Electrochemical biosensor for detection of BCR/ABL fusion gene based on hairpin locked nucleic acids probe

This communication reports on a novel biosensor to study the hybridization specificity by using thiolated hairpin locked nucleic acids (LNA) as the capture probe. The LNA probe was immobilized on the gold electrode through sulfur–Au interaction and could selectively hybridize with its target DNA. Differential pulse voltammetry (DPV) was used to monitor the hybridization reaction on the probe electrode. The decrease of the peak current of methylene blue, an electroactive indicator, was observed upon hybridization of the probe with the target DNA. The results indicated this new method has excellent specificity for single-base mismatch and complementary after hybridization, and a high sensitivity. This LNA probe has been used for assay of fusion gene in Chronic Myelogenous Leukemia (CML) of the real sample with satisfactory result.     

Solution structure and conformational dynamics of deoxyxylonucleic acids (dXNA): an orthogonal nucleic acid candidate

Orthogonal nucleic acids are chemically modified nucleic acid polymers that are unable to transfer information with natural nucleic acids and thus can be used in synthetic biology to store and transfer genetic information independently. Recently, it was proposed that xylose-DNA (dXNA) can be considered to be a potential candidate for an orthogonal system. Herein, we present the structure in solution and conformational analysis of two self-complementary, fully modified dXNA oligonucleotides, as determined by CD and NMR spectroscopy. These studies are the initial experimental proof of the structural orthogonality of dXNAs. In aqueous solution, dXNA duplexes predominantly form a linear ladderlike (type-1) structure. This is the first example of a furanose nucleic acid that adopts a ladderlike structure. In the presence of salt, an equilibrium exists between two types of duplex form. The corresponding nucleoside triphosphates (dXNTPs) were synthesized and evaluated for their ability to be incorporated into a growing DNA chain by using several natural and mutant DNA polymerases. Despite the structural orthogonality of dXNA, DNA polymerase β mutant is able to incorporate the dXNTPs, showing DNA-dependent dXNA polymerase activity.     

1-, 2-, and 4-ethynylpyrenes in the structure of twisted intercalating nucleic acids: structure, thermal stability, and fluorescence relationship

A postsynthetic, on-column Sonogashira reaction was applied on DNA molecules modified by 2- or 4-iodophenylmethylglycerol in the middle of the sequence, to give the corresponding ortho- and para-twisted intercalating nucleic acids (TINA) with 1-, 2-, and 4-ethynylpyrene residues. The convenient synthesis of 2- and 4-ethynylpyrenes started from the hydrogenolysis of pyrene that has had the sulfur removed and separation of 4,5,9,10-tetrahydropyrene and 1,2,3,6,7,8-hexahydropyrene, which were later converted to the final compounds by successive Friedel-Crafts acetylation, aromatization by 2,3-dichloro-5,6-dicyano-1,4-benzoquinone, and a Vilsmeier-Haack-Arnold transformation followed by a Bodendorf fragmentation. Significant alterations in thermal stability of parallel triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in homopyrimidine TINAs. Thus, for para-TINAs the bulge insertion of an intercalator led to high thermal stability of Hoogsteen-type parallel triplexes and duplexes, whereas Watson-Crick-type duplexes were destabilized. In the case of ortho-TINA, both Hoogsteen and Watson-Crick-type complexes were stabilized. Alterations in the thermal stability were highly influenced by the ethynylpyrene isomers used. This also led to TINAs with different changes in fluorescence spectra depending on the secondary structures formed. Stokes shift of approximately 100 nm was detected for pyren-2-ylethynylphenyl derivatives, whereas values for 1- and 4-ethynylpyrenylphenyl conjugates were 10 and 40 nm, respectively. In contrast with para-TINAs, insertion of two ortho-TINAs opposite each other in the duplex as a pseudo-pair resulted in formation of an excimer band at 505 nm for both 1- and 4-ethynylpyrene analogues, which was also accompanied with higher thermal stability.     

PRO_LIGAND: An approach to de novo molecular design. 3. A genetic algorithm for structure refinement

Summary Recently, the development of computer programs which permit the de novo design of molecular structures satisfying a set of steric and chemical constraints has become a burgeoning area of research and many operational systems have been reported in the literature. Experience with PRO_LIGAND—the de novo design methodology embodied in our in-house molecular design and simulation system PRO-METHEUS—has suggested that the addition of a genetic algorithm (GA) structure refinement procedure can add value to an already useful tool. Starting with the set of designed molecules as an initial population, the GA can combine features from both high- and low-scoring structures and, over a number of generations, produce individuals of better score than any of the starting structures. This paper describes how we have implemented such a procedure and demonstrates its efficacy in improving two sets of molecules generated by different de novo design projects.     

