The Cruciform DNA Mobility Shift Assay: A Tool to Study Proteins That Recognize Bent DNA

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

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.

Detection of DNA Autoantibodies by Electrophoretic Mobility Shift Assay

Although the presence of antibodies against double-stranded (ds) DNA is considered the serological hallmark of systemic lupus erythematosus (SLE), it is not detected in all SLE patients by routine laboratory tests. Looking at DNA-anti(ds)DNA interaction as one kind of DNA-protein interaction gave us the grounds for a novel type of assay, easy to perform, and providing a direct insight on DNA-anti(ds)DNA IgG interaction. The assay is an application of the electrophoretic mobility shift assay (EMSA) and is based on the observation that the electrophoretic mobility of a DNA-protein complex is typically less than that of free DNA. The EMSA, performed here with purified bacterial DNA and the purified IgG fraction of sera from systemic lupus erythematosus (SLE) or other patients as well as from healthy individuals, revealed itself to be more sensitive than the routinely used assays for the detection of anti-dsDNA in SLE and discoid lupus erythematosus (DLE) patients. In addition, besides providing a direct visualization of DNA-anti(ds)DNA IgG complexes, the assay offers the possibility to study in detail the nature of DNA-IgG interactions. In a further development, we showed that the assay could be performed successfully with sera.