Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Nextera Miseq custom primers

    Hi,

    I am new to deep sequencing and would like a little help. I am trying to design custom primers to use on one end of my fragmented DNA for a Nextera Miseq. I am wondering if my primers need any modifications such as phosphorylations to be able to bind to the chip, or if I can get away with discluding the i5/i7 sequences.

    I have designed two primers (to match the P7 or P5 end that would be randomly inserted due the random inserts of tagmentation). My primer design looks like this:

    Primer to be paired with P5:
    5' CAAGCAGAAGACGGCATACGAGATGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGTACCCTCCTGCTTAAGGGC


    Primer to be paired with P7:
    5' AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTACCCTCCTGCTTAAGGGC

    *Red = P7/P5 ends complementing chip oligo
    *Green = transposon adaptor sequence
    *3' black end = transposon sequence
    *Brown = complementing region to DNA

    Please let me know if you see any problems in this design and let me know if you think it will work. Thanks.

  • #2
    I wonder if you could indicate what you are trying to do. Primers "complementing DNA region" is the same in both so it cannot be standard custom amplicon.

    You would not need any modification on primers except phosphorothioate bond in some cases where 3' end protection is important.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X