Tunable hydrophobicity in DNA micelles: design, synthesis, and characterization of a new family of DNA amphiphiles

This work describes the synthesis and characterization of a new family of DNA amphiphiles containing modified nucleobases. The hydrophobicity was imparted by the introduction of a dodec-1-yne chain at the 5-position of the uracil base, which allowed precise and simple tuning of the hydrophobic properties through solid-phase DNA synthesis. The micelles formed from these modified DNA sequences were characterized by atomic force microscopy, dynamic light scattering, and polyacrylamide gel electrophoresis. These experiments revealed the role of the quantity and location of the hydrophobic units in determining the morphology and stability of the micelles. The effects of hybridization on the physical characteristics of the DNA micelles were also studied; these results showed potential for the sequence-specific noncovalent functionalization of the self-assembled aggregates.     

Electrogenerated chemiluminescence biosensing for the detection of prostate PC-3 cancer cells incorporating antibody as capture probe and ruthenium complex-labelled wheat germ agglutinin as signal probe

A highly selective and sensitive electrogenerated chemiluminescence (ECL) biosensor for the detection of prostate PC-3 cancer cells was designed using a prostate specific antibody as a capture probe and ruthenium complex-labelled wheat germ agglutinin as a signal probe. The ECL biosensor was fabricated by covalently immobilising the capture probe on a graphene oxide-coated glassy carbon electrode. Target PC-3 cells were selectively captured on the surface of the biosensor, and then, the signal probe was bound with the captured PC-3 cells to form a sandwich. In the presence of tripropylamine, the ECL intensity of the sandwich biosensor was logarithmically directly proportion to the concentration of PC-3 cells over a range from 7.0 × 10² to 3.0 × 10⁴ cells mL⁻¹, with a detection limit of 2.6 × 10² cells mL⁻¹. The ECL biosensor was also applied to detect prostate specific antigen with a detection limit of 0.1 ng mL⁻¹. The high selectivity of the biosensor was demonstrated in comparison with that of a lectin-based biosensor. The strategy developed in this study may be a promising approach and could be extended to the design of ECL biosensors for highly sensitive and selective detection of other cancer-related cells or cancer biomarkers using different probes.     

BODIL: a molecular modeling environment for structure-function analysis and drug design

BODIL is a molecular modeling environment geared to help the user to quickly identify key features of proteins critical to molecular recognition, especially (1) in drug discovery applications, and (2) to understand the structural basis for function. The program incorporates state-of-the-art graphics, sequence and structural alignment methods, among other capabilities needed in modern structure–function–drug target research. BODIL has a flexible design that allows on-the-fly incorporation of new modules, has intelligent memory management, and fast multi-view graphics. A beta version of BODIL and an accompanying tutorial are available at http://www.abo.fi/fak/mnf/bkf/research/johnson/bodil.html     

Synthesis and structure of the first ribbed-functionalized quinoxaline clathrochelate: design of cage complexes for efficient intercalation into DNA structure

Condensation of the dichloride clathrochelate FeBd₂(Cl₂Gm)(BF)₂ precursor (Bd^2– is the -benzyl dioxime dianion, Gm is the glyoxime residue) with quinoxaline-2,3-dithiol in the presence of triethylamine afforded the ribbed-functionalized quinoxaline clathrochelate. The structure of this complex was established by X-ray diffraction analysis.     

A fluorescence turn-on probe for the detection of thiol-containing amino acids in aqueous solution and bioimaging in cells

A turn-on fluorescent probe, based on a water-soluble terphenyl derivative, for the detection of cysteine and homocysteine is reported. The aldehyde groups in the probe play crucial roles in providing reaction with thiol groups in the amino acids, leading to a formation of thiazolidine (from cysteine) or thiazinane ring (from homocysteine). As a result, the new formation of such rings alters the electronic property of the conjugated system in the probe and results in emission enhancement. The probe in aqueous solution exhibits a remarkable increase in its quantum yield upon exposure to cysteine (up to 20-fold) and to homocysteine (up to 700-fold), while slight quenching is observed in the presence of glutathione. Moreover, an investigation on time-resolved fluorescence spectra of the probe in the presence of cysteine and homocysteine reveals potential discriminatory detection of cysteine and homocysteine. Bioimaging of the thiols in live HeLa cells was successfully applied.     

Phenoxazine dyes for dye-sensitized solar cells: relationship between molecular structure and electron lifetime

A series of metal-free organic dyes with a core phenoxazine chromophore have been synthesized and tested as sensitizers in dye-sensitized solar cells. Overall conversion efficiencies of 6.03-7.40% were reached under standard AM 1.5G illumination at a light intensity of 100 mW cm(-2) . A clear trend in electron lifetime could be seen; a dye with a furan-conjugated linker showed a shorter lifetime relative to dyes with the acceptor group directly attached to the phenoxazine. The addition of an extra donor unit, which bore insulating alkoxyl chains, in the 7-position of the phenoxazine could increase the lifetime even further and, together with additives in the electrolyte to raise the conduction band, an open circuit voltage of 800 mV could be achieved. From photoelectron spectroscopy and X-ray absorption spectroscopy of the dyes adsorbed on TiO(2) particles, it can be concluded that the excitation is mainly of cyano character (i.e., on average, the dye molecules are standing on, and pointing out, from the surface of TiO(2) particles).     

