Synthesis of novel di-Se-containing thymidine and Se-DNAs for structure and function studies

The selenium derivatization of nucleic acids and nucleic acid-protein complexes has provided a powerful tool to solve phase problem in X-ray crystallography.Selenium atoms in the nucleotides can serve as fine scattering centers in crystal diffraction.Towards the synthesis of multiple selenium atom-containing nucleotides,which offers strong phasing power to facilitate crystal structure determination,we report here the synthesis of the thymidine analogue containing two Se atoms in one nucleobase.The novel Se-containing nucleoside and oligonucleotide DNAs were synthesized and found with the red-shifted UV spectrum and yellow color.Their unique properties are useful in phase determination,nucleic acid-based detection as well as spectroscopic studies of nucleic acids and nucleic acid-protein complexes.     

Nucleic acids analysis

Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis.During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs.In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.     

Studies on the Binding Mode of Pinacyanol Chloride to Nucleic Acids

The interaction of pinacyanol chloride(PC) with nucleic acids has been investigated by a series of experiments.Extensive hypochromism,appreciable peak shifts,isosbestic points and new peaks of the product of binding to nucleic acids in the spectra were observed.They showed that the interaction between PC and nucleic acids occurred.The results from absorption spectra of DNA,DNA melting,electrophoresis and fluorescence polarization studies have indicated that PC binds to DNA in nonintercalative way.Consistent with the nonintercalation,the studies of fluorescence titration and absorption titration specified that the binding of PC to nucleic acids occurred by an outside stacking binding,in which nucleic acids served for acting templates,The fact that the new absorption peaks of bound PC at ca,485nm are just close to the absorption bands of Haggregate of PC at high concentrations without DNA further supports the outside stacking binding mode,In addition,other evidence indicated that the interaction between PC and nucleic acids is not purely electrostatic.     

Study on the interactions of chlorpromazine hydrochloride and promethazine hydrochloride with nucleic acids by resonance Rayleigh scattering spectrum

The interaction between nucleic acids and medicine molecule is one of the important research fields of nucleic acids, which is very valuable for investigating the interactive mechanisms of anti-cancer and anti-virus medicine, screening medicine in vitro, …     

Resonance Rayleigh scattering spectral characteristics of interaction of nucleic acids with some cationic surfactants and their analytical applications

In near neutral medium, the resonance Rayleigh scattering (RRS) intensities of an alone cationic surfactant and nucleic acid are very weak. However, when they combine with each other to form a complex, the RRS intensity of the solution is enhanced greatly. In this paper the reactions of five cationic surfactants with nucleic acids have been studied. The results show that the reaction conditions and RRS spectral characteristics of these reactions are similar, but their sensitivities are obviously different. Among them, the sensitivity of cetyldimethyl benzylammonium chloride (CDBAC) with an aryl and large molecular weight is the highest, while that of cetyl-trimethylammonium bromide (CTAB) without aryl and with small molecular weight is the lowest. The detection limits for ctDNA and yRNA of the former are 6.6 and 29.4 ng · mL-1, while that of the latter are 13.3 and 53.6 ng · mL-1. The method has better selectivity and can be applied to the determination of trace amounts of nucleic acids. Furthermore, i     

The Study on the Stability Constant and Species Distribution of Eu (III) and Tb (III) Complexes with BDBPH

Biomimetic hydrolysis of DNA or RNA is of increasing importance in biotechnology and medicine. The ability to cleave nucleic acids efficiently, in a non-degradative manner, and with high levels of selectivity for site or structure will be required by many applications for the manipulation of genes, the design of structural probes and the development of novel therapeutics1. There has been much interest in the development of lanthanide complexes as nucleic acid cleavage agents. It has been fou…     

Resonance Rayleigh scattering study of the interaction of bleomycinA_5 with nucleic acids and its analytical application

The interaction of bleomycinA5 with nucleic acids has been investigated by using resonance Rayleigh scattering (RRS), molecular absorption and fluorescence spectra. The result shows that in near pH 2.2 buffer medium and absence of any metal ions, nucleic acids are capable of binding with bleomycinA5 (BLMA5) to form complexes which can remarkably enhance the RRS intensity and result in batho- chromic and hyperchromic molecular absorption of nucleic acids and fluorescence quenching of bleomycinA5. The RRS spectral characteristics for the binding products of bleomycinA5 with various DNA and RNA are similar, and the maximum RRS peaks are at 301 nm for ctDNA and sDNA, 370 nm for hsDNA, 310 nm for RNAtypeVI and RNAtypeIII, respectively. The increments of RRS intensity are greatly different in which DNA enhances greatly and RNA enhances lightly. In this work, the optimum condi- tions of the interaction and some influencing factors have been investigated. The reaction mechanism and a binding model for the interaction of BLMA5 with the nucleic acids are discussed. In addition, a highly sensitive, simple and rapid new method for the determination of DNA has been developed. The detection limits (3σ) are 5.7 ng/mL for ctDNA, 7.4 ng/mL for sDNA and 9.2 ng/mL for hsDNA, respectively. The method can be applied to determination of trace amounts of DNA.     

