devin petersohn poster 2015
TRANSCRIPT
Citations
A Study on the Frequency and Location of Palindromic DNA across 41 Mammalian Genomes
Devin Petersohn1 and Chi-Ren Shyu (Mentor)1,2
1Department of Computer Science, College of Engineering, 2MU Informatics Institute, University of Missouri
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Chimpanzee Palindromes as a Percent of Entire Genome
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Human Palindromes as a Percent of Entire Genome
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Wild Boar Palindromes as a Percent of Entire Genome
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Horse Palindromes as a Percent of Entire Genome
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What is a Palindrome?
Palindrome Locations and Frequencies are not Random
A Palindrome is a word that spells itself backwards. For example:
racecar
Spelled backwards, racecar spells racecar, therefore it is a palindrome.
In DNA, palindromes are patterns that are read the same way forwards and backwards. Because DNA is double stranded, however, palindromes within DNA are different than palindromes in language. For example:
5’ 3’
DNA is read from 5’ to 3’ on each strand. It also pairs such that A pairs with T and C pairs with G. If we were to look at both strands together, they would look like this:
5’ 3’
3’ 5’
If you read the bottom strand from 5’ to 3’, it is the exact same as the opposite strand. Thus, a palindrome is a sequence that is its own reverse complement.
Percent of Palindromes Based on Center Base Pairs Why Study Palindromes?
Acknowledgements
• Palindromes have been shown to form interesting structures in DNA.
• Hairpin Structures:
• Cruciform Structures:
• Palindromes have also been shown to be involved in certain diseases and cancers.
• The mutation rate within “almost” palindromes has been shown to be 300x the normal mutation rate.
• These sequences are strongly selected toward being palindromic
• Palindromes have also been shown to have regulatory functions, and also have functions within binding sites.
[1] Glickman, Barry W., and Lynn S. Ripley. "Structural intermediates of deletion mutagenesis: a role for palindromic DNA." Proceedings of the National Academy of Sciences 81.2 (1984): 512-516.
[2] Tanaka, Hisashi, et al. "Large DNA palindromes as a common form of structural chromosome aberrations in human cancers." Human cell 19.1 (2006): 17-23.
This Project was funded by the MU Engineering Undergraduate Honors Scholar in Research Program