1. Breakdown of Core Concepts XNA (Xeno Nucleic Acids): Refers to all nucleic acid analogs whose chemical structures differ from natural DNA and RNA. Common examples include: HNA (Hexitol Nucleic Acid), FANA (2'-Fluoro Arabino Nucleic Acid), LNA (Locked Nucleic Acid), CeNA (Cyclohexene Nucleic Acid), etc. Key Features of XNA: They typically exhibit greatly enhanced nuclease resistance (higher stability in biological fluids), higher thermal stability, and potentially a more diverse three-dimensional structural space, providing a foundation for discovering high-performance aptamers. Aptamer: A short, single-stranded DNA, RNA, or XNA oligonucleotide that can bind specifically and with high affinity to a target molecule (e.g., a protein, small molecule, cell). It can be considered a "chemical antibody." Functionally Enhanced: Here, it specifically refers to aptamers discovered using an XNA backbone, which inherently possess superior functional properties compared to natural nucleic acid aptamers, such as: Extremely high stability in vivo and in vitro (resistant to degradation). Stronger binding affinity and specificity. Broader tolerance to physicochemical conditions (e.g., pH, temperature range). Parallelized Library Screening: Refers to the use of high-throughput, automated experimental platforms (e.g., microfluidic chips, droplet microfluidics, next-generation sequencing-coupled techniques) to simultaneously screen an XNA random library containing an enormous number of sequences (typically 10^13 - 10^15). This dramatically accelerates the discovery process. 2. Overview of the Technical Workflow The entire discovery process is a…
Aptamers are short, single-stranded oligonucleotides (DNA or RNA) that bind to specific targets (proteins, small molecules, cells) with high affinity and specificity. Their generation has traditionally been dominated by the SELEX (Systematic Evolution of Ligands by EXponential enrichment) process. However, this method has significant limitations, driving innovation toward non-SELEX approaches. 1. Current Predominant Method: SELEX SELEX is an iterative, in vitro selection-amplification process with several variations, each suited for different targets and applications. Core Steps of SELEX: Library Creation: A random oligonucleotide library (10¹³–10¹⁵ sequences) flanked by fixed primer sites. Incubation & Binding: Library exposed to the target. Partitioning: Separation of target-bound sequences from unbound ones. Amplification: PCR (DNA) or RT-PCR (RNA) of bound sequences. Repetition: Typically 8–15 cycles to enrich high-affinity binders. Cloning & Sequencing: Identification of enriched aptamer candidates. Key Variations of SELEX: Cell-SELEX: Uses whole cells as targets, ideal for biomarker discovery. Capture-SELEX: For small molecules, using immobilized targets. Capillary Electrophoresis-SELEX (CE-SELEX): High-efficiency partitioning via electrophoresis. Microfluidic-SELEX: Reduces time and reagent use via automation. Magnetic Bead-Based SELEX: Easy separation using target-coated beads. Limitations of SELEX: Time-Consuming: Multiple cycles take weeks to months. Labor-Intensive: Requires significant hands-on effort. Amplification Bias: PCR can favor certain sequences unrelated to binding. Limited Sequence Diversity: Early high-affinity binders can dominate, reducing diversity. Cost: High reagent and time costs. 2. Emerging Trend: Non-SELEX Approaches…
Excellent choice! Aptamer Screening is the core process for discovering these synthetic, single-stranded DNA or RNA molecules that bind to a specific target with high affinity and specificity. It's often called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Here’s a comprehensive breakdown of aptamer screening, from concept to modern advancements. 1. The Core Principle: SELEX The traditional screening method is an in vitro Darwinian evolutionary process. The basic cycle is repeated until a pool of high-affinity aptamers is obtained. Key Steps: Library Design: Start with a vast random-sequence oligonucleotide library (10^13 - 10^15 different molecules). Each molecule has a central random region (20-60 nucleotides) flanked by constant primer regions for PCR amplification. Incubation: The library is incubated with the target molecule (e.g., a protein, small molecule, cell). Partitioning: Unbound sequences are washed away. Bound sequences (potential aptamers) are retained. This is the most critical step, dictating the success of the entire screen. Elution: The bound sequences are recovered (e.g., by heating, denaturing agents, or target digestion). Amplification: The recovered sequences are amplified by PCR (for DNA) or RT-PCR (for RNA) to create an enriched pool for the next round. Iteration: Steps 2-5 are repeated (typically 5-15 rounds) under increasingly stringent conditions (e.g., shorter incubation time, more washes, competitive agents) to select…
