Current Organic Chemistry - Volume 15, Issue 4, 2011

DNA detection is among the most important and fundamental techniques in molecular biology. More significantly, detection of DNA targets is increasingly important in various application areas such as medical diagnostics, food safety and antibioterrorism. While there have been numerous DNA assay kits in the market, mostly based on polymerase chain reactions (PCR), there have been ever-growing efforts to develop new DNA detection methods to meet the requirements of high sensitivity, high speed and low cost. It is the motivation of this special issue, focused on “Designing DNA probes”, to provide readers a range of new technologies emerging in this area within ten reviews. These approaches might seem to be novel for biologists as they mostly rely on non-traditional approaches such as nanotechnology and functional materials. We hope the introduction of these new and relatively immature technologies will bring new viewpoints in this important area, eventually leading to breakthroughs that will greatly contribute to the society. Since the invention of PCR by Kary Mullis, which awarded him Nobel Prize in chemistry in 1993, this technology has become the paradigm in nucleic acid tests (NATs) due to many unprecedented advantages, particularly unparalleled sensitivity. Despite that, there have been long-lasting efforts to optimize PCR protocols in order to increase its specificity and robustness that hampered its widespread applications in the history. Along this direction, Mi et al. reviewed recent progress on nanomaterials-enhanced PCR protocols in this special issue [ref. 1]. Despite the predominant role of PCR, hybridization-based DNA detection is superior in specificity due to the extremely high recognition specificity of Waston-Crick base pairing. In this issue, several groups presented a range of complementary DNA sensing technologies, including electrochemical DNA sensors [refs. 2,3], cantilever-based mechanical DNA sensors [ref. 4], conjugated polymerbased fluorescent DNA sensors [refs. 5,6] and colorimentric detection with vesicles [ref. 7]. Aptamers are a class of novel functional nucleic acid structures that was discovered in early 1990s. The discovery of aptamers reveals a new function of nucleic acids, high target recognition ability and affinity, which was traditionally regarded as the unique property of proteinbased antibodies. Aptamers are selected via an in-vitro evolution method dubbed SELEX (Systematic Evolution of Ligands by Exponential Enrichment). Two groups reviewed recent progress on aptamer-based detection that extends the range of DNA detection to virtually any target detection with aptamer-based sensors [refs. 8, 9]. The unparalleled recognition ability of DNA makes it possible to construct DNA nanostructures with high precision and design flexibility. Consequently, DNA nanotechnology has emerged as a highly promsing area in nanotechnology. In this context, DNA is regarded as a one-dimensional nanowire rather than a piece of “gene” with biological functions. Despite that, recent studies have well demonstrated that DNA nanostructures can be adapted to serve as platforms for DNA detection. In the last review article of this issue, Zhang et al. reviewed recent progress on design and fabrication of DNA nanostructures, and the application of DNA nanostructures in biodetection [ref. 10]. Clearly, while this special issue provides exciting developments in the area of DNA detection, we could only present a limited number of snapshots for this highly promising area, much less than we would like to cover. Despite that, I feel it a great honor for me to have this chance to compile so many excellent reviews from leading experts from different countries in this special issue. I hope (and believe) readers from many areas including chemistry, materials, biomedical science, nanotechnology would benefit from this special issue and may, hopefully, be inspired to contribute to this exciting area. Last but not least, I would like to appreciate the hard work from all authors and, certainly, the kind help from the editorial office of Current Organic Chemistry.

The most widely studied cationic polyfluorene homopolymers and copolymers are fluorene-containing conjugated polymers with quarternary amine groups on side chains which render them soluble in polar solvents. This review summarizes the polymer structures and various synthetic methods to water-soluble polyfluorenes (PF) and their derivatives which include poly(fluorene-cophenylene)s, poly(fluorene-co-benzothiadiazole)s, poly(fluorene-co-thiophene)s, poly(fluorenevinylene)s and poly(fluorenethynylene)s. This is followed by a brief survey on the polymer optical properties. Finally, the application of cationic PF homopolymers and copolymers in DNA sensing is discussed.

Nucleic acids are unique molecular recognition elements in biosensors having targets that range from ions, small molecules, peptides, proteins and DNA/RNA to virus and whole cells. Pyrene is a polycyclic aromatic compound with very special photophysical characteristics, including long fluorescence lifetime, high quantum yield, and the capability of forming excited state dimers with large Stokes shift. In recent years, pyrene has been used extensively as a novel signaling element in nucleic acid sensors. In this review, we will discuss the optical properties of pyrene and summarize recent progress in the development of pyrene DNA probes for the sensing of nucleic acids, proteins, and small molecules.

Microcantilever based biosensors have attracted much attention as a label-free, real-time and highly sensitive approach to the detection of biomolecules. When specific biomolecular interactions occur between a receptor immobilized on one side of a cantilever and a target analyte in solution, a mechanical bending of the cantilever results due to a change in surface stress, thereby translating biochemical interactions into a concentration-dependent nanomechanical response of the microcantilevers. In this review, we present a general overview of the operation principles, fabrication and preparation of microcantilever biosensors and discuss their uses for a wide range of biosensing applications. The focus of the review is given to probing the biomolecular interactions at the solid-liquid interface by measuring the cantilever bending. In addition to the label-free detection of DNA, protein and cells, the emphasis is also made to discuss about the new development of microcantilever biosensors for label-free probing nanoscale conformational changes of DNA, protein and polymers, and real-time detection of nanomechanical forces from living cells. Finally, the outlook for future development work and challenges is also discussed.

