Dichroism Spectral Changes Research Articles

A DNA‐Based Plasmonic Nanodevice for Cascade Signal Amplification

AbstractHere, we describe a DNA circuit‐aided, origami nanodevice‐based plasmonic system, which performs DNA‐regulated, cascade amplification of faint chemical/biological signals. In this system, two gold‐nanorods (GNRs) are co‐assembled onto a DNA lock‐containing, tweezer‐like DNA origami template. Logic circuits serve as recognition and amplification elements for specific messengers, producing DNA keys for driving conformational changes of the plasmonic nanodevices. In the presence of input signals including nucleic acids, adenosines, chiral tyrosinamides or specific receptors expressed by tumor cells, the plasmonic nanodevices can be activated to perform dynamic structural motions, reporting robust responses via plasmonic circular dichroism (CD) spectral changes. This DNA nanodevice‐based system provides a different design to enrich the strategies for constructing synthetic nanomachines, enabling the customized bottom‐up nanostructure construction for sensitive biological signaling.

A DNA-Based Plasmonic Nanodevice for Cascade Signal Amplification.

Here, we describe a DNA circuit-aided, origami nanodevice-based plasmonic system, which performs DNA-regulated, cascade amplification of faint chemical/biological signals. In this system, two gold-nanorods (GNRs) are co-assembled onto a DNA lock-containing, tweezer-like DNA origami template. Logic circuits serve as recognition and amplification elements for specific messengers, producing DNA keys for driving conformational changes of the plasmonic nanodevices. In the presence of input signals including nucleic acids, adenosines, chiral tyrosinamides or specific receptors expressed by tumor cells, the plasmonic nanodevices can be activated to perform dynamic structural motions, reporting robust responses via plasmonic circular dichroism (CD) spectral changes. This DNA nanodevice-based system provides a different design to enrich the strategies for constructing synthetic nanomachines, enabling the customized bottom-up nanostructure construction for sensitive biological signaling.

Enantioselective assembly and recognition of heterochiral porous organic cages deduced from binary chiral components.

Chiral recognition and discrimination is not only of significance in biological processes but also a powerful method to fabricate functional supramolecular materials. Herein, a pair of heterochiral porous organic cages (HPOC-1), out of four possible enantiomeric products, with mirror stereoisomeric crystal structures were cleanly prepared by condensation occurring in the exclusive combination of cyclohexanediamine and binaphthol-based tetraaldehyde enantiomers. Nuclear magnetic resonance and luminescence spectroscopy have been employed to monitor the assembly process of HPOC-1, revealing the clean formation of heterochiral organic cages due to the enantioselective recognition of (S,S)-binaphthol towards (R,R)-cyclohexanediamine derivatives and vice versa. Interestingly, HPOC-1 exhibits circularly polarized luminescence and enantioselective recognition of chiral substrates according to the circular dichroism spectral change. Theoretical simulations have been carried out, rationalizing both the enantioselective assembly and recognition of HPOC-1.

Hydrostatic Pressure-Controllable Chiroptical Properties of Chiral Perylene Bisimide Dyes: A Chiral Aggregation Case

Hydrostatically pressurized spectroscopic and lifetime decay analyses of optically active perylene bisimides were demonstrated in the pressure range of 0.1-320 MPa to show a π-stacked aggregation. The hydrostatic pressure-induced excitation and circular dichroism spectral changes of the fluorescence perylene dye enabled us to differentiate the slight pressure-sensitive aggregates. This work will lead to a new strategy for creating a pressure-responsive supramolecular polymerization material.

Thermal E/ Z Isomerization in First Generation Molecular Motors.

Determination of a thermal E/ Z isomerization barrier of first generation molecular motors is reported. Stable ( E)-1a directly converts to stable ( Z)-1c without photochemical E/ Z isomerization. The activation Gibbs energy of the isomerization was determined to be 123 kJ mol-1 by circular dichroism spectral changes. Density functional theory calculations show that ( Z)-1c is ∼11.4 kJ mol-1 more stable than ( E)-1a.

