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Determines which sticky ends are optimal for Golden Gate Assembly.
This tool was made so that users can split their DNA into multiple fragments that have complementary sticky ends (that are unlikely to bind to the wrong sticky ends) that will be seamlessly assembled during Golden Gate Assembly.

Instructions:

1. In the first input box, enter the DNA sequence.

2. Click "Index sequence" so that your nucleotides are numbered so that it is easier for you to choose ranges where you want sticky ends.

3. Enter the ranges of the DNA sequence where you would like to produce sticky ends. For example, if you want sticky ends within bases 0 and 5, enter "(0, 5)." Click "Add range" to add a new range where you want sticky ends. Repeat until you have the number of sticky ends you want to produce.

4. Once you have filled out both text boxes with the proper information, press Submit to see your DNA sequences with its optimal sticky ends (within your specified ranges) highlighted.

Step 1: Enter DNA sequence
Index sequence

Indexed sequence:

Step 2: Enter ranges you would like to target (length of range must be at least 4)

For reference, if your sequence is "atgcaatgca" and one of ranges you enter is "0, 3,"
"atgc" will be one possible sticky end.

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   Scoring Sticky End Pairs (score out of 10):

Key:

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Multiple of the same sticky end:


We do not want two of the same sticky end because the complementary sticky end of the wrong
sticky end is likely to bind (which is not what we want). We give this pair a score of 0.

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Palindrome (reverse complement) sticky ends:


If a pair contains palindromes, when performing Golden Gate Assembly, they will likely bind
to each other (which is not what we want). We give palindrome pairs a score of 0.

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3 in a row:


If a sticky end or its complementary sticky end have 3 bases in a row that can bind to a sticky
end in the incorrect location, that pair is not desirable, so we give it a score of 0.

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2 bases not in a row:



If a sticky end and/or its complementary sticky end have bases that are not in a row that can
bind to a sticky end in the incorrect location, we simply subtract how ever many bases can
incorrectly bind together (from both a sticky end and its complementary sticky end) from 10.

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2 bases in a row:



If a sticky end and/or its complementary sticky end have bases that are in a row that can bind
to a sticky end in the incorrect location, we simply subtract from 10 how ever many bases in a
row on each respective strand that can incorrectly bind to another sticky end, multiplied by 2.

The Restriction Site Finder was created by Elise Edman as part of the 2018 Davidson College/Missouri Western SynBio Project.
Send comments, questions, and suggestions to Laurie Heyer at laheyer@davidson.edu