Resonance Rayleigh scattering study of the interaction of bleomycinA<Subscript>5</Subscript> with nucleic acids and its analytical application

The interaction of bleomycinA5 with nucleic acids has been investigated by using resonance Rayleigh scattering (RRS), molecular absorption and fluorescence spectra. The result shows that in near pH 2.2 buffer medium and absence of any metal ions, nucleic acids are capable of binding with bleomycinA5 (BLMA5) to form complexes which can remarkably enhance the RRS intensity and result in bathochromic and hyperchromic molecular absorption of nucleic acids and fluorescence quenching of bleomycinA5. The RRS spectral characteristics for the binding products of bleomycinA5 with various DNA and RNA are similar, and the maximum RRS peaks are at 301 nm for ctDNA and sDNA, 370 nm for hsDNA, 310 nm for RNAtypeVI and RNAtypeIII, respectively. The increments of RRS intensity are greatly different in which DNA enhances greatly and RNA enhances lightly. In this work, the optimum conditions of the interaction and some influencing factors have been investigated. The reaction mechanism and a binding model for the interaction of BLMA5 with the nucleic acids are discussed. In addition, a highly sensitive, simple and rapid new method for the determination of DNA has been developed. The detection limits (3σ) are 5.7 ng/mL for ctDNA, 7.4 ng/mL for sDNA and 9.2 ng/mL for hsDNA, respectively. The method can be applied to determination of trace amounts of DNA.     

Studies on Model Interaction of Keggin-type Polyoxometalates with Nucleic Acid

Keggin anions behave differently from each other when they react with nucleic acids. The molybdenum series exhibits oxidative cleavage activity towards AMP and DNA. The mechanism of AMP damage and DNA cleavage caused by the molybdenum series is mainly oxidation and the oxidation sites are on the ribose parts other than on the adenine parts, while the hydrolysis probably makes significant contributions to the cleavage of DNA and to the damage of AMP caused by the tungsten series.     

Chemical and structural biology of nucleic acids and protein-nucleic acid complexes for novel drug discovery

Since nucleic acids(DNA and RNA) play very important roles in cells,they are molecular targets of many clinically used drugs,such as anticancer drugs and antibiotics.Because of clinical demands for treating various deadly cancers and drug-resistant strains of pathogens,there are urgent needs to develop novel therapeutic agents.Targeting nucleic acids hasn’t been the mainstream of drug discovery in the past,and the lack of 3D structural information for designing and developing drug specificity is one of the ...     

An automated nucleic acid detection platform using digital microfluidics with an optimized Cas12a system

Outbreaks of both influenza virus and the novel coronavirus SARS-CoV-2 are serious threats to human health and life. It is very important to establish a rapid, accurate test with large-scale detection potential to prevent the further spread of the epidemic. An optimized RPA-Cas12a-based platform combined with digital microfluidics(DMF), the RCD platform, was established to achieve the automated, rapid detection of influenza viruses and SARS-CoV-2. The probe in the RPA-Cas12a system was optimized to produce maximal fluorescence to increase the amplification signal. The reaction droplets in the platform were all at the microliter level and the detection could be accomplished within 30 min due to the effective mixing of droplets by digital microfluidic technology. The whole process from amplification to recognition is completed in the chip, which reduces the risk of aerosol contamination. One chip can contain multiple detection reaction areas, offering the potential for customized detection.The RCD platform demonstrated a high level of sensitivity, specificity(no false positives or negatives), speed(≤30 min),automation and multiplexing. We also used the RCD platform to detect nucleic acids from influenza patients and COVID-19 patients. The results were consistent with the findings of q PCR. The RCD platform is a one-step, rapid, highly sensitive and specific method with the advantages of digital microfluidic technology, which circumvents the shortcomings of manual operation. The development of the RCD platform provides potential for the isothermal automatic detection of nucleic acids during epidemics.     

Fluorescence Microscopic Image Analysis of Nucleic Acids Based on The Capillary Flow Directed Assembly Ring of Neutral Red－nucleic Acid Supramolecular Complexes

It is critical to establish a direct and precise method with a high sensitivity and selectivity in analytical chemistry. In this research, making use of a well known phenomenon of capillary flow, we have proposed an image analysis method of nucleic acids at the price of a small amount of sample. When a droplet of the supramolecular complex solution, formed by neutral red and nucleic acids (NA) under an approximate neutral condition, was placed on the hydrophobic surface of dimethyl dichlorosilane pretreated glass slides, and it was evaporated, the supramolecular complex exhibited the periphery of the droplet due to the capillary effect,and accumulated there to form a red capillary-flow-directed assembly ring(CFDAR). A typical CFDAR has an outer diameter of (2r) about 1.18 mm and a ring width(2δ) of about 41 ~m. Depending on the experimental conditions, a variety of CFDAR can be assembled. The experimental results are in agreement with our former theoretical discussion. It was found that when a droplet volume is 0. 1 pI., the fluorescence intensity of the CFDAR formed by the NR-NA is in proportion to the content of calf thymus DNA in the range of 0—0. 28 ng, fish sperm DNA of 0—0. 24 ng and yeast RNA of 0—0. 16 ng with the limit of detection(3σ) of 1.7，1.4 and 0. 9 pg, respectively for the three nucleic acids.     