Switch‐ON Near IR Fluorescent Dye Upon Protonation: Helically Twisted Bis(Boron Difluoride) Complex of π‐Extended Corrorin

A novel helically twisted π-extended corrorin derivative having two boron dipyrrin (BODIPY) moieties at the periphery, a BODIPY DYEmer (6-BF2 ) cross-bridged with π-conjugated dipyrrinylidene unit, was synthesized and characterized. The neutral 6-BF2 is nonfluorescent due to the internal photoinduced charge transfer (CT) character in the excited state as inferred from the femtosecond transient absorption spectroscopy. However, upon protonation, the CT process is suppressed and the species H6-BF2+ becomes near infrared (IR) emissive. With the aid of rigid helical conformations in 6-BF2 , the helical isomers (P- and M-forms) were resolved and their chiroptical property was investigated. The distinct circular dichroism (CD) spectral changes of the enantiomers were observed in the presence of acids, which demonstrates that 6-BF2 can be utilized for potential acid-responsive chiroptical materials.

Effects of cytotoxic cis- and trans-diammine monochlorido platinum(II) complexes on selenium-dependent redox enzymes and DNA

Here we present the preparation of 14 pairs of cis- and trans-diammine monochlorido platinum(II) complexes, coordinated to heterocycles (i.e., imidazole, 2-methylimidazole and pyrazole) and linked to various acylhydrazones, which were designed as potential inhibitors of the selenium-dependent enzymes glutathione peroxidase 1 (GPx-1) and thioredoxin reductase 1 (TrxR-1). However, no inhibition of bovine GPx-1 and only weak inhibition of murine TrxR-1 was observed in in vitro assays. Nonetheless, the cis configured diammine monochlorido Pt(II) complexes exhibited cytotoxic and apoptotic properties on various human cancer cell lines, whereas the trans configured complexes generally showed weaker potency with a few exceptions. On the other hand, the trans complexes were generally more likely to lack cross-resistance to cisplatin than the cis analogues. Platinum was found bound to the nuclear DNA of cancer cells treated with representative Pt complexes, suggesting that DNA might be a possible target. Thus, detailed in vitro binding experiments with DNA were conducted. Interactions of the compounds with calf thymus DNA were investigated, including Pt binding kinetics, circular dichroism (CD) spectral changes, changes in DNA melting temperatures, unwinding of supercoiled plasmids and ethidium bromide displacement in DNA. The CD results indicate that the most active cis configured pyrazole-derived complex causes unique structural changes in the DNA compared to the other complexes as well as to those caused by cisplatin, suggesting a denaturation of the DNA structure. This may be important for the antiproliferative activity of this compound in the cancer cells.

Nucleotide Binding in an Engineered Recombinant Ca2+-ATPase N-Domain.

A recombinant Ca2+-ATPase nucleotide binding domain (N-domain) harboring the mutations Trp552Leu and Tyr587Trp was expressed and purified. Chemical modification by N-bromosuccinimide and fluorescence quenching by acrylamide showed that the displaced Trp residue was located at the N-domain surface and slightly exposed to solvent. Guanidine hydrochloride-mediated N-domain unfolding showed the low structural stability of the α6-loop-α7 motif (the new Trp location) located near the nucleotide binding site. The binding of nucleotides (free and in complex with Mg2+) to the engineered N-domain led to significant intrinsic fluorescence quenching (ΔFmax ∼ 30%) displaying a saturable hyperbolic pattern; the calculated affinities decreased in the following order: ATP > ADP = ADP-Mg2+ > ATP-Mg2+. Interestingly, it was found that Ca2+ binds to the N-domain as monitored by intrinsic fluorescence quenching (ΔFmax ∼ 12%) with a dissociation constant (Kd) of 50 μM. Notably, the presence of Ca2+ (200 μM) increased the ATP and ADP affinity but favored the binding of ATP over that of ADP. In addition, binding of ATP to the N-domain generated slight changes in secondary structure as evidenced by circular dichroism spectral changes. Molecular docking of ATP to the N-domain provided different binding modes that potentially might be the binding stages prior to γ-phosphate transfer. Finally, the nucleotide binding site was studied by fluorescein isothiocyanate labeling and molecular docking. The N-domain of Ca2+-ATPase performs structural dynamics upon Ca2+ and nucleotide binding. It is proposed that the increased affinity of the N-domain for ATP mediated by Ca2+ binding may be involved in Ca2+-ATPase activation under normal physiological conditions.

