Probing the role of RNA-DNA hybrids in instigating trinucleotide repeat instability and their interaction with RNase H1

R-loops are transient intermediates that are formed during the transcription and consist of an\ud RNA-DNA hybrid that is formed between the nascent RNA strand and the template DNA\ud strand and a displaced non-template DNA strand. Formation of R-loops have been detected in\ud organisms from bacteria to humans. If R-loops form more frequently, they impact transcription\ud affecting genome stability, genome integrity and cause a number of diseases. Recently, genome\ud instability caused due to stable RNA-DNA hybrid in R-loop was shown to predominantly\ud associate with expansion of trinucleotide repeats, leading to many incurable neurological and\ud neuromuscular genetic disorders like Myotonic dystrophy1, Fragile X syndrome, Huntington's\ud disease, Friedreich’s ataxia, Spinocerebellar ataxias etc. Till date, the structural information\ud about RNA-DNA hybrids formed by trinucleotide repeat expansions (TREs) are unknown to\ud elucidate the mechanism behind RNA-DNA hybrid in instigating TREs. In this context, we\ud aim here to study the structures of RNA-DNA hybrids consisting of trinucleotide repeats such\ud as dGAA-rUUC, rGAA-dTTC, rCAG-dCTG, rCUG-dCAG, rCGG-dCCG and rCCG-dCGG\ud by employing molecular dynamics (MD) simulation technique. It’s noteworthy that\ud trinucleotide repeat expansion disorders (TREDs) can also be treated at mRNA level, wherein,\ud a short complimentary DNA oligonucleotide is targeted against the mRNA that is followed by\ud the cleavage of the mRNA strand by RNase H1 enzyme. Thus, to understand the efficacy of\ud RNase H1 against TRE containing RNA-DNA hybrid, the interaction of TRE containing RNADNA\ud hybrid with RNase H1 is also probed. Such scenario comes into picture during\ud replication, wherein a transient RNA-DNA hybrid is formed and subsequently, the RNA strand\ud is cleaved by RNase H1. Thus, this investigation is expected to shed light on structural\ud properties of TRE containing RNA-DNA hybrids as well as its complex with RNase H1 to\ud understand the TRE mechanism at replication and transcription levels and their treatment. The\ud study on structure and dynamics of RNA-DNA hybrids consisting of various TREs suggest\ud that these hybrids have both A & B characteristics irrespectively of sequence. The study on\ud HsRNase H1 complexed with TREs containing RNA-DNA hybrids suggest that the protein\ud follow the same cleavage mechanism for all the hybrids irrespective of sequence and thus,\ud antisense strategy can be utilized to treat TREDs at RNA level