Structure and Dynamics of DNA and RNA Double Helices Formed by d(CTG), d(GTC), r(CUG), and r(GUC) Trinucleotide Repeats and Associated DNA–RNA Hybrids

Abstract

Myotonic dystrophy type 1 is the most frequent form of muscular dystrophy in adults caused by an abnormal expansion of the CTG trinucleotide. Both the expanded DNA and the expanded CUG RNA transcript can fold into hairpins. Cotranscriptional formation of stable RNA•DNA hybrids can also enhance the instability of repeat tracts. We performed molecular dynamics simulations of homoduplexes associated with the disease, d(CTG) n and r(CUG) n , and their corresponding r(CAG) n :d-(CTG) n and r(CUG) n :d(CAG) n hybrids that can form under bidirectional transcription and of non-pathological d(GTC) n and d(GUC) n homoduplexes. We characterized their conformations, stability, and dynamics and found that the U•U and T•T mismatches are dynamic, favoring anti−anti conformations inside the helical core, followed by anti−syn and syn−syn conformations. For DNA, the secondary minima in the non-expanding d(GTC) n helices are deeper, wider, and longer-lived than those in d(CTG) n , which constitutes another biophysical factor further differentiating the expanding and non-expanding sequences. The hybrid helices are closer to A-RNA, with the A-T and A-U pairs forming two stable Watson−Crick hydrogen bonds. The neutralizing ion distribution around the non-canonical pairs is also described.

High-Resolution NMR Structures of Intrastrand Hairpins Formed by CTG Trinucleotide Repeats

“…These resonated with our resolved NMR structures for even-numbered dG(CTG) 4 C and dG(CTG) 6 C that adopted blunt-end hairpins with a TGCT loop (Figures –), while the slipping dynamics in odd-numbered repeats might contribute to the smearing PAGE gel bands of dG(CTG) 5 C and dG(CTG) 7 C (Figure S1). Furthermore, our NMR and previous MD simulation works have revealed similar configurations of TGCT tetraloop and T·T mismatches in the hairpins of CTG repeats with varying sequence context. , These biophysical means collectively foster our understanding of the microscopic structural behaviors of trinucleotide repeats associated with neurodegenerative diseases.…”

“…The CTG and CAG trinucleotide repeat expansions have been reported to associate with more than 10 neurodegenerative diseases. , It is only recently that the focus has shifted toward understanding the microscopic structural behaviors of their DNA structures and how they affect important biological processes including replication and transcription. Apart from high-resolution NMR study presented here, smFRET integrated with MD simulations have also emerged as powerful biophysical tools for studying the structures and dynamics of trinucleotide repeats. − To elucidate the hairpin structures of d­(CTG) n and d­(CAG) n repeats, smFRET can be used to determine the slipped states and transition kinetics among various conformations, and MD simulations unveil the stabilizing forces underpinning the dominant loop configurations and mismatch pairing modes. Weninger and co-workers have established that both d­(CTG) n and d­(CAG) n repeats form hairpin structures in a parity-dependent manner; i.e., the even-numbered repeats predominantly adopt blunt-end hairpins, whereas the odd-numbered repeats slip back and forth to form hairpins with 5′ or 3′ overhangs. , In addition, both d­(CTG) n and d­(CAG) n hairpins favor forming tetranucleotide loops.…”

Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

“…However, many more groups are separately working on deriving and optimizing parameters for only either the RNA or DNA. ,− In those cases, the choice of the second nucleic acids ff is arbitrary and difficult to justify, especially when no specific recommendation is given by the ff developers and the hybrids are seldom among the systems used for benchmarking. In fact, there is currently no study systematically assessing the ff performance in MD simulations of hybrid duplexes available in the literature, although computational studies of specific hybrids have been previously carried out. − …”