Palindromic sequence
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Understanding Palindromic Sequences: Structure, Function, and Biological Significance
Introduction to Palindromic Sequences
Palindromic sequences are unique DNA or RNA motifs that read the same forwards and backwards. These sequences can form secondary structures such as hairpins or cruciforms, which have significant implications in various biological processes. This article explores the structural, functional, and evolutionary roles of palindromic sequences across different organisms.
Structural Characteristics of Palindromic Sequences
Formation of Hairpin and Cruciform Structures
Palindromic sequences have the potential to form hairpin or cruciform structures, which are substrates for nucleases and mismatch repair enzymes. In yeast, a 140-bp-long palindromic sequence can induce double-strand breaks during meiosis, acting as a recombination hotspot1. This suggests that longer palindromic sequences are more prone to forming cruciform structures, which are then targeted by structure-specific nucleases.
Imperfect Palindromes in Gene Regulation
In regulatory DNA, palindromic sequences often appear as imperfect repeats, allowing transcription factors to bind as homodimers or heterodimers. These imperfect palindromes play crucial roles in gene regulation, as seen in Drosophila photoreceptor differentiation and mammalian steroid receptor signaling7. The functional significance of these asymmetries remains an area of active research.
Functional Roles of Palindromic Sequences
Genetic Recombination and Stability
Palindromic sequences can influence genetic recombination and stability. In E. coli, dispersed repetitive palindromic units are found in clusters or single occurrences, often between operons. These units can form stem-loop structures that may play roles in transcription and mRNA stability4. Additionally, palindromic sequences in yeast are over-represented in intergenic regions, suggesting a role in genome organization and stability6.
Immunostimulatory Activity
Certain palindromic sequences in synthetic oligonucleotides are essential for inducing interferon (IFN) and augmenting natural killer (NK) cell activity. For instance, oligonucleotides containing the palindromic sequence GACGTC can stimulate IFN production and enhance NK cell activity, highlighting the immunostimulatory potential of specific palindromic motifs5.
Evolutionary Significance of Palindromic Sequences
Y Chromosome Palindromes and Gene Conversion
Palindromic sequences on the Y chromosome exhibit strong recombinational activity through arm-to-arm gene conversion. This mechanism helps remove deleterious mutations and fix beneficial ones, playing a crucial role in the evolution and maintenance of male-specific genes8. The independent appearance of these palindromes across different species underscores their evolutionary importance.
Repetitive DNA in Bacteria
In bacteria, highly repetitive palindromic units can constitute a significant portion of the genome. These units are species-specific and may be involved in mRNA stabilization, processing, or transcription termination. Their ability to bind specific proteins suggests a role in the structural organization of the bacterial nucleoid10.
Conclusion
Palindromic sequences are versatile DNA motifs with significant structural, functional, and evolutionary roles. From inducing genetic recombination in yeast to regulating gene expression in higher organisms, these sequences are integral to various biological processes. Understanding their mechanisms and implications continues to be a vital area of research, offering insights into genome stability, gene regulation, and evolutionary biology.
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Most relevant research papers on this topic
A 140-bp-long palindromic sequence induces double-strand breaks during meiosis in the yeast Saccharomyces cerevisiae.
A 140-bp-long palindromic sequence acts as a meiotic recombination hotspot in yeast, generating double-strand breaks and requiring different repair mechanisms than short hairpin structures.
Highly CitedAn algorithm to find all palindromic sequences in proteins
This algorithm can identify all perfect palindromes in a single protein sequence, aiding in understanding their structural, functional, and evolutionary significance.
ON “VERY PALINDROMIC” SEQUENCES
All palindromic sequences have the required property, even with the additional restriction that we can count only palindromes with at least d digits.
Rigorous JournalA family of dispersed repetitive extragenic palindromic DNA sequences in E. coli.
Palindromic units in E. coli may play a role in transcription and mRNA stability, and may relate to transposition elements and genome modular evolution.
Highly CitedUnique palindromic sequences in synthetic oligonucleotides are required to induce IFN [correction of INF] and augment IFN-mediated [correction of INF] natural killer activity.
Unique palindromic sequences, such as GACGTC, AGCGCT, and AACGTT, are essential for the immunostimulatory activity of oligonucleotides, promoting IFN-alpha/beta production and NK cell activity.
In Vitro StudyHighly CitedPalindrome content of the yeast Saccharomyces cerevisiae genome
Short palindromes (2-12 bp) are under-represented in the yeast genome, while long palindromes (12-12 bp) are over-represented and preferentially located in intergenic regions.
The power of the (imperfect) palindrome: Sequence‐specific roles of palindromic motifs in gene regulation
Imperfect palindromes play a crucial role in gene regulation, potentially aiding in transcriptional outcomes and drug response prediction in steroid receptor signaling.
Y chromosome palindromes and gene conversion
Palindromes on sex chromosomes may have adaptive significance, allowing efficient removal of deleterious mutations and maintaining the structural integrity of male-specific genes.
Rigorous JournalComparison of physical and genetic properties of palindromic DNA sequences
Palindromes with no Chi sites can increase genetic recombination, but their physical properties do not correlate with their biological effects on recombination.
In Vitro StudyPalindromic units: a case of highly repetitive DNA sequences in bacteria
Palindromic units (PUs) are highly repetitive DNA sequences in bacteria, potentially playing roles in mRNA stabilization, transcription termination, and bacterial nucleoid structure.
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