New structural insights into unusual nucleic acid conformations in relevance to mechanisms and pathogeneses of trinucleotide repeat expansion disorders

Kolimi, Narendar and Rathinavelan, Thenmalarchelvi (2018) New structural insights into unusual nucleic acid conformations in relevance to mechanisms and pathogeneses of trinucleotide repeat expansion disorders. PhD thesis, Indian Institute of Technology Hyderabad.

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Trinucleotide repeats belong to the family of microsatellites (a tract of 1 to 6 repetitive nucleotides) that are commonly observed in eukaryotes and exhibit repeat length polymorphism. The inherent ability of trinucleotide repeats to undergo abnormal expansion (viz., increase in repeat length) leads to many incurable genetic disorders, the best known are, Huntington's disease (CAG repeat), fragile X syndrome (CGG repeat), myotonic dystrophy 1 (CTG repeat), Friedreich’s ataxia (GAA repeat) and spinocerebellar ataxias (CAG repeat) that are mainly neurodegenerative. Severity of these disorders is proportional to the number of expanded repeats. Overexpansion of these repeats results in the formation of unusual nucleic acid secondary structures such as hairpins, triplexes, tetraplexes etc. Although many investigations have been carried out to understand the mechanism(s) behind these disorders, the therapeutics of trinucleotide repeat expansion disorders are not well developed. Thus, to facilitate the therapeutics of aforementioned neurological and neuromuscular disorders, the impact of such an overexpansion on DNA & RNA conformations and the concomitant functional implications have to be investigated. We have carried out molecular dynamics simulations (MD), circular dichroism (CD) and electrophoretic mobility shift assay (EMSA) to determine (i) the secondary structural characteristics of DNA hairpin stems that contain CAG (A...A mismatch), GAC (A...A mismatch), CCG (C...C mismatch) & CGG repeat sequences and (ii) the complex model of CAG repeats containing RNA duplex with alternative pre-mRNA splicing regulator muscle blind like protein 1 (MBNL1). MD results revealed that A...A mismatch containing CAG/GAC dictates local B- to Z-DNA transformation irrespective of the starting glycosyl conformation, in sharp contrast to the canonical DNA duplex. This result is further confirmed by CD studies. MD and CD studies further showed that more than four C...C mismatches cannot be accommodated in a RNA duplex formed by CCG repeat, instead, these favor i-motif structure. In contrast, CCG can form duplex structure at the DNA level irrespective of the number of C...C mismatches. Strikingly, CGG repeats prefer to form quadruplex structure both at DNA and RNA levels. The current investigation also explored the binding mode of MBNL1 with RNA duplex that contain CAG repeats. Our study revealed for the first time that MBNL1 binds to the minor groove of the RNA duplex. Thus, the conformational preference for CNG (N=A/C/G) and GAC repeats presented here along with the minor groove binding preference for MBNL1 with CAG repeats containing RNA duplex may facilitate the understanding of trinucleotide repeat expansion mechanism(s) and pathogeneses as well as expedite the drug discovery process to treat these diseases.

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IITH Creators:
IITH CreatorsORCiD
Rathinavelan, Thenmalarchelvi
Item Type: Thesis (PhD)
Subjects: Others > Biotechnology
Divisions: Department of Biotechnology
Depositing User: Team Library
Date Deposited: 03 Jul 2018 05:39
Last Modified: 21 Sep 2019 06:21
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