Bioanalytical applications of isothermal nucleic acid amplification techniques

The most popular in vitro nucleic acid amplification techniques like polymerase chain reaction (PCR) including real-time PCR are costly and require thermocycling, rendering them unsuitable for uses at point-of-care. Highly efficient in vitro nucleic acid amplification techniques using simple, portable and low-cost instruments are crucial in disease diagnosis, mutation detection and biodefense. Toward this goal, isothermal amplification techniques that represent a group of attractive in vitro nucleic acid amplification techniques for bioanalysis have been developed. Unlike PCR where polymerases are easily deactivated by thermally labile constituents in a sample, some of the isothermal nucleic acid amplification techniques, such as helicase-dependent amplification and nucleic acid sequence-based amplification, enable the detection of bioanalytes with much simplified protocols and with minimal sample preparations since the entire amplification processes are performed isothermally. This review focuses on the isothermal nucleic acid amplification techniques and their applications in bioanalytical chemistry. Starting off from their amplification mechanisms and significant properties, the adoption of isothermal amplification techniques in bioanalytical chemistry and their future perspectives are discussed. Representative examples illustrating the performance and advantages of each isothermal amplification technique are discussed along with some discussion on the advantages and disadvantages of each technique.     

Separation and recovery of nucleic acids with improved biological activity by acid‐degradable polyacrylamide gel electrophoresis

One of the fundamental challenges in studying biomacromolecules (e.g. nucleic acids and proteins) and their complexes in a biological system is isolating them in their structurally and functionally intact forms. Electrophoresis offers convenient and efficient separation and analysis of biomacromolecules but recovery of separated biomacromolecules is a significant challenge. In this study, DNAs of various sizes were separated by electrophoresis in an acid‐degradable polyacrylamide gel. Almost 100% of the nucleic acids were recovered after the identified gel bands were hydrolyzed under a mildly acidic condition and purified using anion exchange resin. Further concentration by centrifugal filtration and a second purification using ion exchange column chromatography yielded 44–84% of DNA. The second conventional (non‐degradable) gel electrophoresis confirmed that the nucleic acids recovered from acid‐degradable gel bands preserved their electrophoretic properties through acidic gel hydrolysis, purification, and concentration processes. The plasmid DNA recovered from acid‐degradable gel transfected cells significantly more efficiently than the starting plasmid DNA (i.e. improved biological activity via acid‐degradable PAGE). Separation of other types of nucleic acids such as small interfering RNA using this convenient and efficient technique was also demonstrated.     

Adaptive recognition of small molecules by nucleic acid aptamers through a label-free approach

We report a novel label-free method for the investigation of the adaptive recognition of small molecules by nucleic acid aptamers using capillary electrophoresis analysis. Cocaine and argininamide were chosen as model molecules, and the two corresponding DNA aptamers were used. These single-strand DNAs folded into their specific secondary structures, which were mainly responsible for the binding of the target molecules with high affinity and specificity. For molecular recognition, the nucleic acid structures then underwent additional conformational changes, while keeping the target molecules stabilized by intermolecular hydrogen bonds. The intrinsic chemical and physical properties of the target molecules enabled them to act as indicators for adaptive binding. Thus any labeling or modification of the aptamers or target molecules were made obsolete. This label-free method for aptamer-based molecular recognition was also successfully applied to biological fluids and therefore indicates that this approach is a promising tool for bioanalysis.     

Cyclodextrin-Containing Polymers for Gene Delivery

Cyclodextrin-containing polymers are now being explored as vehicles for delivering nucleic acids into cells. The structures of the cyclodextrin-containing polycations affect the nucleic acid delivery efficiencies and their toxicities. Of interest is the fact that the cyclodextrin-containing polymers reveal lower toxicities than polymers that lack the cyclodextrins. The cyclodextrins endow the nucleic acid delivery vehicles with the ability to be modified by compounds that form inclusion complexes with the cyclodextrins, and these modifications can be performed without disruption of the polymer-nucleic acid interactions. Thus, cyclodextrin-containing polymers provide unique properties for gene delivery.     

Point of attachment and sequence of immobilized peptide-acridine conjugates control affinity for nucleic acids

Screening of combinatorial libraries by spatial arraying strategies requires library members to be solid-phase immobilized. However, for nucleic acid ligands that bind via intercalation, immobilization may inhibit binding if the tethering functionality is present at the edge of the heterocyle that approaches the duplex during the binding reaction. We report here a method for immobilizing peptide-acridine conjugates (PACs) via either their C- or their N-terminus, corresponding to functionalization at either the 4- or the 9-position of acridine, respectively, and for assaying the nucleic acid binding properties of the resulting resins. We find that both the amino acid sequence of the PAC as well as its point of attachment to the solid support are important in determining affinity for duplex nucleic acids. These results have implications for the design of future on-bead and microarray-based selections and in understanding the nucleic acid binding of functionalized intercalators.     

