Nucleic acid based molecular devices

In biology, nucleic acids are carriers of molecular information: DNA's base sequence stores and imparts genetic instructions, while RNA's sequence plays the role of a messenger and a regulator of gene expression. As biopolymers, nucleic acids also have exciting physicochemical properties, which can be rationally influenced by the base sequence in myriad ways. Consequently, in recent years nucleic acids have also become important building blocks for bottom-up nanotechnology: as molecules for the self-assembly of molecular nanostructures and also as a material for building machinelike nanodevices. In this Review we will cover the most important developments in this growing field of nucleic acid nanodevices. We also provide an overview of the biochemical and biophysical background of this field and the major "historical" influences that shaped its development. Particular emphasis is laid on DNA molecular motors, molecular robotics, molecular information processing, and applications of nucleic acid nanodevices in biology.     

Functionalized cryogel monoliths for fast and selective separation of nucleic acids directly from crude lysate

The fast and selective separation of nucleic acids has been attractive recently because of their wide number of applications in the biomedical field such as the development of vaccines for infectious diseases, gene therapy, and diagnosis. Traditional approaches of nucleic acids separation are costlier, lengthy, and associated with possible denaturation because of the use of organic solvents in the elution step. Under this perspective, cryogels represent an attractive choice as a monolith stationary phase in column chromatography, which have proven efficient in recent chromatographic studies. Cryogels are the macroporous hydrogels with interconnecting properties between the pores. They allow the easy flow of large biomolecules with minimum mass transfer resistance. They are spongy in nature and possess good mechanical strength. Current article represents different developed functionalized cryogel monoliths for nucleic acids separation, their separation strategies, and challenges associated with further advancement in separation science.     

Functional Xeno Nucleic Acids for Biomedical Application

Functional nucleic acids(FNAs) refer to a type of oligonucleotides with functions over the traditional genetic roles of nucleic acids, which have been widely applied in screening, sensing and imaging fields. However, the potential application of FNAs in biomedical field is still restricted by the unsatisfactory stability, biocompatibility, biodistribution and immunity of natural nucleic acids(DNA/RNA). Xeno nucleic acids(XNAs) are a kind of nucleic acid analogues with chemically modified sugar groups that possess improved biological properties, including improved biological stability, increased binding affinity, reduced immune responses, and enhanced cell penetration or tissue specificity. In the last two decades, scientists have made great progress in the research of functional xeno nucleic acids, which makes it an emerging attractive biomedical application material. In this review, we summarized the design of functional xeno nucleic acids and their applications in the biomedical field.     

电感耦合等离子体质谱用于多组分免疫分析研究进展

免疫分析在临床医学检测领域具有重要的地位.本课题组提出了基于电感耦合等离子体质谱(ICP-MS)的免疫分析方法,利用元素标记技术结合ICP-MS检测实现多组分免疫分析.随后,研究人员在该领域做了大量研究工作,证明该方法可用于从小分子、蛋白质、核酸到细胞等一系列生物样品的检测.本文综述了基于ICP-MS免疫分析方法的特点,对其发展方向进行了展望,希望为该领域的研究工作提供参考.     

Selective Chemical Modification to the Higher-Order Structures of Nucleic Acids

DNA and RNA can adopt a variety of stable higher-order structural motifs, including G-quadruplex (G4 s), mismatches, and bulges. Many of these secondary structures are closely related to the regulation of gene expression. Therefore, the higher-order structure of nucleic acids is one of the candidate therapeutic targets, and the development of binding molecules targeting the higher-order structure of nucleic acids has been pursued vigorously. Furthermore, as one of the methodologies for detecting the higher-order structures of these nucleic acids, developing techniques for the selective chemical modification of the higher-order structures of nucleic acids is also underway. In this personal account, we focus on the following higher-order structures of nucleic acids, double-stranded DNA containing the abasic site, T−T/U−U mismatch structure, and G-quadruplex structure, and describe the development of molecules that bind to and chemically modify these structures.     

