-C Base Pairs Modulate the Bending and Stiffening of the DNA Double Helix

Abstract

The influence of base composition (and sequence) on the process of interaction between synthetic polynucleotides and spermine, has been investigated using ultraviolet (including second derivative) spectroscopy, and electric dichroism.

Different binding modes of spermine to poly(dG-dC) as compared to A-T containing polynucleotides, were evidenced. An interaction with the N7 and 06 of guanine is probably partially involved in the former case while simple electrostatic interaction with the phosphate groups would dominate in the latter.

In the intermediate binding range (spermine over DNA phosphate molar ratios Sp/P of the order of 0.1 to 0.2), the complexes with poly(dA) · poly(dT) and those with poly(dA-dT) displayed an important contribution of a permanent dipole moment to the orientation mechanism, as detected by the application of bipolar pulses in electric dichroism experiments. Just prior to precipitation (at Sp/P slightly larger than 0.3), these polynucleotides show electric dichroism and relaxation times characteristics corresponding to toroidal particles formation resulting from a bending of their chains. This implies asymmetric binding to phosphate sites on A-T containing polynucleotides. At low Sp/P ratios, spermine induced a stiffening of poly (dG-dC). No influence of spermine on the orientation mechanism of this polynucleotide was detected for Sp/P values ranging from zero to 0.35. The spermine-induced bending of A-T rich regions thus appears to be essential for DNA condensation into toroidal particles.     

Sequence specific hydrogen bond of DNA with denaturants affects its stability: Spectroscopic and simulation studies

BackgroundSeveral different small molecules have been used to target the DNA helix in order to treat the diseases caused by its mutation. Guanidinium(Gdm⁺) and urea based drugs have been used for the diseases related to central nervous system, also as the anti-inflammatory and chemotherapeutic agent. However, the role of Gdm⁺ and urea in the stabilization/destabilization of DNA is not well understood.MethodsSpectroscopic techniques along with molecular dynamics (MD) simulation have been performed on different sequences of DNA in the presence of guanidinium chloride (GdmCl) and urea to decode the binding of denaturants with DNA and the role of hydrogen bond with the different regions of DNA in its stability/destability.Results and conclusionOur study reveals that, Gdm⁺ of GdmCl and urea both intrudes into the groove region of DNA along with the interaction with its phosphate backbone. However, interaction of Gdm⁺ and urea with the nucleobases in the groove region is different. Gdm⁺ forms the intra-strand hydrogen bond with the central region of the both sequences of DNA whereas inter-strand hydrogen bond along with water assisted hydrogen bond takes place in the case of urea. The intra-strand hydrogen bond formation capability of Gdm⁺ with the nucleobases in the minor groove of DNA decreases its groove width which probably causes the stabilization of B-DNA in GdmCl. In contrast, the propensity of the formation of inter-strand hydrogen bond of urea with the nucleobases in the groove region of DNA without affecting the groove width destabilizes B-DNA as compared to GdmCl. This study depicts that the opposite effect of GdmCl and urea on the stability is a general property of B-DNA. However, the extent of stabilization/destabilization of DNA in Gdm⁺ and urea depend on its sequence probably due to the difference in the intra/inter-strand hydrogen bonding with different bases present in both the sequences of DNA.General significanceThe information obtained from this study will be useful for the designing of Gdm⁺ based drug molecule which can target the DNA more specifically and selectively.     

Impact of the Doping Method on Conductivity and Thermopower in Semiconducting Polythiophenes

The development of organic semiconductors for use in thermoelectrics requires the optimization of both their thermopower and electrical conductivity. Here two fundamentally different doping mechanisms are used to investigate the thermoelectric properties of known high hole mobility polymers: poly 3‐hexylthiophene (P3HT), poly(2,5‐bis(3‐tetradecylthiophen‐2‐yl)thieno[3,2‐b]thiophene) (PBTTT‐C₁₄), and poly(2,5‐bis(thiphen‐2‐yl)‐(3,7‐diheptadecantyltetrathienoacene)) (P2TDC₁₇‐FT4). The small molecule tetrafluorotetracyanoquinodimethane (F₄TCNQ) is known to effectively dope these polymers, and the thermoelectric properties are studied as a function of the ratio of dopant to polymer repeat unit. Higher electrical conductivity and values of the thermoelectric power factor are achieved by doping with vapor‐deposited fluoroalkyl trichlorosilanes. The combination of these data reveals a striking relationship between thermopower and conductivity in thiophene‐based polymers over a large range of electrical conductivity that is independent of the means of electrical doping. This relationship is not predicted by commonly used transport models for semiconducting polymers and is demonstrated to hold for other semiconducting polymers as well.     

Comparison of gas phase intrinsic properties of cytosine and thymine nucleobases with their O-alkyl adducts: different hydrogen bonding preferences for thymine versus O-alkyl thymine

In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O⁴-methylthymine, O²-methylcytosine and O²-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair’s hydrogen bonding properties, of these molecules with those in the normal nucleobases thymine and cytosine. The results are of interest for chemical reasons and also possibly for biological purposes since biological media can be quite non-polar. Furthermore, we found that N1-H of O⁴-methylthymine is less acidic than N1-H of thymine, suggesting that alkyl DNA glycosylase enzyme cannot discriminate this damaged nucleobase from a normal thymine nucleobase. This result indicates that the conjugated base anion of O⁴-methylthymine would be a worse leaving group and O⁴-methylthymine is repaired in genome by demethylation rather than enzyme-catalyzed excision at N1.     

Convenient Synthesis of Oligodeoxynucleotides Containing 2′-Deoxy-6-thioinosine

Abstract

A facile synthesis of oligodeoxynucleotides (ODN) containing 2′-deoxy-6-thioinosine (dI^6S) based on the convertible nucleoside O6-phenyl-2′-deoxyinosine is presented. After standard solid-phase DNA synthesis and removal of the cyanoethyl protecting groups with DBU treatment with aqueous sodium hydrogen sulfide introduces the sulfur functionality, deprotects the other nucleobases and cleaves the ODN from the solid support in a one-pot reaction. In addition, the extinction coefficient of 2′-deoxy-6-thioinosine is determined by enzymatic fragmentation of the resulting ODN in the presence of adenosine deaminase.     

Conformational Analysis of 3′-Deoxyribonucleosides using 1D-Noe Difference Spectroscopy

Abstract

The results of PMR studies on 3′Deoxyribo nucleosides (1a-d) reveals that the sugar puckering is predominantly in N state with g⁺ conformation of the 5′-CH₂OH group. Except in 1a, nucleobases in other nucleosides favour anti conformation.