Design of a novel G-quenched molecular beacon: a simple and efficient strategy for DNA sequence analysis

G-quenched MBs are devised from readily available starting materials and used for sequence specific DNA detection with high efficiency.     

A benzimidazole-based single molecular multianalyte fluorescent probe for the simultaneous analysis of Cu and Fe

We synthesized a novel receptor with benzimidazole moieties in a tripodal framework. The receptor displays rarely observed metal specific fluorescence enhancement at two different wavelengths. The receptor was investigated for the simultaneous analysis of Cu²⁺ and Fe³⁺ and successfully quantified the ions without interference over a wide concentration range.     

Calibration of forcefields for molecular simulation: Sequential design of computer experiments for building cost‐efficient kriging metamodels

We present a global strategy for molecular simulation forcefield optimization, using recent advances in Efficient Global Optimization algorithms. During the course of the optimization process, probabilistic kriging metamodels are used, that predict molecular simulation results for a given set of forcefield parameter values. This enables a thorough investigation of parameter space, and a global search for the minimum of a score function by properly integrating relevant uncertainty sources. Additional information about the forcefield parameters are obtained that are inaccessible with standard optimization strategies. In particular, uncertainty on the optimal forcefield parameters can be estimated, and transferred to simulation predictions. This global optimization strategy is benchmarked on the TIP4P water model. © 2013 Wiley Periodicals, Inc.     

Crystal and molecular structure of 5-trifluorothymine, a metabolite from human urine: Role of fluorine in stacking and hydrogen bonded interactions

The crystal structure of the metabolite from urine, 5-trifluorothymine [5F₃T] has been determined by single crystal X-ray diffractometric methods. Crystals of 5F₃T are monoclinic, space group P2₁/c with cell dimensions a = 6.7468(2), b = 15.0740(6), c = 13.4405(6), β = 90.412(2), V = 1366.88(8), Z = 8 (two molecules per asymmetric unit). Crystal structure of 5F₃T was determined with 3039 independent data and refined by full-matrix least squares methods to a final reliability factor of 0.047. Molecules of 5F₃T are connected by dimeric type of NH?O hydrogen bonding linking molecules related by a center of inversion into an extensive layer of dimeric molecules. These layers are stacked on top of each other at a stacking distance of 3.280 Å with a head-to-head stacking of the fluorine atoms on top of each other with no hydrogen bonding involving the fluorine atoms.     

Forward molecular design for highly efficient OLED emitters: a theoretical analysis of photophysical properties of platinum(II) complexes with N-heterocyclic carbene ligands

The electronic structures and photophysical properties of eight Pt-complexes with different N-heterocyclic carbene ligands and potential to serve as light emitting diode materials were investigated by density functional theory and time-dependent density functional theory, employing the BP86 functional for geometry optimisations, SAOP potential for excited state calculations and all-electron TZ2P basis set throughout. Non-radiative and radiative decay rate constants were determined for each system through analyses of the geometric relaxations, d-orbital splitting and spin-orbit couplings at the optimised S(0) and T(1) geometries. Three Pt-systems bound to two N-heterocyclic carbenes were shown to be nonemissive, while a fourth was shown to be emissive from the T(1) excited state. Similar T(1)-initated emission was observed for three other Pt-systems investigated, each bound to four N-heterocyclic carbenes, while a fourth similarly tetra-ligated system showed T(2)-initation of emission. The results highlight the coupling of ligand-identity to photophysical properties and more importantly, the potential for rational optimisation and tuning of emission wavelengths and phosphorescent efficiencies. Encouragingly, two of the tetra-N-heterocyclic carbene ligated systems show strong potential to serve as highly-efficient blue and green light emitting materials, respectively.     

Extensive conformational searches of 13 representative dipeptides and an efficient method for dipeptide structure determinations based on amino acid conformers

Conformations of peptides are the basis for their property studies and the predictions of peptide structures are highly important in life science but very complex in practice. Here, thorough searches on the potential energy surfaces of 13 representative dipeptides by considering all possible combinations of the bond rotational degrees of freedom are performed using the density functional theory based methods. Careful analyses of the conformers of the 13 dipeptides and the corresponding amino acids reveal the connections between the structures of dipeptide and amino acids. A method for finding all important dipeptide conformers by optimizing a small number of trial structures generated by suitable superposition of the parent amino acid conformations is thus proposed. Applying the method to another eight dipeptides carefully examined by others shows that the new approach is both highly efficient and reliable by providing the most complete ensembles of dipeptide conformers and much improved agreements between the theoretical and experimental IR spectra. The method opens the door for the determination of the stable structures of all dipeptides with a manageable amount of effort. Preliminary result on the applicability of the method to the tripeptide structure determination is also presented. The results are the first step towards proving Anfinsen's hypothesis by revealing the relationships between the structures of the simplest peptide and its constituting amino acids. It implies that the structures of peptides are not only determined by their amino acid sequences, but also closely linked with the amino acid conformations. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009