A range of nanometer-sized materials such as metal nanoparticles, semiconductor quantum dots, metal oxide nanostructures, carbon nanomaterials and polymer nanoparticles, have been introduced into polymerase chain reactions (PCR). They have shown to remarkably improve PCR amplification in sensitivity, specificity and extension rate. In this review, we will try to describe the development of nanomaterials-based PCR, including the types of nanomaterials, optimization of properties and mechanisms. In particular, several mechanisms have been introduced in view of special physical and chemical properties of nanomaterials.

Aptamers are with their selectivity and affinity for specific target ligands ideal biorecognition units for any biosensor development. The development of improved techniques for in vitro selection of aptamers with high affinities (comparable to antibodies) for target molecules has transformed aptamers from costly and restrictedly accessible species into readily synthetically available biorecognition material for almost all possible targets - from small molecules to proteins and whole cells. Unsurprisingly, the new potential of aptamers has also been applied for development of novel aptamer-based electrochemical biosensors. In this paper we overview general tendencies and recent advances in this field, exemplified by impedimetric and electrochemical conformational aptamer-based biosensors, electrochemical aptamer-based biosensors exploiting redox indicators, catalytic and quantum dot labels, and inherent redox activity of DNA, and aptamer-modified field-effect transistors.

Electrochemical DNA sensors have been increasingly fascinating due to high sensitivity, specificity, portability and integrated compatibilities with microelectronics. Numerous strategies have been developed to design electrochemical DNA sensors with high sensitivity and selectivity. In this review, we will focus on the efforts toward sensitive electrochemical DNA sensing based on nanomaterials including metal nanoparticles, magnetic nanoparticles, semiconductor nanoparticles and carbon nanomaterials, especially carbon nanotubes. The potential application of the electrochemical DNA sensors in gene analysis, diagnosis, environmental and food safety monitoring will be briefly discussed. At the end of this review, we will give a brief outlook of the future challenges of electrochemical DNA sensors.

Polydiacetylenes (PDAs) have gained much interest in recent years because of their distinctive chromatic transition property. The PDA molecules can be self-assembled into thin films or vesicles that could undergo blue-red transformations in response to different stimuli, like temperature, pH, and the presence of biological molecules. Due to this unique chromatic property, PDA materials have emerged as an attractive option for biosensing applications. Functionalized PDA has been used as a platform for detection of biological analytes, including viruses, microorganisms, and proteins. In this paper, we will review the formation of PDA films and vesicles, their optical properties, and their potential applications as biosensors.

Apart from providing the material for genetic information storage, DNA has also been regarded as a useful building block in the field of nanotechnology, which is known as DNA nanotechnology. Based on the Watson-Crick base-pairing and the famous double helical structure, a library of DNA 2D or 3D nanostructures has been designed, constructed and characterized, by either tile-based or origami- based self-assembly. More significantly, other molecules/nanomaterials can be organized on those DNA ensembles to achieve highly ordered arrays or specific patterns in nanometer spatial resolution. In this review, we summarize recent progress in creating DNA nanoarchitectures, and discuss potential applications in DNA-based nanofabrication.

Signal amplification property and versatility in molecular design of conjugated polymers make them attractive as signal transducers for DNA detection both in homogenous solution as well as on solid support. The aim of the present article is to review recent efforts in the area of DNA biosensor on solid support that employ fluorescent conjugated polymer for signal transduction. Two solid support formats are commented here: microarrays on glass surface and microspheres (or nanoparticles). Combining the convenient signal amplifying properties of conjugated polymers with high-throughput assay of microarray will not only meet the demanding challenges for the development of highly sensitive DNA microarrays, but also broaden the application field of conjugated polymers.

The abundance of small molecules in biological systems, the wide-spread usage of synthetic small molecules as drugs and biological probes, and the escalation of industrial pollutants in our environment, underscore the importance of detection of small molecules for many disciplines. Functional nucleic acids (FNAs) are single-stranded DNA or RNA sequences that are capable of carrying out ligand binding (aptamers), catalysis (nucleic acid enzymes) or both functions (aptazymes). Many FNAs have been shown to be suitable molecular recognition elements for small-molecule targets. In this article, we will present a focused review on FNAs for small molecule binding and detection. First, we will discuss the technique of “in vitro selection” by which artificial FNAs can be isolated from random-sequence DNA or RNA pools. This will be followed by a survey of aptamers for small molecules isolated to date. Next, the diverse functions of natural aptamers, as part of riboswitches (metabolite-sensing RNA regulatory systems that exist in many organisms) will be explored. Efforts in creating aptazymes will also be presented. Finally, we will examine numerous applications of aptamers and aptazymes in the development of fluorescent, colorimetric and electrochemical biosensors and discuss some emerging applications concerning FNAs.

Synthesized nearly one century ago as a saccharine-like sweetener compound, the o-benzenedisulfonimide has received a discontinuous attention in the past. In the last century, various synthetic procedures have been reported, in confirmation of the interest in this intriguing compound. In recent years, it has been used as a leaving group in reactions of nucleophilic substitution of amines with alcohols or phenols to give the corresponding ethers. Its N-fluoroderivative is a stable and efficient fluorinating agent, which has found applications in several asymmetric syntheses. In previous studies, its conjugated base has been extensively used as stabilizing counter-ion of arenediazonium salts; safely isolated and stored in a dry state, ready to use, they have been applied successfully in many dediazoniation reactions, with interesting mechanistic insights. More recently, due to its high acidity, the o-benzenedisulfonimide has been used in catalytic amounts in some common acid-catalyzed organic reactions. Valuable aspects of this catalyst are its easy recovery from the reaction mixture and its reuse in other reactions, with clear economic and ecological advantages. Finally, the disulfonimide functional group has been proposed as a powerful chiral motif for strong Brønsted acids in asymmetric organocatalysis.