Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids

Abstract

Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-strand hairpins on opposing strands. Biophysical and molecular studies of these structures confirm their characterization as four-way junctions and have demonstrated that several factors influence their stability, including overall chromatin structure and DNA supercoiling. Here, we review our understanding of processes that influence the formation and stability of cruciforms in genomes, covering the range of sequences shown to have biological significance. It is challenging to accurately sequence repetitive DNA sequences, but recent advances in sequencing methods have deepened understanding about the amounts of inverted repeats in genomes from all forms of life. We highlight that, in the majority of genomes, inverted repeats are present in higher numbers than is expected from a random occurrence. It is, therefore, becoming clear that inverted repeats play important roles in regulating many aspects of DNA metabolism, including replication, gene expression, and recombination. Cruciforms are targets for many architectural and regulatory proteins, including topoisomerases, p53, Rif1, and others. Notably, some of these proteins can induce the formation of cruciform structures when they bind to DNA. Inverted repeat sequences also influence the evolution of genomes, and growing evidence highlights their significance in several human diseases, suggesting that the inverted repeat sequences and/or DNA cruciforms could be useful therapeutic targets in some cases.

Pithoviruses are invaded by repeats that contribute to their evolution and divergence from cedratviruses

“…These proteins are involved in Holliday Junctions resolution formed by concatemers in Nucleocytoviricota with linear genomes such as Poxviridae (Culyba et al 2009). They are also involved in the cleavage of cruciform (four-way junction) formed by inverted repeats, such as M1 and M2, to serve as intermediates in homologous recombination (Bowater et al 2022). The second candidate, pv_159 in Pithovirus sibericum , is a probable SbcCD subunit D nuclease (Table S6).…”

DNA Motifs and an Accessory CRISPR Factor Determine Cas1 Binding and Integration Activity in Sulfolobus islandicus

“…Furthermore, we have identified a stem-loop structure located in the leader-proximal region which is preferred for Cas1 binding in vitro ( Figure 3 ). Stem-loop structures are targets for binding by many proteins, such as helicase, integrase, and endonuclease, which are involved in many significant DNA metabolism processes, including replication, transcription, recombination, and DNA repair [ 35 ]. In E. coli , Cas1 is reported to recognize a cruciform DNA, and a palindromic motif present in the repeat is important for the specific interaction of Cas1-Cas2 with a CRISPR locus [ 9 , 36 ].…”

Impacts of Molecular Structure on Nucleic Acid–Protein Interactions

“…Zhao and Usdin review the range of structures that can form in specific trinucleotide From the earliest days of genome sequence analysis, it was recognized that natural DNA molecules contain a wide array of repeating sequences [3]. These types of sequences are particularly prone to adoption of non-canonical DNA structures, such as G4s, triplexes, and cruciforms (Figure 1B), which are all explored in this Special Issue [10][11][12][13][14][15][16]. Zhao and Usdin review the range of structures that can form in specific trinucleotide repeats, highlighting how their expansion in length is important in the pathology of fragile X-related disorders in humans [10].…”

“…Left-handed Z-helices can form in both DNAs and RNAs with appropriate sequences, and searching databases containing protein structures identified novel proteins predicted to bind them [11]. A different type of repetitive DNA sequence, inverted repeats, can adopt cruciform structures and many proteins have now been validated to bind to them [12]. A series of articles provide insights about G4s.…”

“…Some proteins recognise sequence-specific targets, but an increasing number are being shown to interact with non-canonical structural aspects of nucleic acids (Figure 1C). We have already referred to some articles in this Special Issue that describe such interactions [11][12][13]. Another study took advantage of available datasets and discovered new correlations between specific amino acid deviations in p53 proteins, showing a direct association between specific amino acid residues in the protein and changes in p53 functionality, and further highlighting the importance of p53 protein in processes that influence lifespan and aging [17].…”