Regardless of specialization within the oligonucleotide manufacturing industry, getting the synthetic DNA or RNA right is imperative. This is where an Oligo Analyzer is a useful tool of choice. It’s imperative when working on DNA oligo synthesis, custom oligos or other processes such as oligonucleotide drug development that one makes use of an Oligo Analyzer to ensure one determines the properties of short nucleic acid sequences. This is important to ensure that your synthesized oligos have fulfilled the standard for research or therapeutic view.

Step 1: Input the Oligo Sequence

The first thing a user must do to use an Oligo Analyzer is enter the DNA or RNA sequence to be analyzed. Many of the analyzers available for use have an interface through which the sequences may be keyed in by the user or uploaded from the synthesizing software. Make sure that the sequence is correct because mistakes can influence analysis.

Next, your sequence will be analysed by the Oligo Analyzer, which can predict its physical and chemical properties. This includes aspects such as melting temperature (Tm), GC content and molecular weight from the two organisms. Such properties are important when selecting oligos for experiments or oligonucleotide drug candidates.

Step 2: Investigate Melting Temperature (Tm)

A key value when using an Oligo Analyzer is melting temperature. It suggests the temperature, which affects fifty percent of the DNA strands' separation. The Tm plays a significant role in simplifying oligonucleotide manufacturing and the development of drugs by assisting in understanding your oligos' behavior under different experimental conditions.

If the Tm of your Tma is too low then the oligos will not be able to bind to their target sequence efficiently. If it is set high, they might bond, which would complicate matters in the experiment being conducted. Depending on the Tm results you may swap or add some of the nucleotides to design the effective oligos for your study.

Step 3: Evaluate GC Content

There is much more to learn about Oligo Analyzer, and the following steps involve looking at the GC content. This fraction measures the dosages of guanine (G) and cytosine (C) bases in your oligonucleotide. Interestingly, the stability in the oligo increases with the GC percent, thus enhancing binding to any complementary DNA or RNA strand.

Many oligo synthesis companies employ this analysis to ensure the high quality of their products. In any case, extremes in GC content should be avoided, as they can reduce the oligo's efficiency in research or drug substance manufacturing.

Step 4: Search for More Levels

The Oligo Analyzer generates information regarding the secondary structures of compounds in addition to its other features. Unwanted interactions occur within the oligo itself, leading to the folding or looping of the structure. These secondary structures can have detrimental effects that influence the way that the oligo is able to perform, for secondary structures are known to be particularly problematic in sensitive areas of research, such as that of oligonucleotide drugs.

The analyzer can help shift the sequence to decrease these structures, so the oligos should be arranged properly according to their function.

Conclusion

An oligo analyzer must be used to ensure accurate and functional oligos for use in research or therapeutic applications. From the input of the sequence to determining its melting temperature and GC content, all stages contribute to the control of the final product quality. These tools are godsends when engaged in oligo synthesis and design within a research lab or when participating in a CDMO drug development project. Veliter Bio offers a wide range of oligo synthesis and analysis services to guarantee your oligo synthesis process will be accurate from the ground up.