Sampling the structure of the noncanonical lin-4:lin-14 microRNA:mRNA complex by molecular dynamics simulations

Balasubramanian, Chandramouli ; Ojha, Rajendra Prasad ; Maiti, Souvik ; Desideri, Alessandro (2010) Sampling the structure of the noncanonical lin-4:lin-14 microRNA:mRNA complex by molecular dynamics simulations The Journal of Physical Chemistry B, 114 (49). pp. 16443-16449. ISSN 1520-6106

Full text not available from this repository.

Official URL: http://pubs.acs.org/doi/abs/10.1021/jp104193r

Related URL: http://dx.doi.org/10.1021/jp104193r

Abstract

siRNA and microRNA (miRNA) are two classes of noncoding RNAs that carry out post-transcriptional gene regulation by interacting with the target mRNA. The structural features of siRNA/miRNA−mRNA complex play a crucial role in gene silencing. Here we have used computer modeling and simulation approach to (i) elucidate the possible structures of the partially complementary lin-4:lin-14 miRNA-mRNA complex and (ii) compare the structural features with the fully complementary lin-4:lin-14 siRNA-mRNA complex. The fully complementary siRNA complex maintains a canonical helical shape while the presence of mismatch base pairs and bulge induce a kinked structure in the miRNA complex. Docking of the simulated duplex models on to the argonaute protein gives a direct indication that in the siRNA−mRNA structure, the scissile phosphate of the mRNA strand is more accessible to the catalytic site as compared to the miRNA−mRNA structures, providing an explanation for the less prevalence of the cleavage in the later case.

Item Type:Article
Source:Copyright of this article belongs to American Chemical Society.
ID Code:103397
Deposited On:02 Feb 2018 03:48
Last Modified:02 Feb 2018 03:48

Repository Staff Only: item control page