Conformational variability of recombination R-triplex formed by the mammalian telomeric sequence

Alignment of three nucleic acids strands, in which the third strand is identical to one of the DNA duplex strands, occurs in various cellular systems. In the case of telomeric t-loops, recognition between the DNA duplex and the homologous single strand is likely to be mediated by proteins through formation of the transient recombination-type R-triplex. Earlier, using 2-aminopurine as a fluorescent reporting base, we evaluated the thermodynamic characteristics of intramolecular R-triplex formed by a mixed nucleotide sequence. Here, we used this approach to explore a propensity of the telomeric TTAGGG repeat to form the R-triplex. The circular dichroism spectral changes detected upon formation of the R-triplex suggest that this process is accompanied by specific conformational changes in DNA, including a local destabilization of the target duplex next to a GGG run revealed by the fluorescence of the reporting 2-aminopurine base. Surprisingly, stability of the R-triplex formed by telomeric sequence depends strikingly on the counter ion, being higher for Na+ than for Li+. Taken together these findings indicate a significant conformational variability of telomeric DNA in the context of recombination-type R-triplex, a phenomenon of possible biological relevance.

Folding and Hydrodynamics of a DNA i-Motif from the c-MYC Promoter Determined by Fluorescent Cytidine Analogs

The four-stranded i-motif (iM) conformation of cytosine-rich DNA has importance to a wide variety of biochemical systems that range from their use in nanomaterials to potential roles in oncogene regulation. The iM structure is formed at slightly acidic pH, where hemiprotonation of cytosine results in a stable C-C+ basepair. Here, we performed fundamental studies to examine iM formation from a C-rich strand from the promoter of the human c-MYC gene. We used a number of biophysical techniques to characterize both the hydrodynamic properties and folding kinetics of a folded iM. Our hydrodynamic studies using fluorescence anisotropy decay and analytical ultracentrifugation show that the iM structure has a compact size in solution and displays the rigidity of a double strand. By studying the rates of circular dichroism spectral changes and quenching of fluorescent cytidine analogs, we also established a mechanism for the folding of a random coil oligo into the iM. In the course of determining this folding pathway, we established that the fluorescent dC analogs tC° and PdC can be used to monitor individual residues of an iM structure and to determine the pKa of an iM. We established that the C-C+ hydrogen bonding of certain bases initiates the folding of the iM structure. We also showed that substitutions in the loop regions of iMs give a distinctly different kinetic signature during folding compared with bases that are intercalated. Our data reveal that the iM passes through a distinct intermediate form between the unfolded and folded forms. Taken together, our results lay the foundation for using fluorescent dC analogs to follow structural changes during iM formation. Our technique may also be useful for examining folding and structural changes in more complex iMs.

Synthesis of chiral inducers having double stereogenic centers for electrochemical polymerization in cholesteric liquid crystal medium

An enantiomeric pair of chiral inducers with double chiral carbons was synthesized by a simple three-step reaction strategy. The process affords the chiral inducers with good yield, high enantiomeric excess, and good compatibility with nematic liquid crystal. Addition of a small amount of the chiral inducers thus synthesized in this study produced cholesteric architecture. Electrochemical polymerization in the asymmetric liquid crystal environment affords chiroptically active polymers as atropisomers. The electrochemical polymerization under magnetic field of 4T affords polymer films with linear dichroism. The polymers exhibit a significant color change from dark-green in the oxidized state to light-green in the reduced state. The redox process of the polymer films in an electrolyte provides a reversible absorption, circular dichroism, and linear dichroism spectral changes.

Cyclodextrin‐Assisted Synthesis of a Metallosupramolecular Terbium(III) Polymer and Its Fluorescence Properties and Chiral Recognition

Hold and connect! Inclusion of a bridging ligand into cyclodextrin (CD), followed by the addition of Tb(III) leads to a polyrotaxane-type metallosupramolecular polymer (see figure, L=4,4'-biphenyldicarboxylic acid). This polymer can recognize chirality and differentiate enantiomers by fluorescence and circular dichroism spectral changes.

Study of the Mode and Efficiency of DNA Binding in the Damage Induced by Photoactivated Water Soluble Porphyrins

We have investigated the DNA binding interactions and in vitro photoactivated DNA damage induced by a neutral water soluble porphyrin derivative 5,10,15,20-tetrakis(2,4,6-trihydroxyphenyl)porphyrin (TTHPP) and its zinc derivative 5,10,15,20-tetrakis(2,4,6-trihydroxyphenyl)porphyrinato zinc(II) (Zn-TTHPP) upon visible light irradiation through various spectroscopic techniques and employing repair endonucleases. These porphyrin derivatives exhibited high affinity toward DNA through groove binding interactions as evidenced through the UV-vis absorption, emission, circular dichroism spectral and viscosity changes. Interestingly, the free base porphyrin derivative, TTHPP generated efficient singlet oxygen mediated DNA damage sensitive to formamidopyrimidine-DNA glycosylase (Fpg protein), when compared with its metal derivative and to the well-known photosensitizer, hematoporphyrin. These results provide direct evidence for the role of DNA binding mode as well as extent of interactions with DNA in the efficiency of photoactivated DNA damage induced by the neutral porphyrins, which are believed to be the ideal candidates for photodynamic therapeutic applications.

