The quest to improve the detection of biomolecules and cells in health and life sciences has led to the discovery and characterization of various affinity bioprobes. Libraries of synthetic oligonucleotides (ssDNA/ssRNA) with randomized sequences are employed during Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to select highly specific affinity probes called aptamers. With much focus on the generation of aptamers for a variety of target molecules, conventional SELEX protocols have been modified to develop new and improved SELEX protocols yielding highly specific and stable aptamers. Various techniques have been used to analyze the binding interactions between aptamers and their cognate molecules with associated merits and limitations. This article comprehensively reviews research advancements in the generation of aptamers, analyses physicochemical conditions affecting their binding characteristics to cellular and biomolecular targets, and discusses various field applications of aptameric binding. Biophysical techniques employed in the characterization of the molecular and binding features of aptamers to their cognate targets are also discussed.

Peptide aptamers are combinatorial protein molecules with specific bind affinity to given target proteins under intracellular conditions. The typical structure of peptide aptamers is a short peptide region inserted within a scaffold protein. The short peptide region is responsible for binding with its target protein and the scaffold protein helps to enhance the binding affinity and specificity through restriction on the conformation of the binding peptide. This unique structural feature allows peptide aptamers to bind with their target proteins with strong affinity and high specificity. Applications of peptide aptamers thus vary from in vitro detection of various proteins in a complex mixture to in vivo modulation on proteins and cell functions. Peptide aptamers have also been considered as therapeutic molecules because of their anticancer and antivirus activity. Due to the importance of peptide aptamers, a general review on the structure, selection and applications of peptide aptamers in biological study as well as in therapeutics will be presented in this paper.

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Chapter 1 -Introduction 1.1 Applications of peptide ligation 1.2 Peptide ligation tools 1.3 Ligases from Nature 1.3.1 Sortase A and Gram-Positive Bacteria Cell Wall 1.3.2 Plant Asparaginyl Endopeptidase Engineered Ligases