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Related Concept Videos

MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay
12:49

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Published on: May 25, 2015

Tertiary structure-based analysis of microRNA-target interactions.

Hin Hark Gan1, Kristin C Gunsalus

  • 1Department of Biology, New York University, New York, NY 10003, USA. hhg3@nyu.edu

RNA (New York, N.Y.)
|February 19, 2013
PubMed
Summary

We developed a new computational method to model microRNA (miRNA) interactions using tertiary structures. This approach accurately predicts miRNA-target binding energies and reveals structural insights beyond secondary structure analysis.

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Area of Science:

  • Computational biology
  • Molecular biology
  • Biophysics

Background:

  • Current microRNA (miRNA) interaction analysis relies heavily on primary and secondary structure.
  • Realistic modeling of miRNA-mediated translational repression requires computationally efficient tertiary structure-based methods.

Purpose of the Study:

  • To develop and validate a novel pipeline for modeling miRNA-target duplex binding energies using tertiary structure.
  • To enable more accurate predictions of molecular interactions in miRNA-mediated translational repression.

Main Methods:

  • Incorporation of algorithms for predicting RNA duplex structures, ionic strength effects, entropy, and free energy.
  • Utilizing an all-atom RNA description and Poisson-Boltzmann equation for ionic interactions.
  • Docking of duplex-Argonaute protein complexes to model binding.

Main Results:

  • Predicted conformations of Caenorhabditis elegans let-7 miRNA-target duplexes with high accuracy (∼3.8 Å RMSD to NMR structures).
  • Computed thermodynamic parameters (enthalpy, entropy, free energy) for miRNA-target duplexes showed agreement with experimental titration calorimetry data.
  • Analysis revealed that seed region mismatches destabilize duplex hybridization and Argonaute association.

Conclusions:

  • Tertiary structure-based modeling provides a more realistic approach to studying miRNA interactions.
  • This method uncovers structural mechanisms of miRNA activity that are not accessible through secondary structure analysis alone.
  • The developed pipeline accurately predicts miRNA-target binding and offers insights into the role of structural distortions in miRNA function.