Custom User Defined Oligonucleotide Pools or Libraries

Pools or Libraries

Explanation

CRISPR sgRNA

A collection of thousands of unique guide RNAs designed to target specific genes or genomic regions.

Knockout Libraries are designed to create a library of guide RNAs (gRNAs) that will each knock out a specific gene in a cell's genome to screen for genes that, when inactivated, produce a specific phenotype, for example, indicating drug resistance or cell death.

Interference (CRISPRi) and Activation (CRISPRa) Libraries contain gRNAs that don't cut DNA but instead recruit proteins to a gene's promoter to either turn its expression off (CRISPRi) or turn it on (CRISPRa), allowing for high-throughput screening of gene function.

Gene Synthesis

Mutagenesis Libraries or Variant Libraries contain a defined set of gene variants, often with specific point mutations, insertions, or deletions, useful for directed evolution studies, where researchers can screen a large number of protein variants to find one with improved properties, for example, with higher enzymatic activity or stability.

Gene Assembly Pools consist of overlapping oligonucleotides that can be assembled into full-length genes using PCR-based methods like Golden Gate Assembly, which is a highly efficient way to synthesize a library of custom genes for synthetic biology or protein engineering.

Short hairpin RNA (shRNA)

To silence gene expression through RNAi

Functional Genomics Pools for high-throughput screens to systematically knock down every gene in the genome to determine its function in a specific biological process or disease.

Disease Modeling Pool to create cell lines or animal models with a specific gene knocked down to study the aetiology and progression of a disease.

Target Validation in Drug Discovery Pools to validate potential drug targets by confirming that silencing a gene of interest leads to a desired therapeutic effect.

Gene Therapy shRNA Pools to explore short hairpin oligonucleotides as a therapeutic tool for treating diseases caused by the overexpression of a harmful gene by selectively silencing genes.

NGS pools for target sequencing

"Capture panels" or "bait libraries," to "fish" for specific DNA or RNA sequences from a complex sample before sequencing.

Exome Sequencing Panels are designed to capture all the protein-coding regions (exomes) of the genome. By only sequencing the exome, researchers can significantly reduce the cost and time of sequencing while still capturing the vast majority of disease-related genetic variants.

Custom Target Panels are highly specific libraries designed to capture only a pre-defined set of genes or genomic regions of interest. They are widely used in clinical research for focused studies on specific diseases, such as cancer or genetic disorders.

FISH

Chromosome Painting pools are used to "paint" entire chromosomes, making them easy to identify and study, invaluable for karyotyping and detecting large-scale chromosomal abnormalities like translocations, inversions, and aneuploidy.

3D Genome Organization utilize different fluorophores to simultaneously paint multiple genomic regions for the study of how chromosomes are organized and interact within the nucleus in three-dimensional space.

Gene and RNA Localization Pools can be designed to visualize the location and abundance of specific genes or RNA transcripts within a cell, providing insight into gene expression and function.

Molecular Diagnostic Pools or oligo-FISH allow to diagnose genetic diseases and cancers by detecting specific chromosomal rearrangements or gene amplifications.

Comparative Genomics Pools are used to compare the chromosomal structure and evolution across different species.

Mutation Libraries

Random Mutagenesis Libraries introduce mutations randomly throughout a gene sequence to broadly sample the "sequence space" without a specific hypothesis about which amino acids are important.

Error-Prone PCR (epPCR) involves a modified PCR reaction with a low-fidelity DNA polymerase and non-optimal conditions, such as altered dNTP concentrations or adding manganese, that increase the rate of random nucleotide errors.

DNA Shuffling involves fragmenting related genes and then reassembling them through PCR to create a library of hybrid genes that contain a mix of mutations and sequences from the parent genes.

Targeted Mutagenesis Libraries introduce mutations at specific, pre-determined locations in the sequence which is more precise and is used when there is a hypothesis about which amino acids or regions are important for function.

Site-Saturation Mutagenesis (SSM) is a common method for creating targeted libraries involving degenerate codons, for example, NNK or NNS, which encode all 20 amino acids and one stop codon, in the synthesis of oligonucleotides, allowing for every possible amino acid substitution to be systematically tested at a single position or a small group of positions.

Combinatorial Mutagenesis is an extension of SSM where multiple positions are mutated simultaneously to create a combinatorial library of variants. This is used to test for synergistic effects between mutations.

Truncation Libraries are designed to test the importance of different regions of a protein by systematically deleting parts of the gene from either the 5' or 3' end.

High-Precision Libraries or Synthetic Libraries are highly precise mutation libraries.

DNA Data Storage or Barcoding

Cellular Barcoding for cell labeling a unique barcode from the pool, allowing tracking individual cells or cell lineages during an experiment.

Perturb-seq uses DNA barcodes to link a specific genetic or chemical perturbation to the gene expression profile of a cell. The barcodes in the pool are designed to be read out via sequencing to identify which perturbation was applied to which cell.

Random or

Degenerate Libraries

Randomized Primers are used in PCR to amplify DNA from a sample where the sequence is unknown or highly variable.

Random Peptide Libraries are used to screen for peptides that bind to a specific target molecule, which can be useful in drug discovery. The oligo pool encodes a random set of amino acids, which are then expressed as peptides for screening.