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。     

Fluorescent Probes Based on Charge and Proton Transfer for Probing Biomolecular Environment

Fluorescent probes for sensing fundamental properties of biomolecular environment, such as polarity and hydration, help to study assembly of lipids into biomembranes, sensing interactions of biomolecules and imaging physiological state of the cells. Here, we summarize major efforts in the development of probes based on two photophysical mechanisms: (i) an excited-state intramolecular charge transfer (ICT), which is represented by fluorescent solvatochromic dyes that shift their emission band maximum as a function of environment polarity and hydration; (ii) excited-state intramolecular proton transfer (ESIPT), with particular focus on 5-membered cyclic systems, represented by 3-hydroxyflavones, because they exhibit dual emission sensitive to the environment. For both ICT and ESIPT dyes, the design of the probes and their biological applications are summarized. Thus, dyes bearing amphiphilic anchors target lipid membranes and report their lipid organization, while targeting ligands direct them to specific organelles for sensing their local environment. The labels, amino acid and nucleic acid analogues inserted into biomolecules enable monitoring their interactions with membranes, proteins and nucleic acids. While ICT probes are relatively simple and robust environment-sensitive probes, ESIPT probes feature high information content due their dual emission. They constitute a powerful toolbox for addressing multitude of biological questions.     

Study on suitability of KOD DNA polymerase for enzymatic production of artificial nucleic acids using base/sugar modified nucleoside triphosphates

Recently, KOD and its related DNA polymerases have been used for preparing various modified nucleic acids, including not only base-modified nucleic acids, but also sugar-modified ones, such as bridged/locked nucleic acid (BNA/LNA) which would be promising candidates for nucleic acid drugs. However, thus far, reasons for the effectiveness of KOD DNA polymerase for such purposes have not been clearly elucidated. Therefore, using mutated KOD DNA polymerases, we studied here their catalytic properties upon enzymatic incorporation of nucleotide analogues with base/sugar modifications. Experimental data indicate that their characteristic kinetic properties enabled incorporation of various modified nucleotides. Among those KOD mutants, one achieved efficient successive incorporation of bridged nucleotides with a 2'-ONHCH?CH?-4' linkage. In this study, the characteristic kinetic properties of KOD DNA polymerase for modified nucleoside triphosphates were shown, and the effectiveness of genetic engineering in improvement of the enzyme for modified nucleotide polymerization has been demonstrated.     

An Update of Nucleic Acids Aptamers Theranostic Integration with CRISPR/Cas Technology

The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system is best known for its role in genomic editing. It has also demonstrated great potential in nucleic acid biosensing. However, the specificity limitation in CRISPR/Cas has created a hurdle for its advancement. More recently, nucleic acid aptamers known for their high affinity and specificity properties for their targets have been integrated into CRISPR/Cas systems. This review article gives a brief overview of the aptamer and CRISPR/Cas technology and provides an updated summary and discussion on how the two distinctive nucleic acid technologies are being integrated into modern diagnostic and therapeutic applications     

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.     

Homopolymeric pyrrolidine-amide oligonucleotide mimics: Fmoc-synthesis and DNA/RNA binding properties

By chemically modifying or replacing the backbone of oligonucleotides it is possible to modulate the DNA and RNA recognition properties and fine-tune the physiochemical properties of oligomers. This is important because it challenges our understanding of natural nucleic acid structural and recognition properties and can lead to nucleic acid mimics with a wide range of applications in nucleic acid targeting, analysis or diagnostics. In this paper we describe the solid phase synthesis of pyrrolidine-amide oligonucleotide mimics (POMs) using Fmoc-peptide chemistry. This required the synthesis of adeninyl, cytosinyl, thyminyl and guaninyl pyrrolidine monomers, with Fmoc- and standard acyl-protecting groups on the exocyclic amino groups and nucleobases respectively. These monomers were used to synthesise several thyminyl and adeninyl POM pentamers, with modest coupling efficiency. The pentamers were purified by RP-HPLC, characterised by mass spectrometry and their DNA and RNA binding properties were investigated using UV thermal denaturation/renaturation experiments. This revealed that all the pentamers exhibit strong affinity for complementary nucleic acids. The further evaluation of longer mixed-sequence POMs is described in a second accompanying paper (R. J. Worthington et al., Org. Biomol. Chem., 2006, DOI: 10.1039/b613386j).     

Lipophilic nucleic acids — A flexible construction kit for organization and functionalization of surfaces

Lipophilic nucleic acids have become a versatile tool for structuring and functionalization of lipid bilayers and biological membranes as well as cargo vehicles to transport and deliver bioactive compounds, like interference RNA, into cells by taking advantage of reversible hybridization with complementary strands. This contribution reviews the different types of conjugates of lipophilic nucleic acids, and their physicochemical and self-assembly properties. Strategies for choosing a nucleic acid, lipophilic modification, and linker are discussed. Interaction with lipid membranes and its stability, dynamic structure and assembly of lipophilic nucleic acids upon embedding into biological membranes are specific points of the review. A large diversity of conjugates including lipophilic peptide nucleic acid and siRNA provides tailored solutions for specific applications in bio- and nanotechnology as well as in cell biology and medicine, as illustrated through some selected examples.     

