Our platform’s Oligo Designer Agent is a versatile tool tailored for designing high-quality oligonucleotides (oligos) for a wide range of molecular biology applications, including primers for PCR, sequencing, or probes for hybridization assays. This tool simplifies the process of creating custom oligos by offering flexible input parameters, allowing users to precisely define the characteristics needed for their experiments. Whether you are designing single oligos or oligo pairs, the Oligo Designer ensures optimized sequences that meet your experimental requirements.

Input Options:

• Gene Name or Sequence:

  • Users can provide either the name of the target gene (e.g., "GAPDH") or the specific nucleotide sequence they want to target. When entering a gene name, the tool will automatically retrieve the corresponding gene sequence from the database. Alternatively, users can paste a custom nucleotide sequence if they are working with regions outside of annotated genes, such as regulatory elements or non-coding RNAs.

• Probe Type:

  • The Oligo Designer supports two primary probe types:

    • Single Oligo: Ideal for applications like hybridization or simple PCR-based methods where only one oligonucleotide is required.

    • Pair of Oligos: Used for designing primer pairs for PCR amplification or other dual-oligo techniques like qPCR or cloning.

• Organism:

  • Specify the organism of interest (e.g., Homo sapiens, Saccharomyces cerevisiae, Mus musculus), ensuring that the designed oligos are compatible with the genome or transcriptome you are working with. The Oligo Designer can retrieve gene sequences based on the selected organism and adjust for species-specific sequence features.

• Melting Temperature (Tm):

  • Melting Temperature Minimum (Tm Min): Set the minimum melting temperature for the oligos, which influences their binding stability to the target sequence. A higher Tm typically increases the binding specificity of the oligo.

  • Melting Temperature Maximum (Tm Max): Define the maximum Tm to prevent overly stable oligos, which may lead to non-specific binding or poor performance in temperature-sensitive applications like PCR.

  • These parameters ensure the oligos are optimized for conditions where hybridization and binding temperature are critical, such as PCR cycling or hybridization assays.

• Length:

  • Length Minimum: Define the minimum length (in nucleotides) for the oligos, ensuring they are long enough to provide specificity to the target sequence. Shorter oligos may be faster to synthesize but can suffer from reduced specificity.

  • Length Maximum: Set the maximum allowable length, as excessively long oligos may form secondary structures or lead to off-target binding. This parameter balances the need for specificity with synthesis cost and performance.

• GC Content:

  • GC Content Minimum: Set a lower limit for the percentage of guanine (G) and cytosine (C) nucleotides in the oligo. GC-rich regions are more stable due to stronger hydrogen bonding, which can be crucial for binding in certain experimental conditions.

  • GC Content Maximum: Define the maximum GC content to prevent the oligos from being overly GC-rich, which could lead to problems such as high secondary structure formation or difficulty in denaturation during PCR.

Output Options:

• Optimized Oligo Sequences:

  • The Oligo Designer will generate a list of potential oligos that meet the user’s input criteria. For single oligos, the tool outputs one optimized sequence, while for pairs (such as primers), it provides complementary forward and reverse oligos designed to target the region of interest.

• Melting Temperature (Tm):

  • Each oligo is accompanied by its calculated melting temperature, allowing users to assess whether it falls within the specified range. This ensures that the oligos will perform efficiently under the experimental conditions, especially for thermal cycling applications like PCR.

• Length:

  • The exact length of each oligo is provided, ensuring compliance with the user-defined length parameters. This helps avoid oligos that are too short (leading to low specificity) or too long (potentially forming secondary structures).

• GC Content (%):

  • The tool outputs the GC content of each designed oligo, helping users choose oligos with optimal binding stability without risking secondary structure issues or poor denaturation properties. Balancing GC content is key to achieving efficient amplification or hybridization.

• Specificity and Targeting Information:

  • For gene or sequence-based designs, the tool ensures that each oligo binds specifically to the intended region. For paired oligos (e.g., PCR primers), the tool also calculates the optimal annealing temperature based on the Tm and avoids regions prone to forming secondary structures or primer-dimers.

• Ranked Recommendations:

  • The Oligo Designer provides a ranking of the designed oligos based on their predicted performance, considering factors such as Tm, GC content, and the likelihood of non-specific binding. This helps users easily identify the best candidates for synthesis and experimentation.

Applications and Flexibility:

The Oligo Designer is an essential tool for a variety of molecular biology workflows:

• PCR and qPCR: Design primers that are highly specific and optimized for efficient amplification of target sequences.

• Sequencing: Create primers for Sanger sequencing or next-generation sequencing (NGS) that are well-suited for high fidelity and specificity.

• Probes for Hybridization: Generate oligos for hybridization-based applications such as fluorescent in situ hybridization (FISH) or microarray analysis, ensuring high binding specificity to the target sequence.

By offering precise control over key oligo design parameters like length, melting temperature, and GC content, the Oligo Designer Agent provides a reliable and efficient solution for creating oligonucleotides tailored to your experimental needs. Whether you are conducting gene expression studies, cloning, or probe-based assays, this tool ensures that your oligos will perform optimally, saving time and resources in your research process.