Perspectives on analyses of nucleic acid constituents: the basis of genomics

The recent mapping of the human genome was a tremendous achievement made possible to a large degree by the development of analytical methods for sequencing purine and pyrimidine bases in nucleic acids. In the last 3 decades, the number of analyses of nucleic acids and their constituents by HPLC and capillary electrophoresis (CE) has exploded. These techniques have been used not only for genomics, but also for the determination of free nucleotides, nucleosides and their bases in body fluids and tissues. Although a large number of HPLC and CE papers have been published on nucleic acid constituent applications, relatively little has been written on the mechanisms of the separations. However, to optimize analytical conditions knowledgeably and rapidly, it is important to know why and how these separations occur and the factors that affect them. The HPLC methods for the analysis of nucleic acid constituents and the information available on some of the mechanisms of separation of nucleotides, nucleosides and their bases, as well as the analysis of these compounds by CE and the factors that affect these separations are discussed.     

A eole for the MS analysis of nucleic acids in the post-genomics age

The advances of mass spectrometry in the analysis of nucleic acids have tracked very closely the exciting developments of instrumentation and ancillary technologies, which have taken place over the years. However, their diffusion in the broader life sciences community has been and will be linked to the ever evolving focus of biomedical research and its changing demands. Before the completion of the Human Genome Project, great emphasis was placed on sequencing technologies that could help accomplish this project of exceptional scale. After the publication of the human genome, the emphasis switched toward techniques dedicated to the exploration of sequences not coding for actual protein products, which amount to the vast majority of transcribed elements. The broad range of capabilities offered by mass spectrometry is rapidly advancing this platform to the forefront of the technologies employed for the structure-function investigation of these noncoding elements. Increasing focus on the characterization of functional assemblies and their specific interactions has prompted a re-evaluation of what has been traditionally construed as nucleic acid analysis by mass spectrometry. Inspired by the accelerating expansion of the broader field of nucleic acid research, new applications to fundamental biological studies and drug discovery will help redefine the evolving role of MS-analysis of nucleic acids in the post-genomics age.     

Microfluidic chip electrophoresis for biochemical analysis

Microfluidic chip electrophoresis has been widely employed for separation of various biochemical species owing to its advantages of low sample consumption, low cost, fast analysis, high throughput, and integration capability. In this article, we reviewed the development of four different modes of microfluidics‐based electrophoresis technologies including capillary electrophoresis, gel electrophoresis, dielectrophoresis, and field (electric) flow fractionation. Coupling detection schemes on microfluidic electrophoresis platform were also reviewed such as optical, electrochemical, and mass spectrometry method. We further discussed the innovative applications of microfluidic electrophoresis for biomacromolecules (nucleic acids and proteins), biochemical small molecules (amino acids, metabolites, ions, etc.), and bioparticles (cells and pathogens) analysis. The future direction of microfluidic chip electrophoresis was predicted.     

质谱技术在核酸研究领域的应用

质谱技术具有快速、准确、灵敏度高等优点,近年来在生物分析方面得到了广泛的应用.核酸作为生命的基本物质,一直是生命领域的研究热点,进展日新月异.而质谱方法也成为了科学家研究核酸的强有力工具,具有广阔的发展前景.本文介绍了核酸检测的质谱技术,并简要综述了质谱在核酸的高级结构研究、与小分子相互作用、DNA损伤与修饰等领域的应用,重点介绍了中国学者的研究成果.     

生物膜层干涉技术在生物分子分析和检测中应用的研究进展

生物膜层干涉技术是基于光干涉信号实现对生物分子动力学分析或快速检测的非标记分析检测技术。因具有实时提供分析物信息、分析速度快和样品耗量少等优点,该技术已被应用于蛋白质、核酸、脂质、糖类及其他生物分子之间相互作用的分析;所需样品量少、特异性强等优点也为该技术应用于快速检测奠定了基础。该文介绍了生物膜层干涉技术的基本原理,综述了其在动力学分析和快速检测领域的相关应用研究,并对其发展趋势和应用前景进行了展望。     

Analytical methods for locating modifications in nucleic acids

We reviewed and summarized the established methods and the breakthrough of the techniques for locating modifications in nucleic acids. In addition, we discussed the principles, applications, advantages and drawbacks of these methods.     

