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Oligonucleotides are short strands of nucleotides with specifically designed sequences that hybridize with target gene mRNA or pre-mRNA through complementary base pairing, enabling the selective regulation of any target gene or protein expression. Alfa Chemistry offers a comprehensive range of high-quality oligonucleotide products, including antisense oligonucleotides, siRNA, miRNA, aptamers, and CpG oligonucleotides. These products are meticulously designed to meet the diverse requirements of researchers across various fields. We are committed to delivering exceptional oligonucleotide solutions and custom services to support scientific advancements worldwide.
* Our products and services are for research use only and cannot be used for any clinical purposes.
Classification of Oligonucleotides
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Oligonucleotide Synthesis
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Modification of Oligonucleotides
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Oligonucleotide-based therapeutics exert their effects through diverse mechanisms depending on their structural and chemical properties. Therapeutic nucleic acids typically bind to complementary nucleic acids via Watson-Crick base pairing. Based on their mechanisms of action, oligonucleotides can be categorized into the following types:
ASOs are short, single-stranded oligodeoxynucleotides (8~50 bases) that represent a targeted and systematic approach to gene silencing. By modifying RNA and blocking protein expression, ASOs act via several mechanisms, which can be broadly classified into two categories: 1) Splice Modulators and Steric Blockers. 2) Gene Expression Inhibitors.
RNAi is a novel and efficient gene-silencing strategy observed in many organisms. It involves small RNA molecules that inhibit or degrade mRNA, thereby preventing protein synthesis. Key types include:
siRNAs are short, non-coding RNA molecules that regulate gene expression by targeting specific mRNAs. Their mechanism involves post-transcriptional gene silencing through mRNA cleavage and degradation.
miRNAs are single-stranded RNA fragments, 21–25 nucleotides long, that play a crucial role in regulating gene expression. Synthesized from precursor miRNAs via RNase-II/III enzymes, miRNAs inhibit translation by binding to complementary mRNA sequences.
CpG oligonucleotides are short, single-stranded oligonucleotides containing unmethylated CpG dinucleotides in specific regions. They act as immune stimulators for cells expressing Toll-like receptor 9 (e.g., macrophages, B cells, dendritic cells, and monocytes). Based on structural differences and induced immune responses, they are classified into four types: K-Type/B-Type, D-Type/A-Type, C-Type, and P-Type.
Aptamers are short, synthetic RNA or DNA oligonucleotides or peptides that bind selectively and with high affinity to target molecules, often inhibiting protein-protein interactions. Unlike other oligonucleotides, their activity relies on forming 3D structures to bind targets, rather than Watson-Crick base pairing.
Decoys are single-stranded RNA oligonucleotides designed to target transcription factors. These molecules are modified with 2′-O-methylation on the ribose moieties of the nucleotide chain. When delivered into cells, decoys containing specific consensus-binding sequences for a target transcription factor are recognized and bound by the factor. This interaction not only sequesters the transcription factor but also inhibits its ability to bind to the promoter regions of pathogenic target genes, thereby obstructing gene activation.
Mechanism of action of antisense oligonucleotides (AS-ODN), siRNAs and aptamers. (Khar RK, et.al. 2010)
References
Oligonucleotides can be formed enzymatically either by breakage of larger biomolecules or by targeted chemical synthesis. In the latter approach, organic nucleotide synthesis involves chemical processes to produce nucleoside phosphoramidites, which are the key monomeric units for oligonucleotide assembly. These phosphoramidites are derived from natural or synthetic nucleosides and are required building blocks.
Nucleotides consist of nucleosides covalently linked to a phosphate group arranged in a specific sequence to produce the desired product. Oligonucleotides are short fragments of nucleic acids linked together to form single-stranded biopolymers. Typically, they consist of up to 20 nucleotide units, although longer sequences are possible, categorizing them as small biomolecules.
The synthesis process requires precise control of factors such as temperature, pH, and substrate quality. As nucleotide sequences become longer and more complex, the challenge of meeting yield, purity, and cost goals increases. To address these challenges, Process Analytical Technology (PAT) plays a key role in optimizing and ensuring the efficiency of oligonucleotide production.
Standard DNA or RNA sequences (oligonucleotide drugs) that are not additionally chemically modified are rapidly degraded in vivo by nuclease enzymes and have suboptimal drug-forming properties. Chemical modification is one of the most effective ways to improve oligonucleotide drug delivery.
The main types of oligonucleotide modifications include the following, each of which aims to improve the pharmaceutical properties of the oligonucleotide, such as stability, targeting, and pharmacokinetic properties.
The desired properties of oligonucleotides can be customized by formulating targeted advanced drug carrier systems. The ADME properties of carrier-based delivery compositions are largely dependent on the characteristics of the delivery system and are independent of the oligonucleotide. The type of targeting can be passive or active.
Alfa Chemistry is dedicated to developing different delivery systems for oligonucleotide therapeutics. Our liver-targeted drug delivery technologies have been developed and matured to support the rapid entry of drug candidates into the clinical phase. Our team of experts is currently exploring novel delivery methods and technologies suitable for extrahepatic tissues.
We also offer a number of polymers and lipids for oligonucleotide drug delivery, among others.
Q1 How to select a suitable oligonucleotide sequence?
When selecting a suitable oligonucleotide sequence, the specificity of the target sequence, length, GC content, and possible secondary structure need to be considered. We recommend contacting our technical support team for customized advice.
Q2 How do you ensure the quality and purity of the oligonucleotides?
Our oligonucleotides are quality-controlled using highly efficient HPLC or mass spectrometry analysis to ensure a high standard of purity in each batch. A common purity standard is >95%, and different purification levels are available to meet specific needs.
Q3 What are the storage conditions for oligonucleotides?
To maintain the stability of the oligonucleotides, it is recommended to store them in a refrigerated environment at -20°C, avoiding high temperatures and humidity. If they are not to be used for a long time, please store them in dry and low-temperature conditions.
Q4 Is it possible to customize the oligonucleotide sequence?
Yes, we offer customization of oligonucleotides. We can synthesize any specified sequence according to the specific needs of our customers, and offer a choice of different lengths, modification types, and purification levels.
Q5 How do you solve common problems in oligonucleotide synthesis?
If you encounter difficulties or poor results in synthesis, you can try to adjust the experimental conditions, such as temperature, pH or ionic strength. Also, consult our technical support team for optimized solutions.
Q6 Do you provide technical support and consulting services for oligonucleotides?
Yes, we provide professional technical support and consulting services to our customers. Whether it is in the selection of appropriate oligonucleotide sequences, experimental design, or optimization of the experimental process, we can provide assistance.
What are Oligonucleotides?
What is the Mechanism of Oligonucleotide Therapeutics?
Chemical Modification Strategies for Oligonucleotides
FDA-Approved Oligonucleotide Drugs: A Detailed Overview
Comprehensive Guide to Oligonucleotide Synthesis: Techniques, Optimization, and Purification Strategies
Comprehensive Guide to 5'-DMTr-3'-OH Oligomers: Properties, Applications, and Synthesis
What are 3'-Phosphoramidite Oligomers?
What Are 3'-Protected Monomers and Their Role in Oligonucleotide Synthesis?
Linkers in Oligonucleotide Conjugates
Our products and services are for research use only and cannot be used for any clinical purposes.
As a specialist in oligonucleotide therapeutics, Alfa Chemistry offers consumers a wealth of raw materials and a full range of technologies and services.
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