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Part II: Molecular Recognition in Protein Assay
Part II
Molecular Recognition in Protein Assay A biosensor, consisting of a biorecognition element, a biotransducer component, and a signal output system, employs the biomolecules such as antibodies, nucleic acids, peptides, and small molecules for the detection of analytes by converting a biological response into an electrical or optical signal. One of the essential components in the fabrication of a biosensor for protein analysis is the molecular recognition part that is capable of identifying the protein of interest in a given sample and ensuring a high degree of selectivity. So, the establishment of the molecular recognition part is the first step for the fabrication of nano-inspired biosensor, which plays a crucial role in protein assay. Molecular recognition refers to the specific interaction between two or more molecules through noncovalent bonding such as hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, π π interactions, halogen bonding, electrostatic, and/or electromagnetic effects. It can occur in between receptor ligand, antigen antibody, DNA protein, peptide protein, small molecule protein/peptide, etc. Among them, antigen antibody interaction is a specific chemical interaction between antibodies produced by B cells of the white blood cells and antigens during immune reaction. The antibodies specifically bind to antigens to form an antigen antibody complex through weak and noncovalent interactions such as electrostatic interactions, hydrogen bonds, Van der Waals forces, and hydrophobic interactions. Each antibody is capable of binding to only one specific antigen and the specificity of the binding is due to the specific chemical constitution of each antibody. For DNA protein interaction, it occurs when a protein binds to a molecule of DNA to regulate the biological function of DNA. Generally, the proteins can specifically or nonspecifically bind to DNA in the major groove. The specific interaction between DNA and protein can be utilized for the detection of protein. Up to now, a type of single-stranded oligonucleotide (called aptamer), screened from a large random DNA or RNA library, represents a promising alternative for antibodies in the field of molecule recognition, in view of the advantages including the comparable binding affinity and selectivity towards protein of interest,
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PART | II Molecular Recognition in Protein Assay
cost-effective chemical synthesis, high stability and remarkable flexibility, and convenience in design and modification. Apart from antigen or antibody and aptamer, protein can also be specifically recognized by peptides. For example, Peptide T, a short peptide derived from the HIV envelope protein gp120, can bind to the CCR5 receptor so as to block binding and infection of viral strains. In addition, small molecule ligands with high specificity and affinity can interact with the protein/peptide. For instance, the antibiotic vancomycin selectively binds to the peptides with terminal D-alanyl-D-alanine in bacterial cells through five hydrogen bonds. In this part, we aim to provide an overview of major advances in the field of nano-inspired biosensors for detecting disease protein biomarkers with a special focus on the recognition elements. According to the molecular recognition component and mechanism, the biosensors can be classified as immune-biosensor, aptasensors, peptide-based biosensors, and biosensorbased on protein small molecule interaction, and so on.
Molecular Recognition in Protein Assay A biosensor, consisting of a biorecognition element, a biotransducer component, and a signal output system, employs the biomolecules such as antibodies, nucleic acids, peptides, and small molecules for the detection of analytes by converting a biological response into an electrical or optical signal. One of the essential components in the fabrication of a biosensor for protein analysis is the molecular recognition part that is capable of identifying the protein of interest in a given sample and ensuring a high degree of selectivity. So, the establishment of the molecular recognition part is the first step for the fabrication of nano-inspired biosensor, which plays a crucial role in protein assay. Molecular recognition refers to the specific interaction between two or more molecules through noncovalent bonding such as hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, π π interactions, halogen bonding, electrostatic, and/or electromagnetic effects. It can occur in between receptor ligand, antigen antibody, DNA protein, peptide protein, small molecule protein/peptide, etc. Among them, antigen antibody interaction is a specific chemical interaction between antibodies produced by B cells of the white blood cells and antigens during immune reaction. The antibodies specifically bind to antigens to form an antigen antibody complex through weak and noncovalent interactions such as electrostatic interactions, hydrogen bonds, Van der Waals forces, and hydrophobic interactions. Each antibody is capable of binding to only one specific antigen and the specificity of the binding is due to the specific chemical constitution of each antibody. For DNA protein interaction, it occurs when a protein binds to a molecule of DNA to regulate the biological function of DNA. Generally, the proteins can specifically or nonspecifically bind to DNA in the major groove. The specific interaction between DNA and protein can be utilized for the detection of protein. Up to now, a type of single-stranded oligonucleotide (called aptamer), screened from a large random DNA or RNA library, represents a promising alternative for antibodies in the field of molecule recognition, in view of the advantages including the comparable binding affinity and selectivity towards protein of interest,
114
PART | II Molecular Recognition in Protein Assay
cost-effective chemical synthesis, high stability and remarkable flexibility, and convenience in design and modification. Apart from antigen or antibody and aptamer, protein can also be specifically recognized by peptides. For example, Peptide T, a short peptide derived from the HIV envelope protein gp120, can bind to the CCR5 receptor so as to block binding and infection of viral strains. In addition, small molecule ligands with high specificity and affinity can interact with the protein/peptide. For instance, the antibiotic vancomycin selectively binds to the peptides with terminal D-alanyl-D-alanine in bacterial cells through five hydrogen bonds. In this part, we aim to provide an overview of major advances in the field of nano-inspired biosensors for detecting disease protein biomarkers with a special focus on the recognition elements. According to the molecular recognition component and mechanism, the biosensors can be classified as immune-biosensor, aptasensors, peptide-based biosensors, and biosensorbased on protein small molecule interaction, and so on.