基于化学衍生-质谱技术的生物与临床样本中核酸修饰分析

除了经典碱基外,核酸(DNA和RNA)中还包含许多化学修饰。迄今为止,已经在核酸中鉴定了超过150多种化学修饰。这些化学修饰不会改变核酸的序列,但会改变它们的结构和生化特性,最终调节基因的时空表达。阐明这些修饰的功能可以促进对生命体生理调控机制的深入认识和理解。然而,核酸修饰在体内的丰度通常很低。因此,高灵敏和特异的检测方法对破译这些修饰的功能至关重要。化学衍生与质谱技术相结合对内源性低丰度核酸修饰展现出很好的分析能力。在过去几年中,研究者建立了多种基于化学衍生-质谱分析的分析方法,用于灵敏、高效地分析核酸修饰。该文总结了通过化学衍生-质谱分析方法来破译核酸修饰的最新进展,希望能促进未来对核酸修饰功能的深入研究。     

Detection of biomolecules in electrophoresis gels with salts of imidazole and zinc II: a decade of research

The proven ability of gel electrophoresis to simultaneously resolve, in a single experiment, many components from complex biological samples, has determined its preference over a variety of well-established chromatographic methods. Therefore, procedures placed at the interface between gel separation and microanalysis have earned increasing significance with respect to the overall success of the microanalytical strategy. The first of these procedures is the detection technique. The most important requirement for compatibility with further analysis or bioapplications is that the staining method does not compromise the chemical integrity and the biological properties of micropurified biomolecules. Procedures for negative detection of proteins with metal salts that have been proven to comply with this condition have been known for about 15 years. Only recently have these procedures been extended to the field of nucleic acids and lipopolysaccharides. The focus of this review is to chronicle the development and current status of the negative or reverse stain procedure based on the in-gel reaction of imidazole with zinc salts and its applications forthe micropurification and analysis of unmodified proteins, nucleic acids and bacterial lipopolysaccharides. We highlight the common aspects in the detection of the three types of biomolecules, and their applications to structural and biological analyses. Emphasis is given on the mechanism underlying imidazole-zinc staining, as it contributes to a deeper understanding of a general detection mechanism with metal salts. Finally, we discuss the latest applications of the techniques in proteomics and their possible impact on the characterization of gel-separated single components from complex lipopolysaccharides.     

毛细管电泳在生物大分子分析中的应用研究进展

近年来,毛细管电泳技术以其高效、微量、分离模式多样等优势,在生物大分子分析领域得到了日益广泛的应用.综述了毛细管电泳技术在多糖、蛋白质、核酸和脂质中的应用,并对其相关的样品制备、毛细管内壁吸附、仪器的研制等方面存在的问题进行分析和展望,以期为毛细管电泳技术在生物大分子领域的推广应用提供借鉴.     

PNA-DNA duplexes, triplexes, and quadruplexes are stabilized with trans-cyclopentane units

Peptide nucleic acids (PNAs) are non-natural nucleic acid mimics that bind to complementary DNA and RNA with high affinity and selectivity. PNA can bind to nucleic acids in a number of different ways. Currently, the formation of PNA-oligonucleotide duplex, triplex, and quadruplex structures have been reported. PNAs have been used in numerous biomedicial applications, but there are few strategies to predictably improve the binding properties of PNAs by backbone modification. We have been studying the benefits of incorporating (S,S)-trans-cyclopentane diamine units (tcyp) into the PNA backbone. In this Communication, we report the improvement in stability associated with tcyp incorporation into PNA-DNA duplexes, triplexes, and quadruplexes. The broad utility of this modification across multiple types of PNA structures is unique and should prove useful in the development of applications that rely on PNA.     

Nanomaterial-based electrochemical DNA sensing strategies

DNA sensing strategies have recently been varieted with the number of attempts at the development of different biosensor devices based on nanomaterials, which will further become DNA microchip systems. The investigations at the side of material science in connection with electrochemical biosensors open new directions for detection of specific gene sequences, and nucleic acid-ligand interactions.An overview is reported here about nanomaterial-based electrochemical DNA sensing strategies principally performed for the analysis of specific DNA sequences and the quantification of nucleic acids. Important features of electrochemical DNA sensing strategies, along with new developments based on nanomaterials are described and discussed.