Four‐peptide‐nanotube bundle formation by self‐assembling of cyclic tetra‐β‐peptide using g‐quartet motif

A hydrophilic cyclic tetra-β-peptide having guanine at the side chain (CPG) was synthesized to construct a four-peptide-nanotube bundle with the formation of guanine quadruplex (G-quartet). CPG was so soluble in water that molecular association of CPG was very limited in water. However, in the presence of potassium ion, circular dichroism spectral change showed initial molecular association due to the G-quartet formation followed by a slow growth into peptide nanotubes. Transmission electron microscope observation and electron diffraction analysis revealed that CPG self-assembled into a four-peptide-nanotube bundle with a uniform diameter of 7-8 nm.

Phosphate derivative-induced supramolecular assembly and NIR-emissive behaviour of alkynylplatinum(ii) terpyridine complexes for real-time monitoring of enzymatic activities

Polyanionic phosphate derivatives, ATP and phosphopeptide, were shown to induce the supramolecular assembly of cationic alkynylplatinum(II) terpyridine complexes via the formation of metal–metal and π–π stacking interactions with significant UV-vis, near-infrared (NIR) emission and circular dichroism spectral changes. The induced supramolecular assembly behaviours of these platinum(II) complexes were shown to be sensitive towards microenvironmental changes as well as the negative charge densities of the phosphate derivatives, providing the complexes with the capability of distinguishing the target substrates from their respective metabolic products by sole structural differences. Through the monitoring of the NIR emission spectral changes that are dependent on the extent of the assembly/disassembly of the platinum(II) complexes, the conversion of the target substrates catalyzed by ATPase, v-Src kinase and alkaline phosphatase could be signaled and probed on a real-time basis. The kinetic parameters of the enzymatic activities have also been determined.

Multi-spectroscopic DNA interaction studies of sunset yellow food additive

The use of food dyes is at least controversial due to their essential role. Synthetic color food additives occupy an important place in the food industry. Moreover many of them have been related to health problems mainly in children that are considered the most vulnerable group. The purpose of this work is to present spectrophotometric methods to analyze the interaction of native calf thymus DNA (CT-DNA) with sunset yellow (SY) at physiological pH. Considerable hyperchromism and no red shift with an intrinsic binding constant of 7 × 10(4 )M(-1) were observed in UV absorption band of SY. Binding constants of DNA with complex were calculated at different temperatures. Slow increase in specific viscosity of DNA, induced circular dichroism spectral changes, and no significant changes in the fluorescence of neutral red-DNA solutions in the presence of SY suggest that this molecule interacts with CT-DNA via groove binding mode. Furthermore, the enthalpy and entropy of the reaction between SY and CT-DNA showed that the reaction is exothermic and enthalpy favored (∆H = -58.19 kJ mol(-1); ΔS = -274.36 kJ mol(-1) ) which are other evidences to indicate that van der Waals interactions and hydrogen bonding are the main running forces in the binding of the mentioned molecule and mode of interaction with DNA.

Anion-Controlled Circular Dichroism Spectral Changes in Hg2+ Complexes with a Chiral Bidentate Ligand

Anion-controlled circular dichroism (CD) spectral changes in Hg(2+) complexes with a chiral bidentate ligand are reported. Although the Hg(CF(3)SO(3))(2) and Hg(CF(3)CO(2))(2) complexes with (R)-(-)-1-(naphthalen-1-yl)-N,N-bis(pyridin-4-ylmethyl)ethanamine, (R)-(-)-1, show significant CD spectral changes, no CD spectral changes were observed in the HgCl(2), HgBr(2), Hg(CN)(2), or Hg(CH(3)CO(2))(2) complexes. X-ray analysis indicates that both the (R)-(-)-1-Hg(CF(3)SO(3))(2) and (R)-(-)-1-HgCl(2) complexes form a coordination polymer and a discrete 2:3 [=(R)-(-)-1/HgCl(2)] complex with a figure-eight structure. X-ray crystallography revealed that (i) the Hg-Hg distances bridged by anions vary depending on the anions used and (ii) a coordination polymer cannot be formed when the Hg-Hg distances are too short. Therefore, the formation of a coordination polymer is required to give the observed significant CD spectral changes.