Ribosome Display is a cell-free (in vitro) display technology used to evolve and select peptides or proteins by keeping a physical connection between phenotype (the translated peptide/protein) and genotype (the encoding mRNA). Instead of relying on a living host (as in phage or yeast display), ribosome display uses a stalled translation complex so that the newly made polypeptide remains associated with the ribosome, which in turn remains associated with its mRNA—forming a non-covalent ternary complex that can be selected for binding or function. 1) What Ribosome Display Is (And Why the mRNA Link Matters) Display technologies work best when every “candidate molecule” can be traced back to the genetic information that produced it. In ribosome display, this tracking is achieved by stabilizing a complex often described as: nascent polypeptide – ribosome – mRNA Because the polypeptide and its mRNA remain physically connected through the ribosome, any selection step that enriches for a desired function (for example, binding to a target) can be followed by recovery of the encoding mRNA, conversion to cDNA, and amplification—creating an iterative loop of evolution entirely in vitro. 2) Core Mechanism: How the Ribosome “Holds” the Peptide to the mRNA The stalled translation complex…
1) What “Bacterial Display” Means (and Why It Matters) Bacterial Display (also called bacterial surface display) is a protein/peptide engineering method where a bacterium is genetically programmed to present a peptide (or protein fragment) on its outer surface, while the DNA encoding that peptide remains inside the same cell. This physically links phenotype (binding/function) to genotype (the encoding sequence), enabling efficient discovery and optimization of peptides from large libraries. 2) Core Principle: Surface Presentation + High-Throughput Selection A typical bacterial display workflow looks like this: Build a peptide library Create DNA encoding millions of peptide variants (often randomized regions) and clone them into a plasmid or genomic locus. Fuse peptides to a “surface scaffold” The library peptides are genetically fused to a bacterial surface-localized protein (the scaffold) so they are exported and exposed externally. Common scaffold classes include outer membrane proteins, autotransporters, fimbriae/flagella, and engineered systems like circularly permuted outer membrane proteins used for peptide display. Expose library cells to a target The target might be a purified protein, a receptor domain, a small molecule conjugate, or even whole cells (depending on the goal). Select the winners Enriched cells are collected using methods like FACS (fluorescence-activated cell sorting)…
Yeast Display (also called Yeast Surface Display, YSD) is a protein engineering and screening technology that presents peptides or proteins on the outside surface of yeast cells, effectively turning each yeast cell into a “living bead” that physically links a displayed molecule (phenotype) to its encoding DNA inside the cell (genotype). This makes it especially powerful for building and screening peptide libraries to discover binders, optimize affinity, and study molecular interactions. 1) What “Yeast Display” Means in Practice In yeast display, researchers genetically fuse a peptide (or protein) to a yeast surface-anchor system so that the peptide is exported through the secretory pathway and tethered to the cell wall. A classic and widely used anchoring strategy in Saccharomyces cerevisiae is the Aga1p–Aga2p system, where a fusion partner (often Aga2p) helps attach the displayed peptide to the cell surface, while the encoding plasmid remains inside the same cell. This one-cell-one-variant format is what makes library screening so efficient. 2) Why Yeast Is a Strong Host for Display Libraries Yeast is a eukaryote, so it can support more complex folding and quality control than many prokaryotic systems. For many peptide/protein scaffolds, this can translate into improved display of properly folded…
mRNA Display is an in vitro selection and directed-evolution technology that physically couples a peptide (or protein) to the mRNA sequence that encodes it through a covalent bond. This genotype–phenotype “fusion” allows researchers to screen enormous molecular libraries and then recover the winning sequences by amplification, enabling fast, iterative optimization under tightly controlled experimental conditions. 1) The Core Idea: Genotype–Phenotype Coupling Without Cells Every selection technology needs a reliable way to keep “what a molecule does” attached to “the information that made it.” In mRNA Display, that attachment is literal: the newly made peptide becomes covalently linked to its own mRNA, producing a stable fusion that survives stringent washing and enrichment steps. This is a major conceptual advantage over systems where the linkage is non-covalent or depends on living cells for propagation. Because the entire workflow is performed in vitro, the experimenter can tune conditions (buffers, salts, temperature, denaturants, competitors) to match the target biology and the selection pressure they want to apply. 2) How the Covalent Link Is Formed: Puromycin at the 3′ End The “magic” reagent behind classic mRNA Display is puromycin, a molecule that mimics the 3′ end of an aminoacyl-tRNA. When puromycin is physically…