Molecular modeling on Zn(II) binding modes of Alzheimer''''s amyloid β-peptide in insoluble aggregates and soluble complexes

Alzheimers disease (AD) is a progressive neu-rodegenerative illness relative to aging. One of the major pathological characters is that senile plaques (SP) occur in the brains of patients. Amyloid b-peptide (Ab) is the major constituent of senile plaques. The peptide is produced from a precursor membrane pro-tein (APP) by normal proteolytic processing and is released into extracellular fluids as a soluble peptide of 39—42 amino acids[1,2]. For AD patients, Ab ag-gregates and accumulates …     

Studies on cyclopent-2-enone——Ⅱ.The diastereoselectivity in Lewis acid mediated reactions of enol silyl ether of cyclopent-2-enone with aldehydes

The aldol reaction of the silyl enol ether of cyclopent-2-enone with aldehydes is mediatedby various Lewis acids.Threo isomers are the major diastereoisomers formed in most cases.A reversediastereoselectivity was observed when the reaction was mediated by TBAF.The results have beendiscussed in detail by structure and transition state analysis.     

Synthesis, Characterization, Crystal Structure and Stability of a Ternary Cu（Ⅱ） complex with 1, 10-Phenanthroline and L-Valinate

It is important to research the mixed-ligand copper complexes containing bioligands, such as amino acids, nucleic acids and proteins, in exploring the functional mechanism of microelement copper in organism because the reaction of any micronutrient with two or more bioligands in the concentrated bioligands background gives mixed-ligand ternary complexes, which are more stable and related with storage of substance and transportationof metal ions in the life process.     

Synthesis and Crystal Structure of a New Ternary Mixed Ligand Complex [Cu（ampym）（bapa）Cl]（ClO4） （ampym = 2-Aminopyrimidine, bapa = Bi（3-aminopropyl）amine）

1 INTRODUCTION The pyrimidine substructure plays a vital role in physiological system. It occurs not only in organisms such as nucleic acids, vitamins and coenzymes[1~3], but also frequently presents in commercially availa- ble drugs such as antibiotics, antiatherosclerotic and antihypertensive agent[4, 5]. Studying the interaction of pyrimidine derivatives and metal ions is important as a means of understanding the role of pyrimidine ring in biological systems. This paper describes the …     

HPLC Determination of the Major Non-protein Amino Acids and Common Biogenic Amines in Lathyrus sativus Using a Novel Extraction Method

An assay is presented for simultaneously determining 5 biogenic amines and the major non-protein amino acids: the toxin β-N-oxalyl-L-α，β-diaminopropanoic acid (β-ODAP), its isomer α-ODAP and homoarginine in Lathyrus sativus extracts using the HPLC system after derivatization with para-nitrobenzyloxycarbonyl chloride (PNZ-Cl). However, it is more worthy of noting that this paper also describes a new extraction method using 0.2 mol/L HClO4. The new method has some advantages: shorter extraction-time, simultaneous extraction of free amino acids and polyamines, better inhibiting the isomerization of β-ODAP to α-ODAR and so on.     

Electronic Structures and Spectra of the Bases and Base Pairs of Nucleic Acids

The present paper covers electronic structures and spectra of the bases and the base pairs of nucleic acids calculated by using the INDO/S method. For free bases we give the energy levels of ground states and transition energies of low-lying excited states and discuss the band characters. The results indicate that the calculated spectra are in good agreement with experimental values. On the other hand, our calculations for A-T and G-C pairs are very beneficial to understanding hydrogen bond properties of these pairs.     

Studies on Interaction Between Gallocyanine and DNA

IntroductionConsiderable attention has been focused onnew DNA- binding and DNA- modifying agents fromnatural ones to wholly synthetic designs due totheir usage as probes of deciphering the structureand the function of nucleic acids and as potentialchemotherapeutic agents[1— 4] . The application ofthose molecules must be based on the preciseunderstanding of the structural details about thebinding of the agents with the target molecule,double- helical DNA. The interaction of smallmolecules …     

BORONIC ACIDS AS LIGANDS FOR AFFINITY CHROMATOGRAPHY

 A review on the principles and applications of boronic acids as affinity ligands for the chromatographic separation of carbohydrates, nucleic acid components, glycoproteins, and other small biomolecules. The mechanisms of interactions between boronate ligands and analytes are described. Various boronate ligands and supports are discussed. Examples of the use of boronate affinity chromatography for separation of each class of analytes are presented.