Answers.Body: <p>Orthogonal DNA sequences are the shortest possible single stranded nucleotide stretches constructed. These sequences are used as probes in DNA hybridization. Because of its length and construction it has least chance of binding with other probes. </p>
  
  <p>This technique improves the efficacy and specificity and is clinically used to detect genetic disorders in shortest time duration.</p>
  
  <p>Via:
  <a href="https://www.nature.com/articles/srep24650" rel="nofollow noreferrer">https://www.nature.com/articles/srep24650</a></p>
  
  <p><a href="https://www.pnas.org/content/106/7/2289" rel="nofollow noreferrer">https://www.pnas.org/content/106/7/2289</a></p>
  
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Answers.Text: Please upvote if you found it useful :)
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Answers.Text: No problem! I have upvoted. I was told that my vote was recorded, but it wouldn't change the publicly post score because my reputation in the system was less than 15.
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Body: <p>When reading <a href="https://doi.org/10.1093/nar/gkt809" rel="nofollow noreferrer">a paper</a>, I came across the following statement</p>
  
  <blockquote>
    <p>Standard vectors were constructed, flanked by pairs of homology sequences derived from yeast barcodes at the ends of each expression cassette. We reasoned that as these barcode sequences were designed to be <strong>orthogonal</strong>, they could serve a dual purpose of reducing the probability of mis-annealing and dictating the assembly order of multiple cassettes.</p>
  </blockquote>
  
  <p>I am not sure what the "orthogonal" means here. I think it is about synthetic biology.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-22T06:12:15.253Z
Comments.Text: Could you please put your question in contact? What is the reason for asking? How does this relate to your research area? Otherwise Google it
Comments.UserDisplayName: M__
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Comments.CreationDate: 2019-10-22T12:02:34.750Z
Comments.Text: Could you be referring to orthologous? We can't answer this without more context.
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2019-10-22T16:57:31.007Z
Comments.Text: You are talking about synthetic biology, right? If you mean the orthogonal Shine-Dalgano sequences, it depends on the system and all are experimental and not as established as Amber supression codons. See [wiki](https://en.wikipedia.org/wiki/Expanded_genetic_code#Orthogonal_ribosomes)
Comments.UserDisplayName: Matteo Ferla
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Comments.CreationDate: 2019-10-25T03:47:14.173Z
Comments.Text: Thank you all very much! When I read a paper, it says, "Standard vectors were constructed, flanked by pairs of homology sequences derived from yeast barcodes at the ends of each expression cassette. We reasoned that as these barcode sequences were designed to be **orthogonal**, they could serve a dual purpose of reducing the probability of mis-annealing and dictating the assembly order of multiple cassettes." I am not sure what the "orthogonal" means here. I think it is about synthetic biology. Thanks!
Comments.UserDisplayName: Luhui Zhang
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-03T09:48:18.807Z
Comments.Text: Orthogonal in that case means what it means normally. Namely, different enough to not cross-talk. Say A interacts with a and B with b, but A does not with b. If A did interact with b, it would not be orthogonal but it be non-orthogonal/cross-talking/cross-reaction (if chemical).
Comments.UserDisplayName: Matteo Ferla
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Comments.CreationDate: 2019-12-06T04:24:29.400Z
Comments.Text: @MatteoFerla Thanks so much!
Comments.UserDisplayName: Luhui Zhang
Tags: <phylogenetics>
Title: What are Orthogonal DNA Sequences?
ThreadText: # What are Orthogonal DNA Sequences?
  
  (Asked by: username_0 on 2019-10-22)
  
  When reading [a paper](https://doi.org/10.1093/nar/gkt809), I came across the following statement
  
  > Standard vectors were constructed, flanked by pairs of homology sequences derived from yeast barcodes at the ends of each expression cassette. We reasoned that as these barcode sequences were designed to be **orthogonal**, they could serve a dual purpose of reducing the probability of mis-annealing and dictating the assembly order of multiple cassettes.
  
  I am not sure what the "orthogonal" means here. I think it is about synthetic biology.
  
  **Tags:** phylogenetics
  
  > **Comments:**
  > **username_1**: Could you please put your question in contact? What is the reason for asking? How does this relate to your research area? Otherwise Google it  
  > **username_2**: Could you be referring to orthologous? We can't answer this without more context.  
  > **username_3**: You are talking about synthetic biology, right? If you mean the orthogonal Shine-Dalgano sequences, it depends on the system and all are experimental and not as established as Amber supression codons. See [wiki](https://en.wikipedia.org/wiki/Expanded_genetic_code#Orthogonal_ribosomes)  
  > **username_0**: Thank you all very much! When I read a paper, it says, "Standard vectors were constructed, flanked by pairs of homology sequences derived from yeast barcodes at the ends of each expression cassette. We reasoned that as these barcode sequences were designed to be **orthogonal**, they could serve a dual purpose of reducing the probability of mis-annealing and dictating the assembly order of multiple cassettes." I am not sure what the "orthogonal" means here. I think it is about synthetic biology. Thanks!  
  > **username_3**: Orthogonal in that case means what it means normally. Namely, different enough to not cross-talk. Say A interacts with a and B with b, but A does not with b. If A did interact with b, it would not be orthogonal but it be non-orthogonal/cross-talking/cross-reaction (if chemical).  
  > **username_0**: @username_3 Thanks so much!  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2019-11-01. Score: 1
  
  Orthogonal DNA sequences are the shortest possible single stranded nucleotide stretches constructed. These sequences are used as probes in DNA hybridization. Because of its length and construction it has least chance of binding with other probes.
  
  This technique improves the efficacy and specificity and is clinically used to detect genetic disorders in shortest time duration.
  
  Via:
  <https://www.nature.com/articles/srep24650>
  
  <https://www.pnas.org/content/106/7/2289>
  
  > **Comments:**
  > **username_0**: Thank you! @username_4  
  > **username_4**: Please upvote if you found it useful :)  
  > **username_0**: No problem! I have upvoted. I was told that my vote was recorded, but it wouldn't change the publicly post score because my reputation in the system was less than 15.  
  
  ---
  
  