Aptamers for DNA Damage and Repair

Multi-aptamer-mediated hairpin allosteric and aptamer-assisted CRISPR system for detection of S. pneumoniae and S. aureus

A novel nucleic acid aptamer nanoprobes-mediated hairpin allosteric and aptamer-assisted CRISPR system for detection of Streptococcus pneumoniae and Staphylococcus aureus is presented. In this fluorescence assay system, utilizing the hairpin allosteric effect caused by the aptamer binding to the target bacteria, the detection of S. pneumoniae is first achieved through changes in fluorescence due to FRET. Subsequently, a Cas12a protein mixture is added to detect S. aureus. The amplified output signal is triggered by two methods to ensure the sensitivity of the method: the synergistic FRET effect is achieved by the assembly of multi-aptamer through the conjugation of streptavidin-biotin, and the trans-cleavage function of CRISPR/Cas 12a. Under the optimized conditions, the proposed hairpin allosteric aptasensor could achieve high sensitivity (a detection limit of 135 cfu/mL) and broad-concentration quantification (dynamic range of 103-107 cfu/mL) of S. pneumoniae. The aptamer-assisted CRISPR system for S. aureus detection showed good linearity (R2 = 0.996) in the concentration range 102-108 cfu/mL, with a detection limit of 39 cfu/mL. No cross-reactivity with other foodborne pathogenic bacteria was observed in both systems. Taking only 55 min, this method of multiple pathogen detection proved to be promising.

High-sensitivity small-molecule detection of microcystin-LR cyano-toxin using a terahertz-aptamer biosensor

We demonstrate the rapid and highly sensitive detection of a small molecule, microcystin-LR (MC-LR) toxin using an aptasensor based on a terahertz (THz) emission technique named the terahertz chemical microscope (TCM). The main component of the TCM is the sensing plate, which consists of a thin silicon layer deposited on a sapphire substrate, with a natural SiO₂ layer formed on the top of the Si layer. The DNA aptamer is linked to the oxidized top surface of the silicon layer by a one-step reaction (click chemistry) between the DBCO-labeled aptamer and an azido group that binds to the surface. Using density functional theory (DFT) calculations, the number of active sites on the surface has been estimated to be 3.8 × 10¹³ cm^-2. Aptamer immobilization and MC-LR binding have been optimized by adjusting the aptamer concentration and the binding buffer composition. When MC-LR binds with the DNA aptamer, it causes a change in the chemical potential at the surface of the sensing plate, which leads to a change in the amplitude of the THz signal. Compared with other bio-sensing methods such as surface plasmon resonance (SPR), TCM is a rapid assay that can be completed in 15 min (10 min incubation and 5 min data acquisition). Moreover, our results show that the aptamer-based TCM can detect MC-LR with an excellent detection limit of 50 ng L^-1, which is 20 times more sensitive compared with SPR measurements of MC-LR.

Food components and diet habits: chief factors of cancer development

Food is a vital need for everyone. Today, there is food for all, but the world still suffers from under- and over-nutrition and risk of cancer development and chronic diseases can follow both cases. Worldwide, cancer is a leading cause of mortality after cardiovascular disease; it is considered the second reason for death globally. Role of nutritional habits, the quality of food, the consumption of canned foods, genetically modified fruits and vegetables and exposed food to certain pesticides and carcinogens agents, and unhealthy lifestyle behaviours such as smoking, alcohol, obesity, and fast-foods consumption may be at risk to the development of some cancers. In recent decades, researchers have carried out attention in this field to improve the quality of life and to limit nutrition problems. Thus, this study aims to summarize current evidence on the relationship between nutritional factors and cancer expansion, how nutrition can be a heal and a source of fatal illness leading to death. In detail, this review will highlight the influence of specific foodstuffs on the threat of cancer incidence and recurrence by providing some examples of most carcinogenic compounds.

DNA repair and neurological disease: From molecular understanding to the development of diagnostics and model organisms

In both replicating and non-replicating cells, the maintenance of genomic stability is of utmost importance. Dividing cells can repair DNA damage during cell division, tolerate the damage by employing potentially mutagenic DNA polymerases or die via apoptosis. However, the options for accurate DNA repair are more limited in non-replicating neuronal cells. If DNA damage is left unresolved, neuronal cells die causing neurodegenerative disorders. A number of pathogenic variants of DNA repair proteins have been linked to multiple neurological diseases. The current challenge is to harness our knowledge of fundamental properties of DNA repair to improve diagnosis, prognosis and treatment of such debilitating disorders. In this perspective, we will focus on recent efforts in identifying novel DNA repair biomarkers for the diagnosis of neurological disorders and their use in monitoring the patient response to therapy. These efforts are greatly facilitated by the development of model organisms such as zebrafish, which will also be summarised.

Aptamers: an emerging class of bioaffinity ligands in bioactive peptide applications

The food and health applications of bioactive peptides have grown remarkably in the past few decades. Current elucidations have shown that bioactive peptides have unique structural arrangement of amino acids, conferring distinct functionalities, and molecular affinity characteristics. However, whereas interest in the biological potency of bioactive peptides has grown, cost-effective techniques for monitoring the structural changes in these peptides and how these changes affect the biological properties have not grown at the same rate. Due to the high binding affinity of aptamers for other biomolecules, they have a huge potential for use in tracking the structural, conformational, and compositional changes in bioactive peptides. This review provides an overview of bioactive peptides and their essential structure-activity relationship. The review further highlights on the types and methods of synthesis of aptamers before the discussion of the prospects, merits, and challenges in the use of aptamers for bioaffinity interactions with bioactive peptides.

Three decades of nucleic acid aptamer technologies: Lessons learned, progress and opportunities on aptamer development

Aptamers are short single-stranded nucleic acid sequences capable of binding to target molecules in a way similar to antibodies. Due to various advantages such as prolonged shelf life, low batch to batch variation, low/no immunogenicity, freedom to incorporate chemical modification for enhanced stability and targeting capacity, aptamers quickly found their potential in diverse applications ranging from therapy, drug delivery, diagnosis, and functional genomics to bio-sensing. Aptamers are generated by a process called SELEX. However, the current overall success rate of SELEX is far from being satisfactory, and still presents a major obstacle for aptamer-based research and application. The need for an efficient selection strategy consisting of defined procedures to deal with a wide variety of targets is significantly important. In this work, by analyzing key aspects of SELEX including initial library design, target preparation, PCR optimization, and single strand DNA separation, we provide a comprehensive analysis of individual steps to facilitate researchers intending to develop personalized protocols to address many of the obstacles in SELEX. In addition, this review provides suggestions and opinions for future aptamer development procedures to address the concerns on key SELEX steps, and post-SELEX modifications.

Imaging cellular responses to antigen tagged DNA damage

Repair pathways of covalent DNA damage are understood in considerable detail due to decades of brilliant biochemical studies by many investigators. An important feature of these experiments is the defined adduct location on oligonucleotide or plasmid substrates that are incubated with purified proteins or cell free extracts. With some exceptions, this certainty is lost when the inquiry shifts to the response of living mammalian cells to the same adducts in genomic DNA. This reflects the limitation of assays, such as those based on immunofluorescence, that are widely used to follow responding proteins in cells exposed to a DNA reactive compound. The lack of effective reagents for adduct detection means that the proximity between responding proteins and an adduct must be assumed. Since these assumptions can be incorrect, models based on in vitro systems may fail to account for observations made in vivo. Here we discuss the use of a detection tag to address the problem of lesion location, as illustrated by our recent work on replication dependent and independent responses to interstrand crosslinks.