Inquiry of Palindromic DNA, Its Role in Escheria coli , And Contribution of Bioinformatics to Research in Palindromic DNA Lee Hong, Dong Jin Shin, Chris Straka CompSci 4G, Genome Revolution Focus, Duke University, 2006. Applications to Bioinformatics
And Contribution of Bioinformatics to Research in Palindromic DNA
Lee Hong, Dong Jin Shin, Chris Straka CompSci 4G, Genome Revolution Focus, Duke University, 2006
Applications to Bioinformatics
Bioinformatics is essential to the study of palindromic DNA sequences. First and foremost, bioinformatics, specifically a java program, must be used to find the number of occurrences and locations of palindromic sequences in long chains of given DNA. Studies have consistently shown that there are several hundred occurrences of palindromes in the E. coli genome. Specifically, differing amounts of four and six base pair palindromic sequences are found in E. coli. More generally, these four and six base pair sequences are found in almost all sequenced genomes and are thought to preserve both structural and content integrity during DNA replication. Bioinformatics can be used analyze the composition and frequency of these clusters. Using this information, an algorithm could theoretically be written to find correlation between the structures and the functions of different palindromic clusters. Relatively little is currently known about the precise correlation between different DNA structures and their function; further analyses of different palindromic sequences could be the first step to solving many of the unknowns in DNA structure.
What is palindromic DNA?
Palindromic DNA is a DNA sequence that is complimentary when read from 5’ to 3’ and vice versa. Thus, the shape of a palindromic DNA sequence is usually that of a hairpin.
For example, the following sequence is a palindromic DNA sequence:
If the sequence is split in half, one can see the complimentary strands:
ATCG A CGAT
Thus, the “hairpin” structure would look like this (the lines at center represent hydrogen bonds between nucleotides):
(Right) A more complicated structure
of quasi-palindromic DNA undergoing
“strand switch” in E. coli:
Frequency of Palindromic DNA in E. coli
Using a rough extrapolation, it can be inferred from experimental results that the consensus stem should be present at least several hundred times on the E. coli chromosome. This means that the consensus stems are not random events (frequency in prokaryotes is of the same order as that of the consensus stem). Furthermore, the structure and location of the PUs in bacteria are suggestive of at least two possible roles: a role in gene expression and a role in genome evolution.
Also, units of palindromic DNA sequences (also called Palindromic Units or PU’s) are known to be organized into clusters. "Palindromic units are part of a new bacterial interspersed mosaic element" describes a unique quality of the PUs of DNA: that each PU cluster is made up of a "mosaic combination" of PU and of other "sequence motifs."
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Above: Palindromic DNA, due to their structure, facilitate the mutation of DNA and the genome.
(Right) An example of how both perfect and imperfect palindromic sequences facilitate gene mutation: once “strand switch” takes place, two distinct forms of “branch mutation” may result.
(Left) an example of quasi-palindromic DNA strand, which has hairpin loops attached to the main cruciform structure.