Unique Length-Dependent Biophysical Properties of Repetitive DNA

Abstract

Expansion of a trinucleotide repeat (TNR) sequence is the molecular signature of several neurological disorders. Formation of non-canonical structures by the TNR sequence is proposed to contribute to the expansion mechanism. Furthermore, it is known that the propensity for expansion increases with repeat length. In this work we use calorimetry to describe the thermodynamic parameters (ΔH, TΔS, and ΔG) of the non-canonical stem-loop hairpins formed by the TNR sequences (CAG)n and (CTG)n, and also the canonical (CAG)n/(CTG)n duplexes, for n = 6–14. Using a thermodynamic cycle, we calculated the same thermodynamic parameters describing the process of converting from non-canonical stem-loop hairpins to canonical duplex. In addition to these thermodynamic analyses, we used spectroscopic techniques to determine the rate at which the non-canonical structures convert to duplex, and the activation enthalpy ΔH‡ describing this process. We report that the thermodynamic parameters of unfolding the stem-loop (CTG)n and (CAG)n hairpins, along with the thermodynamic and kinetic properties of hairpin to duplex conversion, do not proportionally corresponding to the increase of length, but rather show a unique pattern that depends on whether the sequence has an even or odd number of repeats.

Uncovering the mechanism for aggregation in repeat expanded RNA reveals a reentrant transition

“…and tetramers forming at extremely low fractions. We find that for certain concentrations, the system forms either monomers or dimers depending on the parity of n, in agreement with experimental results [17]; however, this parity does not significantly affect aggregation. We plot the results of Nguyen et al on top of our predictions as colored points, finding excellent agreement between the two.…”

“…studies [7, 19]. Our work provides a unified framework to explain both dimerization and aggregation phenomena in CAG repeat systems [17, 19] and extends these to arbitrary sequences, temperatures, and concentrations, thus setting the stage for the construction of novel materials and new techniques based on programmable RNA condensates.…”

Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches

“…The stability trends of (CNG) n are the same as observed in other melting experiments. [117][118][119] However, for (GNC) 5 repeats with N ¼ A, C, or T, Fig. 13b, the displacements are very large.…”

Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops

“…Hairpins represent perhaps the most common pathogenic secondary structure associated with TREDs [18] , [19] , [20] , [21] , [22] , [23] , [24] , [25] , [26] , [27] , [28] . Because relatively little is known about these structures at the molecular level, our work has focused on the structural and dynamical characteristics of both homoduplexes (representing the stem of a long hairpin) and hairpins.…”

“…However, it could probably become stable for longer sequences where two C-quartets could become “sandwiched” between four-layered G-tetrads. We also studied the stability of quadruplexes as a function of K + and Na + ions [25] . Both types of ions favor a stable twist distribution with Na + giving smaller twist angles.…”