Applications to Bioinformatics

1. 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 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: ATCGACGAT 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): ATCG A TAGC (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." • Bacterial Interspersed Mosaic Elements (BIME) and their implications • Two sets of similar sequences, A & B, constitute about half of the left external segments, though no such set exists on the right. • Sorting of internal segments in 5 sets based on size & sequence  5 defined motifs (4 sharply defined sizes, & last can be considered as combo between A & B) • The L motif (Long sequences) corresponds to a repetitive DNA with a high level of sequence homogeneity along the genome. • Since PUs are part of BIME (larger genetic element w/other sequence motifs), a greater question can be asked: what is the role of each particular motif in each function? Literature cited Cromie, G.A., Millar, C.B., Schmidt, K.H., and Leach, D.R. (2000). Palindromes as substrates for multiple pathways of recombination in Escherichia coli. Genetics 154, 513–522. Gilson, E., Saurin, W., Perrin, D., Bachellier, S., and Hofnug, M. (1991). Palindromic units are part of a new bacterial interspersed mosaic element (BIME) [electronic version]. Nucleic Acids Research, 19, 1375-1383. Glickman, B.W., and Ripley, L.S. Structural Intermediates of Deletion Mutagenesis: A Role for Palindromic DNA [electronic version]. Proc. Natl. Acad. Sci., 81, 512-516. Rattray, A.J. (2004) A method for cloning and sequencing long palindromic DNA junctions. Nucleic Acids Res,. 32, e155 Ripley, L. S. (1982). Model for the Participation of Quasi-Palindromic DNA Sequences in Frameshift Mutation [electronic version]. Proc. Natl. Acad. Sci., 79, 4128-4132. Seurinck S., Verstraete W., Siciliano SD. (2003) Use of 16S-23S rRNA Intergenic Spacer Region PCR and Repetitive Extragenic Palindromic PCR Analyses of Escherichia coli Isolates To Identify Nonpoint Fecal Sources. Appl Environ Microbiol,. 69(8), 4942-4950 • Significance of Palindromic DNA • Two findings described in the original report of the palindromic sequence suggested that palindromic strands are a key component of the DNA’s mechanism. • Using a rough extrapolation, the authors can predict that the consensus stem should be present at least several hundred times on the E. coli chromosome. Such a minimal figure is compatible with the fact that in some cases (malB, ndh and metJBLF) several clusters of p.u.s are found in the same genetic system. • Consensus stems are not random events (frequency in prokaryotes is of the same order as that of the consensus stem.) • Meanwhile, other observations suggested various possibilities on the roles of the palindromic strands: genetic expression and genome evolution. • Neither the consensus stem nor variations with one difference were found in the complete genome of X or T7 phages. (P.U.s are unique) • The structure and location of the p.u.s in bacteria are suggestive of at least two possible roles: a role in gene expression and a role in genome evolution. • Transcription termination is a complex phenomenon which often involves several DNA palindromic structures as well as several steps (Wu et al., 1981; Cau et al., 1982). P.u.s could play a role in some of these steps. • Palindromic Sequences are associated with gene expressions. TATA boxes are examples of palindromic sequences that can predict the beginnings of genes Above: Palindromic DNA, due to their structure, facilitate the mutation of DNA and the genome. • Quasi-Palindromic Sequences • (Imperfect Palindromes) • Imperfect palindromes are Palindromic sequences that have non-palindromic sets of nucleotides located at any point on the otherwise perfectly palindromic DNA strand. These will result in small hairpin-loops forming along the DNA strand extending from the main cruciform structure, in a shape that resembles corals. These structures have similar roles as the perfect palindromes in the process of gene mutation and expression. • The Quasi-Palindromic model: • The DNA secondary-structure model that the paper describes predicts the participation of a variety of structural intermediates in deletion formation. • The model provides a basis for understanding how deletion end points might be joined through metabolic events in which misaligned DNA structures participate as substrates or templates. (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. • For More Information • Palindromic DNA sample APT Problem: • http://www.duke.edu/~djs9/ • Contacts: • DJ Shin: djs9@duke.edu • Lee Hong: lee.hong@duke.edu • Chris Straka: chris.straka@duke.edu • Owen Astrachan, Ph.D: ola@cs.duke.edu (Left) an example of quasi-palindromic DNA strand, which has hairpin loops attached to the main cruciform structure.