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Violation of DNA neighbor exclusion principle in RNA recognition | JoVE Visualize

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Violation of DNA neighbor exclusion principle in RNA recognition

Muhammad Yousuf^1,2, Il Seung Youn^1,2, Jeonghun Yun^1,2

¹Pohang University of Science and Technology , Pohang 790-784 , Korea.

Chemical Science|July 13, 2018

View abstract on PubMed

Summary

Naphthalene-based probes selectively bind to RNA, unlike DNA, by violating the neighbor-exclusion principle. This discovery enables specific RNA sensing and dynamic observation for biological studies.

Area of Science:

Biochemistry
Molecular Biology
Materials Science

Background:

DNA intercalation is crucial for functional material design.
RNA intercalation is generally assumed to mirror DNA intercalation.

Purpose of the Study:

Investigate the mechanism of naphthalene-based cationic probe intercalation in RNA.
Determine the selectivity of these probes for RNA over DNA.
Understand the structural basis for selective RNA sensing.

Main Methods:

Experimental characterization of probe-RNA interactions using fluorescence and circular dichroism (CD).
Computational modeling to reproduce experimental data.
Molecular dynamics (MD) simulations to analyze structural changes.

Main Results:

Naphthalene-based probes violate the neighbor-exclusion principle in RNA, unlike in DNA.
Intercalation occurs via π-π interactions and is stabilized by hydrogen bonds, conferring RNA selectivity.
MD simulations show probe intercalation leads to RNA unfolding.
Experimental and computational data support the proposed mechanism.

Conclusions:

The study elucidates a novel mechanism for selective RNA sensing using naphthalene-based probes.
This mechanism relies on the violation of the neighbor-exclusion principle in RNA.
Understanding this selective binding is key for developing tools for dynamic RNA observation and biological role studies.

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Violation Of Dna Neighbor Exclusion Principle In Rna Recognition