In biological and biomedical sciences, the term “target” refers to a specific molecule or structure within a living system that researchers aim to observe, influence, or regulate. Although often discussed in the context of drug discovery, targets extend far beyond that domain and include proteins, receptors, enzymes, nucleic acids, and even cell-surface markers that influence physiological and pathological processes. Understanding how targets function provides essential insight into cellular signaling, disease mechanisms, and therapeutic innovation. 1. What Is a Biological Target? A biological target is any molecular entity that participates in a measurable biological activity. It may act as a signal transmitter, structural component, metabolic regulator, or interaction hub within a biochemical pathway. Researchers identify and characterize targets to understand how biological responses are initiated and how they can be modulated to achieve desired outcomes. Common categories of targets include: Proteins – structural proteins, transport proteins, transcription factors Receptors – membrane-bound or intracellular sensors that respond to chemical signals Enzymes – catalysts that regulate metabolic reactions Cell surface markers – characteristic molecules on the external cell membrane used to identify and classify cell types Ion channels – regulators of cellular electrical activity Nucleic acids – DNA or RNA sequences involved…
Amino acids are essential organic molecules that serve as the primary building blocks of peptides and proteins—structures at the core of nearly every biological process. Their unique chemical properties allow them to assemble into countless configurations, enabling life to grow, repair, and operate with extraordinary precision. What Are Amino Acids? Amino acids are small, nitrogen-containing compounds composed of an amino group, a carboxyl group, and a distinct side chain. This side chain—also called the R-group—defines each amino acid’s characteristics, dictating how it interacts with others and influencing the structure of peptides and proteins. Amino Acids as the Basis of Peptides Peptides form when amino acids link together through peptide bonds. This occurs via a condensation reaction, where the carboxyl group of one amino acid connects to the amino group of another. As more amino acids join the chain, they develop into polypeptides, which eventually fold into complex, three-dimensional protein structures. These proteins then serve roles in catalysis, structure, signaling, immunity, and metabolism. Types of Amino Acids Amino acids can be classified into several categories based on their chemical characteristics: Essential amino acids: Cannot be synthesized by the body and must be obtained through diet. Non-essential amino acids:…
Peptide screening is a foundational technique in modern molecular biology, pharmaceutical research, and bioengineering. It enables scientists to identify peptides—short chains of amino acids—that possess specific biological activities or desirable physicochemical properties. As interest in peptide-based therapeutics, diagnostics, and biomaterials continues to rise, understanding how peptide screening works has become more important across research and industry. ⸻ What Is Peptide Screening? Peptide screening refers to the systematic identification of functional peptides from a large and diverse peptide library. These peptide libraries may contain millions—or even billions—of unique sequences. The goal is to pinpoint peptides with properties such as high binding affinity, antimicrobial action, enzyme inhibition, cell-penetrating ability, or structural stability. Screening technologies are designed to mimic biological interactions, allowing researchers to observe how peptides behave under controlled conditions. The method chosen typically depends on the intended application, desired specificity, and throughput requirements. ⸻ Why Peptide Screening Matters Peptide screening is essential because it significantly accelerates peptide discovery compared to traditional trial-and-error approaches. Its importance spans multiple fields: 1. Drug Discovery & Therapeutics Peptides can act as signaling molecules, enzyme regulators, immune modulators, or receptor agonists/antagonists. Screening allows rapid discovery of therapeutic candidates with: •High specificity •Low toxicity •Modifiable structures 2.…