In silico Complexes of Amino Acids and Diamondoids

We report on the specific interaction of a small diamond-like molecule, known as diamondoid, with single amino-acids forming nano/bio molecular complexes. Using time-dependent density-functional theory calculations we have studied two different relative configurations of three prototypical amino acids, phenylalanine, tyrosine, and tryptophan, with the diamondoid. The optical and charge-transfer properties of these complexes exhibit amino acid and topology specific features which can be directly utilized for in the direction of novel biomolecule detection schemes.     

Intermolecular Interactions in Photodamaged DNA from Density Functional Theory Symmetry‐Adapted Perturbation Theory

The intermolecular interactions of the photodamaged cyclobutane pyrimidine dimer (CPD) lesion with adjacent nucleobases in the native intrahelical DNA double strand are investigated at the level of density functional theory symmetry‐adapted perturbation theory (DFT‐SAPT) and compared to the original (or repaired) case with pyrimidines (TpT) instead of CPD. The CPD aggregation is on average destabilized by about 6 kcal mol^?1 relative to that involving TpT. The effect of destabilization is asymmetric, that is, it involves a single H‐bonding (Watson–Crick (WC) type) base‐pair interaction.     

Metal‐Ion Selectivity of Chemically Modified Uracil Pairs in DNA Duplexes

DNA duplexes containing 5‐modified uracil pairs (5‐bromo, 5‐fluoro, and 5‐cyanouracil) bind selectivity to metal ions. Their selectivity is sensitive to the pH value of the solution (see picture), as the acidities of the modified uracil bases vary according to the electron‐withdrawing properties of the substituents.

     

Identification of Compounds that Selectively Stabilize Specific G‐Quadruplex Structures by Using a Thioflavin T‐Displacement Assay as a Tool

Small molecules are used in the G‐quadruplex (G4) research field in vivo and in vitro, and there are increasing demands for ligands that selectively stabilize different G4 structures. Thioflavin T (ThT) emits an enhanced fluorescence signal when binding to G4 structures. Herein, we show that ThT can be competitively displaced by the binding of small molecules to G4 structures and develop a ThT‐displacement high‐throughput screening assay to find novel and selective G4‐binding compounds. We screened approximately 28 000 compounds by using three different G4 structures and identified eight novel G4 binders. Analysis of the structural conformation and stability of the G4 structures in presence of these compounds demonstrated that the four compounds enhance the thermal stabilization of the structures without affecting their structural conformation. In addition, all four compounds also increased the G4‐structure block of DNA synthesis by Taq DNA polymerase. Also, two of these compounds showed selectivity between certain Schizosaccharomyces pombe G4 structures, thus suggesting that these compounds or their analogues can be used as selective tools for G4 DNA studies.     

Probing DNA Mismatched and Bulged Structures by Using 19F NMR Spectroscopy and Oligodeoxynucleotides with an 19F‐Labeled Nucleobase

In this study, DNA local structures with bulged bases and mismatched base pairs as well as ordinary full‐matched base pairs by using ¹⁹F NMR spectroscopy with ¹⁹F‐labeled oligodeoxynucleotides (ODNs) were monitored. The chemical shift change in the ¹⁹F NMR spectra allowed discrimination of the DNA structures. Two types of ODNs possessing the bis(trifluoromethyl)benzene unit (F‐unit) at specified uridines were prepared and hybridized with their complementary or noncomplementary strands to form matched, mismatched, or bulged duplexes. By using ODN F1, in which an F‐unit was connected directly to a propargyl amine‐substituted uridine, three local structures, that is, full‐matched, G–U mismatch, and A‐bulge could be analyzed, whereas other structures could not be discriminated. A molecular modeling study revealed that the F‐unit in ODN F1 interacted little with the nucleobases and sugar backbone of the opposite strand because the linker length between the F‐unit and the uridine base was too short. Therefore, the capacity of ODN F1 to discriminate the DNA local structures was limited. Thus, ODN F2 was designed to improve this system; aminobenzoic acid was inserted between the F‐unit and uridine base so the F‐unit could interact more closely with the opposite strand. Eventually, the G‐bulge and T–U mismatch and the three aforementioned local structures could be discriminated by using ODN F2. In addition, the dissociation processes of these duplexes could be monitored concurrently by ¹⁹F NMR spectroscopy.     

Rational Design for Cooperative Recognition of Specific Nucleobases Using β‐Cyclodextrin‐Modified DNAs and Fluorescent Ligands on DNA and RNA Scaffolds

We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β‐cyclodextrin (β‐CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase‐specific heterocycle and an environment‐sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β‐CyD. Three reporter ligands, MNDS (naphthyridine–dansyl linked ligand), MNDB (naphthyridine–DBD), and DPDB (pyridine–DBD), were used for DNA and RNA probing with 3′‐end or 5′‐end modified β‐CyD – ODN conjugates. For the DNA target, the β‐CyD tethered to the 3′‐end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site ( MNDS and DPDB ). Meanwhile the β‐CyD on the 5′‐end of the ODN interacted with the fluorophore in the minor groove ( MNDB and DPDB ). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.     