功能化核酸适体的筛选及分子识别应用

核酸适体是从寡核苷酸文库中筛选获得的一段单链寡核苷酸. 由于能与多种靶标分子高特异性结合, 核酸适体已发展成为一种新兴的分子识别工具, 广泛应用于生物医学等领域. 天然核酸文库有限的化学组成限制了核酸适体的结构和功能, 进而限制了其在分子识别中的应用. 功能化核酸适体通过引入特定的化学官能团使核酸序列具有更丰富的构象和功能, 增强其分子识别能力. 然而, 功能化核酸很难与核酸扩增方法兼容, 因而难以使用传统筛选方法进行功能化核酸的筛选. 因此, 优化筛选方法对于获得具有优异性能的功能化核酸适体至关重要. 本综述总结了功能化核酸适体的筛选方法, 并介绍了其作为分子识别工具在生物医学领域中的应用.     

Aptasensors – the future of biosensing?

Aptamers are artificial nucleic acid ligands that can be generated against amino acids, drugs, proteins and other molecules. They are isolated from combinatorial libraries of synthetic nucleic acid by an iterative process of adsorption, recovery and reamplification. Aptamers, first reported in 1990, are attracting interest in the areas of therapeutics and diagnostics and offer themselves as ideal candidates for use as biocomponents in biosensors (aptasensors), possessing many advantages over state of the art affinity sensors. The properties of aptamers, their applicability to biosensor technology, current research and future prospects are addressed in this short review.     

Convertible and Constrained Nucleotides: The 2’-Deoxyribose 5’-C-Functionalization Approach,a French Touch

Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5’-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson–Crick base-pairing. We show that 5’-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5’-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C₂NA) providing unique tools to functionalize and stabilize nucleic acids.     

Structure and nuclease resistance of 2',4'-constrained 2'-O-methoxyethyl (cMOE) and 2'-O-ethyl (cEt) modified DNAs

Combining the structural elements of the second generation 2'-O-methoxyethyl (MOE) and locked nucleic acid (LNA) antisense oligonucleotide (AON) modifications yielded the highly nuclease resistant 2',4'-constrained MOE and ethyl bicyclic nucleic acids (cMOE and cEt BNA, respectively). Crystal structures of DNAs with cMOE or cEt BNA residues reveal their conformational preferences. Comparisons with MOE and LNA structures allow insights into their favourable properties for AON applications.     

Spherical Nucleic Acid Nanoparticle Conjugates Enhance G‐Quadruplex Formation and Increase Serum Protein Interactions

To understand the effect of three‐dimensional oligonucleotide structure on protein corona formation, we studied the identity and quantity of human serum proteins that bind to spherical nucleic acid (SNA) nanoparticle conjugates. SNAs exhibit cellular uptake properties that are remarkably different from those of linear nucleic acids, which have been related to their interaction with certain classes of proteins. Through a proteomic analysis, this work shows that the protein binding properties of SNAs are sequence‐specific and supports the conclusion that the oligonucleotide tertiary structure can significantly alter the chemical composition of the SNA protein corona. This knowledge will impact our understanding of how nucleic acid‐based nanostructures, and SNAs in particular, function in complex biological milieu.     

Invited Article Liquid-crystalline dispersions of nucleic acids

The formation and properties of dispersions of double stranded natural and synthetic nucleic acids are described. Evidence is given for the liquid-crystalline state of the nucleic acid within the dispersed droplets in these phases. The exploitation of nucleic acid dispersions in biosensors is discussed.     

Single-walled carbon nanotube as an effective quencher

Over the past few years, single-walled carbon nanotubes (SWNTs) have been the focus of intense research motivated by their unique physical and chemical properties. This review specifically summarizes recent progress in the development of fluorescence biosensors that integrate the quenching property of SWNTs and the recognition property of functional nucleic acids. SWNTs are substantially different from organic quenchers, showing superior quenching efficiency for a variety of fluorophores, with low background and high signal-to-noise ratio, as well as other advantages derived from the nanomaterial itself. As the second key component of biosensors, functional nucleic acids can bind to either their complementary DNA or a target molecule with the ability to recognize a broad range of targets from metal ions to organic molecules, proteins, and even live cells. By taking advantage of the strengths and properties of both SWNTs and nucleic acid based aptamers, a series of fluorescence biosensors have been designed and fabricated for the detection of a broad range of analytes with high selectivity and sensitivity.     

Supramolecular Materials Comprising Nucleic Acid Biopolymers

We have generated a supramolecular self-assembling film by exchanging the counter-ions of the phosphate moieties in nucleic acid with those of cationic amphiphiles as didodecyldimethylammonium bromide (or DDAB). SAXS and WAXS data for all film samples showed similar harmonic peaks suggesting a lamellar multilayer structure with layers of nucleic acids being separated by lipid bilayers of DDAB. AFM height images also showed that double stranded nucleic acid film can form the step or plateau type of structure and shorter nucleic acid film showed shorter step feature. Moreover, the length and the molecular structure of DNA and RNA can be used to manipulate the mechanical properties of these self-assembled films.