Carbonyl side-chain of catechol compounds is a key structure for the suppression of copper-associated oxidative DNA damage in vitro

Catechol is possibly carcinogenic to humans (International Agency for Research on Cancer, IARC). The key mechanism could include its oxidative DNA-damaging effect in combination with reductive–oxidative metals like Cu. We found that DNA damage was suppressed by introducing an α-carbonyl group to catechol at C4-position to produce carbonyl catechols. During the oxidative DNA-damaging process, catechols but not carbonyl catechols were oxidized to o-quinone; however, coexisting Cu(II) was reduced to Cu(I). Carbonyl catechols were possibly arrested at the oxidation step of semiquinones in the presence of Cu(II). Cu(I)-binding to DNA was stronger than Cu(II)-binding, on the basis of the circular dichroism spectral change. None of the carbonyl catechols induced such change, suggesting sequestration of Cu(I) from DNA. Solid-phase extraction experiments and spectrophotometric analyses showed the formation of semiquinone chelates with Cu(I). Thus, chelate formation could explain the suppression mechanism of the Cu–catechol-dependent DNA damage by terminating the reduction–oxidation cycle. Structural modifications such as introducing an α-carbonyl group to catechol at C4-position would contribute to reducing the risk and improving industrial and medical potentials of aromatic/phenolic compounds sustaining our daily lives.

In vitro interaction between calf thymus DNA and Escherichia coli LPS in the presence of divalent cation Ca2+

With increasing addition of Escherichia coli LPS to calf thymus DNA, both dissolved in CaCl2, absorption maxima of DNA at 260 nm decreased gradually with the appearance of isosbastic points at both ends of spectra, which implied some binding between DNA and LPS. Hill plot of absorbance data showed that the binding interaction was positive cooperative in nature. For any fixed concentration of DNA and LPS, extent of interaction increased as concentration of CaCl2 was raised from 1.0 to 100 mM, signifying the electrostatic nature of the interaction, mediated through Ca2+ ion. Stepwise addition of EDTA, a chelating agent for divalent cations, to DNA-LPS bound complex gradually reversed the spectral shift with increase in absorbance at 260 nm, which implied opening up of the complex, that is, reversible nature of the interaction. Circular dichroism spectral changes of DNA by the addition of LPS indicated partial transition of DNA from B to A form. Isothermal titration calorimetric (ITC) study showed that the DNA-LPS binding was an exothermic and enthalpy-driven phenomenon. Moreover, in the presence of 100 mM CaCl2, binding constant of the interaction was found to be 2.6 x 10(4) M(-1) and 3.1 x 10(4) M(-1) from the analysis of Hill plot and ITC result, respectively. DNA-melting study showed that the LPS binding had increased the melting temperature of DNA, indicating more stabilization of DNA double helix. The binding of LPS to DNA made the complex resistant to digestion with endonucleases EcoRI and DNase I.

The Quadruplex−Duplex Structural Transition of Polyriboguanylic Acid

The vibrational infrared (IR) absorption and vibrational circular dichroism (VCD) spectral changes of polyriboguanylic acid (polyG) as a function of time, temperature and pH have been investigated to establish how changes in spectral features relate to the structural modifications of polyG. From the progression of IR and VCD spectral features with respect to time, it is observed that stabilization of the quadruplex structure at pH 6.4 (near-neutral environment) takes place within 5 days. This stabilization process is most clearly evidenced by a downshift of the carbonyl absorption band and the corresponding positive VCD couplet, from 1689 to approximately 1682 cm(-1) in time. Time-induced spectral modifications also indicated that, in an acidic environment (pH 3.1) and within a 5 day waiting period, polyG develops a duplex structure. An additional positive VCD couplet associated with an absorption band at 1589 cm(-1) is identified as a marker of the polyG duplex structure. From the progression of spectral features with respect to temperature at pH 6.4, it is found that heating induces structural changes that favor the formation of a duplex structure. This duplex structure, at pH 6.4, would not form at room temperature simply by the passage of time. When polyG is in an acidic environment (pH 3.1), heating accelerates the conversion to the duplex structure that could also be obtained with passage of time at that pH. On the basis of the comparison of experimental and quantum theoretical VCD spectra for polyG, the key spectral signature for the quadruplex form is considered to be a single positive VCD couplet, while the spectral signature for a duplex form is considered to contain an additional positive VCD couplet at a lower frequency.