Factors deciding oligo length ?

In summary, the conversation discusses the question of why different companies use different lengths for oligonucleotides in microarray projects. The speaker is looking for literature or information on the reasoning behind these different lengths and whether there is a generalization or if it varies depending on the experiment. They also mention that some research papers suggest that melting point may be more significant than length.
  • #1
Lele
4
0
Hi! All,

Here's a specific question I need to address in a Microarray project.

1) Different companies have oligos (oligonucletides) with different lengths. My understanding is, the oligo length should be sample specific. However a glance at company websites tells me that each one has come up with their own lengths (25-mer, 60-mer etc.). I need to know what makes them choose one over the other? I am looking for literature answering the same. Shall highly appreciate if someone can direct me to a good source or send a detailed reply.

Thanks,
Lele
 
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  • #3


Could someone explain in very basic terms. On research papers it seems like melting point is more significant than the length. Is there any generalization to the length of the probe or it depends from experiment to experiment ?

Thanks,
lele
 

1. What is the optimal length for an oligo?

The optimal length for an oligo can vary depending on the specific experiment or application. Generally, oligos that range from 15-30 nucleotides in length are considered optimal for most applications.

2. How does the length of an oligo affect its specificity?

The length of an oligo can greatly impact its specificity. Longer oligos have a higher melting temperature and are less likely to bind to non-target sequences, making them more specific. However, shorter oligos may be more suitable for specific applications, such as PCR.

3. What factors should be considered when deciding the length of an oligo?

When deciding the length of an oligo, factors such as the target sequence, melting temperature, and desired specificity should be considered. Other factors include the presence of secondary structures and the potential for non-specific binding.

4. Can the length of an oligo affect its efficiency?

Yes, the length of an oligo can affect its efficiency. Longer oligos may be more efficient in certain applications, such as hybridization-based assays, while shorter oligos may be more efficient in others, such as PCR.

5. How can I determine the appropriate length for my oligo?

Determining the appropriate length for an oligo can involve trial and error, as well as considering the factors mentioned above. Utilizing tools such as oligo design software can also help determine the optimal length for your specific experiment or application.

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