Temperature‐Dependent Prediction of the Liquid Entropy of Ionic Liquids

Modeling of the temperature‐dependent liquid entropy of ionic liquids (ILs) with great accuracy using COSMO‐RS is demonstrated. The minimum structures of eight IL ion pairs are investigated and the entropy, calculated from ion pairs, is found to differ on average only 2 % from the available experimental values (119 data points). For calculations with single ions, the average error amounts to 2.6 % and stronger‐coordinating ions tend to give higher deviations. Additionally, the first parameterization of the standard liquid entropy for ILs is presented in the context of traditional volume‐based thermodynamics (S_l⁰=1.585 kJ mol^?1 K^?1 nm^?3?r_m³+14.09 J mol^?1 K^?1), which sheds light on the statistical treatment of ionic interactions. The findings provide the first direct access to accurate predictions of liquid entropies of ILs, which are tedious and time‐consuming to measure.     

Microarray‐Based Detection of Dye‐Labeled DNA by SERRS Using Particles Formed by Enzymatic Silver Deposition

The growing interest in DNA diagnostics is addressed today by microarrays with fluoresence detection. In our approach, we utilize spatially defined arrays of short oligonucleotides on a modified glass surface. Surface enhanced resonance Raman scattering (SERRS) is used to obtain molecularly specific spectra of the Raman‐active dye‐labeled DNA. Nanoparticles produced by enzymatic silver deposition are used as SERS‐active substrate. They grow directly on the modified oligonucleotides and only in the spatially defined areas on the chip. Furthermore, they potentially offer several advantages for SERS detection. The nanoparticles are characterized and their ability for use as SERS‐ and SERRS‐active substrate is estimated. Three different Raman‐active dyes are investigated for their potential for involvement in sequence specific DNA analysis.     

DNA Interaction with 17α‐Ethinylestradiol Studied Using Electrochemical Biosensors and Biosensing in Solution

The synthetic estrogen 17α‐ethinylestradiol (EE2) is an active component of oral contraceptives. It is considered as an endocrine disrupting compound that, once incorporated into an organism, affects the hormonal balance of animals and humans. In this study we characterized the DNA‐EE2 interaction using an electrochemical biosensor and biosensing in solution phase with the double stranded DNA from salmon sperm and deoxyguanosine monophosphate (dGMP). Differential pulse voltammetry method has been applied based on voltammetric anodic responses of the deoxyguanine (dGuo) and deoxyadenine (dAdo) as well as EE2 in the medium of phosphate buffer solution pH 7.0. Binding of EE2 to the nucleobases leads to a decrease of their anodic signals. Association constant for DNA‐EE2 interaction has been estimated to be about 1.1 ? 10³ L mol^?1 and 1.4 ? 10³ L mol^?1 for dGuo and dAdo responses, respectively. The association is reversible as indicated by decrease of the EE2 response in pure buffer solution due to leaching of EE2 from the surface attached DNA. The DNA‐EE2 association has been confirmed also by UV‐vis spectrometric experiments.     

DNA Photosensitization by an “Insider”: Photophysics and Triplet Energy Transfer of 5‐Methyl‐2‐pyrimidone Deoxyribonucleoside

The main chromophore of (6‐4) photoproducts, namely, 5‐methyl‐2‐pyrimidone (Pyo), is an artificial noncanonical nucleobase. This chromophore has recently been reported as a potential photosensitizer that induces triplet damage in thymine DNA. In this study, we investigate the spectroscopic properties of the Pyo unit embedded in DNA by means of explicit solvent molecular‐dynamics simulations coupled to time‐dependent DFT and quantum‐mechanics/molecular‐mechanics techniques. Triplet‐state transfer from the Pyo to the thymine unit was monitored in B‐DNA by probing the propensity of this photoactive pyrimidine analogue to induce a Dexter‐type triplet photosensitization and subsequent DNA damage.     

Enzyme‐Regulated Activation of DNAzyme: A Novel Strategy for a Label‐Free Colorimetric DNA Ligase Assay and Ligase‐Based Biosensing

The DNA nick repair catalyzed by DNA ligase is significant for fundamental life processes, such as the replication, repair, and recombination of nucleic acids. Here, we have employed ligase to regulate DNAzyme activity and developed a homogeneous, colorimetric, label‐free and DNAzyme‐based strategy to detect DNA ligase activity. This novel strategy relies on the ligation‐trigged activation or production of horseradish peroxidase mimicking DNAzyme that catalyzes the generation of a color change signal; this results in a colorimetric assay of DNA ligase activity. Using T4 DNA ligase as a model, we have proposed two approaches to demonstrate the validity of the DNAzyme strategy. The first approach utilizes an allosteric hairpin‐DNAzyme probe specifically responsive to DNA ligation; this approach has a wide detection range from 0.2 to 40 U mL^?1 and a detection limit of 0.2 U mL^?1. Furthermore, the approach was adapted to probe nucleic acid phosphorylation and single nucleotide mismatch. The second approach employs a “split DNA machine” to produce numerous DNAzymes after being reassembled by DNA ligase; this greatly enhances the detection sensitivity by a signal amplification cascade to achieve a detection limit of 0.01 U mL^?1.