What is known, however, is that such rearrangements are associated with the progression and prognosis of the cancer, Rattray said. How these events arise is not well understood. Some cancer cells exhibit massive genome rearrangements, which include gene amplifications, translocations, and deletions, and these rearrangements are often associated with the presence of a palindrome, suggesting a possible correlation between the palindrome and the gene rearrangements. “Small hairpins are not problematic, but when palindromes are long (more than 100 base pairs), they interfere with normal cellular processes such as transcription and replication,” she explained. For example, the sequence GGATCC on one strand of DNA is considered a palindrome because the sequence on its complementary strand is CCTAGG.īecause of the sequence complementarity, palindromic sequences can also fold back onto themselves, forming hairpin loops or cruciforms that are extruded from the normal double helix, Rattray said. What Is a DNA Palindrome?Ī palindromic sequence of nucleotides (which are labeled A, T, C, or G) occurs when complementary strands of DNA read the same in both directions, either from the 5-prime end or the 3-prime end. Rattray is a major contributor to research reported in BMC Genomics that describes the group’s newly developed method for genome-wide sequencing of DNA palindromes in a cancer cell line. The arrangement turned out to be a DNA palindrome, “opening the door to studying these elusive DNA motifs,” she said.Ī staff scientist in GRCBL, NCI Center for Cancer Research, Rattray said that, while their discovery occurred a number of years ago, their group continues to study DNA repair and rearrangements that result in abnormal repair “because of the association with certain cancers.” The group’s goal is to better understand the origin of these rearrangements, she added. The DNA exhibited a “very specific, but weird, rearrangement,” she explained. When Alison Rattray and colleagues in the Gene Regulation and Chromosome Biology Laboratory (GRCBL) examined a mutant yeast cell they had isolated in a screen, they noticed something strange. Craig Reynolds, associate director, National Cancer Institute, from among the most recently published Platinum Publications. 2012.Editor's note: Platinum Highlight articles are noteworthy publications selected periodically by Dr. When the complementary strand is read backwards, the sequence is 5’-GGATCC-3’ which is identical to the first one, making it a palindromic sequence. This is the sequence where the restriction endonuclease, BamHI, binds to and cleaves at a specific cleavage site. An example of a palindromic sequence is 5’-GGATCC-3’, which has a complementary strand, 3’-CCTAGG-5’. So if a sequence is palindromic, the nucleotide sequence of one strand would be the same as its reverse complementary strand. The pairing of nucleotides within the DNA double-helix is complementary which consist of Adenine (A) pairing with either Thymine (T) in DNA or Uracil (U) in RNA, while Cytosine (C) pairs with Guanine (G). Recognition sites of many restriction enzymes are palindromic. The sequence is the same when one strand is read left to right and the other strand is read right to left. A DNA sequence whose 5'-to-3' sequence is identical on each DNA strand.
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