Custom Degenerated Oligo Synthesis Service
Introduction
Our Custom Degenerated Oligo Synthesis service accelerates genetic discovery via advanced mixed base synthesis, high-throughput platforms, and strict quality control, delivering high-quality probes/primers to identify novel genetic targets. Creative Biolabs delivers accurate, customized solutions for intricate genetics, facilitating gene cloning, whole-genome amplification, and novel gene family discovery through optimized designs to ensure dependable outcomes.
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Custom Degenerated Oligo Synthesis
Custom Degenerated Oligo Synthesis is a key molecular biology technique using the genetic code's degeneracy. By integrating mixed bases at specific sites, these artificial DNA/RNA sequences act as adaptable probes/primers, assisting in gene cloning, whole-genome amplification, and exploration amid sequence ambiguities. They account for codon redundancy, ensuring matches to target sequences even with limited precise information, empowering researchers in complex genetic studies.
Tab.1 The corresponding rules of degenerate base symbols.
| Degenerate base | Normal Base | Naming Rules |
|---|---|---|
| B | C,G,T | not A, B follows A |
| D | A,G,T | not C, D follows C |
| H | A,C,T | not G, H follows G in the alphabet |
| K | G,T | Keto |
| M | A,C | aMino |
| N | A,C,G,T | aNy |
| R | A,G | puRine |
| S | C,G | Strong interaction (3 hydrogen bonds) |
| V | A,C,G | not T (not-U), V follows U |
| W | A.T | Weak interaction (2 hydrogen bonds) |
| Y | C,T | pYrimidine |
Workflow
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Required Starting Materials
- Protein Subsequence: The amino acid sequence of the target protein or a conserved region within a protein family.
- Target Gene Family Information: Any known nucleotide sequences of related genes or information about conserved motifs.
- Specific Research Objective: A clear outline of your experimental goals (e.g., gene cloning, cDNA screening, WGA, homologous gene discovery).
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Synthesis
- Mixed Phosphoramidite Method: Most common approach, adding different phosphoramidite monomers in specific ratios at a synthesis step to incorporate mixed bases at that position.
- Mixed Bases Method: Overarching strategy for designing/synthesizing oligonucleotides with mixed bases at designated positions to accommodate genetic degeneracy.
- Split-and-Pool Method: For high complexity, splits reactions into aliquots (adding one specific base to each), then pools them before the next steps, iteratively ensuring all sequence combinations are included.
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Purification
Following the chemical synthesis, the crude oligonucleotide product contains not only the desired full-length degenerated sequences but also truncated sequences, unreacted reagents, and other impurities. Creative Biolabs utilizes advanced purification techniques, such as HPLC and PAGE.
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Quality Control
Our comprehensive quality assurance protocols include:
- Mass Spectrometry (MS): Verifies exact molecular weight to confirm correct sequence and successful mixed base incorporation, providing accurate composition data.
- HPLC: Assesses product purity, ensuring freedom from truncated sequences and impurities that could affect results.
- Functional Testing (Optional): On request, confirms activity as PCR primers or hybridization probes via specific functional assays.
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Estimated Timeframe
The typical timeframe for this service ranges from 2 to 4 weeks, depending on the complexity of the degenerated sequence design, the length of the oligonucleotide, and the required purification and quality control measures.
What we can offer
Accurate Mixed Base Integration
Professional synthesis abilities for exact insertion of mixed phosphoramidites and bases at any degenerate spot, guaranteeing thorough target coverage.
Flexible Degeneracy Planning
Custom-made design approaches for degenerated oligonucleotides according to your particular protein sequences, gene family data, and research aims.
Assistance for Various Uses
Fine-tuned degenerated oligos for a broad spectrum of applications, such as gene cloning, cDNA screening, homologous gene finding, and Whole Genome Amplification (WGA).
Scalable Synthesis Capabilities
Ability to synthesize degenerated oligonucleotides at various scales, from research-grade quantities to larger requirements for high-throughput studies.
Expert Consultation and Support
A Dedicated scientific team providing professional guidance from initial design to final delivery, ensuring your project's success.
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FAQs
What is the primary advantage of using degenerated oligonucleotides over specific ones when the target sequence is unknown?
The key advantage is targeting sequences with incomplete information: degenerated oligos leverage genetic code redundancy, ensuring at least one molecule in the pool matches the target, boosting success in gene cloning/amplification vs. using a single specific sequence.
Can Creative Biolabs incorporate specific non-standard or modified bases into degenerated oligonucleotides?
Creative Biolabs offers extensive capabilities to incorporate non-standard bases and modifications at degenerate or other positions. Discuss your specific needs with our experts during consultation.
Is Custom Degenerated Oligo Synthesis suitable for whole-genome amplification (WGA) from very limited DNA samples?
Degenerated oligonucleotides are key to techniques like DOP-PCR, used for WGA from low-copy DNA (including single cells). Though conventional DOP-PCR has coverage limits, our high-quality custom oligos support such sensitive applications.
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