Exploiting the optical sensing of fluorophore-tagged DNA nucleobases on hexagonal BN and Al-doped BN sheets: a computational study.

Hexagonal boron nitride (h-BN) sheets possess high fluorescence quenching ability and high affinity towards DNA/RNA, and they can be used as a sensing platform for rapid detection. We report the absorption and emission properties of DNA nucleobases such as adenine (A), cytosine (C), guanine (G), and thymine (T) tagged with benzoxazole on h-BN and aluminium-doped h-BN (Al_hBN) sheets. The binding affinity of studied nucleobases on h-BN sheets at the M062X/6-31G* level of theory showed the following adsorption trend: G ≥ T ≥ A > C, which is in good agreement with the previous results. The calculated stability trend of nucleobases on the Al_hBN sheet follows as C > G > A > T at the same level of theory. The physically adsorbed behavior of nucleobases to h-BN sheets was confirmed by the non-covalent interactions (NCIs) and the total density of states (TDOS) plots. The NCI results indicated that van der Waals interactions contribute significantly to the adsorption of nucleobases on h-BN sheets. Atoms in molecules (AIM) calculations revealed the electrostatic interactions between nucleobases and the Al_hBN sheet. The quenching phenomenon of nucleobase-tagged fluorophores on h-BN and Al_hBN sheets was investigated by TD-DFT calculations using the same level of theory. The thymine-tagged fluorophore upon adsorption to the pristine h-BN sheet was found to be blue-shifted (∼43 nm); however, the guanine-tagged fluorophore with Al_hBN showed a remarkable difference from other nucleobase-tagged fluorophores in the absorption and emission spectrum. Guanine-tagged fluorophores showed a smaller blue shift (∼7 nm) in the absorption spectrum; however, it showed a larger red shift (∼55 nm) than the other nucleobase-tagged fluorophores on Al_hBN sheets and can be useful in recognizing a sequence-specific phenomenon as a fluorescent biosensor of DNA and RNA to ascertain the presence of such nucleobases.

Recyclable Functionalized Material for Sensitive Detection and Exceptional Sorption of Hexavalent Chromium and Permanganate Ions with Biosensing Applications.

Environmental remediation with a single platform for selective sensing and removal of toxic analytes with recyclability of the material has always been a desirable system for sustainability. However, materials comprising all the abovementioned advantages are rarely known for oxoanions. We herein developed a fluorogenic napthalimide-based functionalized mesoporous silica material (SiO2@NBDBIA) as a signaling and remediation system for oxoanions (CrO42-, Cr2O72-, and MnO4-) from a pool of several anions. The fluorescence quenching of the SiO2@NBDBIA material in the presence of CrO42-, Cr2O72-, and MnO4- ions gives the limit of detection (LOD) values of 6.23, 25.2, and 20.32 ppb, respectively, which are well below the maximum contaminant level demarcated by the United States Environmental Protection Agency. The maximum adsorption capacities of the material for the abovementioned oxoanions are found to be 352, 363, and 330 mg/g, respectively, which are well above those mentioned in the literature reports. Contrary to the literature-dominated irreversible ion-exchange mechanism, the reversible hydrogen-bonded binding of the material with the oxoanions leads to the recyclability of the material easily, which is very rare in the literature. The DFT calculations were performed to examine the interactions between the material and oxoanions. For real applications, this material was also used as a fluorescence probe to detect these oxoanions in the actual water samples, and more interestingly, used as a biosensing probe for these oxoanions in the living organism Artemia salina through fluorescence imaging. Thus, the SiO2@NBDBIA material is a unique example of recyclable material for detecting and remediating oxoanions.

Role of the backbone of nucleic acids in the stability of Hg2+-mediated canonical base pairs and thymine-thymine mispair: a DFT study.

Metal-mediated base pairs have attracted attention in nucleic acid research and molecular devices. Herein, we report a systematic computational study on Hg2+-mediated base pairs with canonical and TT mispair dimers. The computed results revealed that the model DTTD (thymine-thymine with DNA backbone) mispair is more energetically favored than the canonical base pairs. The DTTTTD mispair dimer is more energetically stable by ∼36.0 kcal mol-1 than the corresponding canonical DATGCD base pairs. The Hg⋯Hg metallophilic interaction was observed with the DTTTTD mispair and not the canonical base pairs. The DATGCD (adenine: thymine, guanine: cytosine) base pairs were significantly perturbed upon interaction with the mercury ion; however, the TTTT mispairs were aligned upon interaction with the Hg2+ ion. The DTTTTD mispair adopts a B-type conformation with proper alignment of its nucleobases along the axis. The MESP calculations showed a larger V min value for the interacting nitrogen centers of the thymine nucleobase, supporting its stronger binding with the Hg2+ ion compared to the other nucleobases. The role of the backbone is crucial in nucleic acids to determine many useful properties, and PNAs have been exploited extensively in the literature. Thus, this study was further extended to metal-mediated PNA-containing dimer mispairs such as DTTTTP (thymine-thymine dimer model with hybrid DNA and PNA backbone) and PTTTTP (thymine-thymine dimer model with PNA backbone). The calculated results showed that the PTTTTP PNA mispair is thermodynamically more stable than the canonical dimers. The enthalpy calculated for DTTTTD and PTTTTP at the B3LYP-D3/6-31G* level of theory showed that PTTTTP is ∼3.0 kcal mol-1 more stable than DTTTTD. The metallophilic interaction of Hg2+ ions in the PTTTTP mispair was not observed; however, the metal ions interact with the nitrogen of the thymine bases, presumably enhancing the stability of this mispair by strong electrostatic interactions. These interactions arise due to the P-type conformations of PNAs, which lack metallophilic interactions between the metal ions and can adopt a wider and more unwounded helix. The interaction of the mispair dimers with the explicit water molecules also showed a similar stability trend to that observed with the implicit solvation model. The metallophilic interaction (Hg⋯Hg) was found to be conserved in DTTTTD. The AIM analysis performed for these dimers revealed that the interactions are primarily electrostatic in nature. The UV-vis absorption spectra of the mispair systems calculated at the B3LYP-D3/6-31G* level of theory using the TD-DFT method in the aqueous phase suggested that the absorption maximum is located at a longer wavelength in the case of PTTTTP compared to the corresponding DTTTTD and can be a signature to identify the formation of metal-mediated nucleic acid systems.

Role of backbones on the interaction of metal ions with deoxyribonucleic acid and peptide nucleic acid: A DFT study.

Metal ion interaction with deoxyribonucleic acid and peptide nucleic acid were studied using B3LYP-D3/6-311++g(d,p)//B3LYP/6-31 + G(d) level of theory in aqueous phase employing polarized continuum (PCM) model. This study reports the role of backbones on deoxyribonucleic acid and peptide nucleic acid for complexation with different metal ions. The systematic study performed with DFT calculations reveals that central binding (Type-4) shows the strongest binding compared to the other binding modes because of the involvement of the backbone as well as the nitrogenous bases. The charged backbone of DNA nucleotides contributes significantly towards binding with the metal ions. The deoxyguanosine monophosphate (dGMP) clearly indicates the strongest binding upon complexation with Mg2+ (-49.6 kcal/mol), Zn2+ (-45.3 kcal/mol) and Cu2+ (-148.4 kcal/mol), respectively. The neutral backbone of PNA also assists to complex the metal ions with PNA nucleotides. The Mg2+ and Cu2+ prefer to bind with the PNA-Cytosine (-32.9 kcal/mol & -132.9 kcal/mol) in central binding mode (type-4). PNA-Adenine-Zn2+ (-29.1 kcal/mol) is the preferred binding mode (type-4) compared to other modes of interaction for this metal ion with PNA-Adenine nucleotide. The Cu2+ ion showed the superior complexation ability with deoxyribonucleic acid and peptide nucleic acid compared to Mg2+ and Zn2+ ions. The cation-π complexation with the bases of nucleotides was also obtained with Cu2+ ion. The AIM (atoms in molecule) theory has been applied to examine the nature of the interaction of Mg2+, Zn2+, and Cu2+ ion to the deoxyribonucleic acid and peptide nucleic acid. The alkaline earth metal, Mg2+ ion shows electrostatic nature while interaction with deoxyribonucleic acid and peptide nucleic acid, however, the transition metal ions (Zn2+, Cu2+) showed partly covalent nature as well with deoxyribonucleic acid and peptide nucleic acid. The optical properties calculated for the binding of metal ions with deoxyribonucleic acid and peptide nucleic acid showed a diagnostic signature to ascertain the interaction of metal ions with such nucleotides. Cu2+ ion showed larger red shifts in the absorption spectrum values upon complexation with the DNAs and PNAs. The calculated results suggest that such metal ions would prefer to bind with the DNA compared to PNA in DNA-PNA duplexes. The preference for the binding of metal ions with DNA nucleotides is largely attributed to the contribution of charged backbones compared to the neutral PNA backbones.

Estimation of bisulfate in edible plant foods, dog urine, and drugs: picomolar level detection and bio-imaging in living organisms.

In order to explore the properties of any species in solution, the actual, i.e. equilibrium concentration of the free species should be taken into account. Researchers have not paid attention to the deprotonation equilibrium between HSO4- and SO42- while probing bisulfate ion. In this study, we have addressed this concern and developed two zwitterions, CG (coumarin-integrated glycine) and CA (coumarin-integrated alanine), for the selective detection of HSO4- at a picomolar level (50 to 325 pM) with very high binding affinity (∼108 M-1) in pure water at physiological pH. The principle of HSO4- recognition was established via UV-vis and fluorescence techniques. DFT calculations suggested that the H-bonding interactions between the probes and HSO4- are the driving force for this unforeseen selectivity. The membrane penetration ability and nontoxicity of CG/CA enable them to function as staining agents in living brine shrimps and bacteria. The use of these probes for the estimation of HSO4- in various day-to-day edible foods and drugs along with urine samples is unprecedented. The significance and novelty of this study lies in the application and development of assays for estimating bisulfate in several real-world samples that are predominantly aqueous in nature, which are the first of their kind.

Probing the Structural and Electronic Effects on the Origin of π-Facial Stereoselectivity in 1-Methylphosphole 1-Oxide Cycloadditions and Cyclodimerization.

We have examined the π-facial stereoselectivity in the Diels-Alder reactions of phosphole oxides computationally. The experimentally observed syn-cycloadditions have been rationalized with the Cieplak model and distortion-interaction model. The natural bond orbital analysis suggests that the hyperconjugative interactions are energetically preferred between the antiperiplanar methyl group present in the -P=O unit and the developing incipient (-C-C-) bond in syn-adducts in accordance with the Cieplak model. The distortion-interaction analysis carried out for syn and anti transition states of Diels-Alder reactions of 1-substituted phosphole 1-oxide with different dienophiles reveals that the syn selectivity is favored by distortions and interaction energies compared with the anti selectivity. The formation of a syn adduct is also stabilized by the πCC-σ*PO orbital interaction, and the repulsive n-π interaction destabilizes the anti adduct that leads to the 7.0 kcal/mol thermodynamic preference for the former adduct. Furthermore, the distortion-interaction model rationalizes the formation of stereospecific products in these Diels-Alder reactions, which however is not explicable with the much-debated Cieplak model.