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The antibiotic viomycin traps the ribosome in an intermediate state of translocation

Dmitri N Ermolenko
P Clint Spiegel
Harry F Noller
Research21 May 2007
Nature Structural & Molecular Biology

Volume: 14, P: 493-497
Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation

This study shows that rather than high thermodynamic stability, specific length and structure enable regulatory mRNA stem-loops to pause translation. These findings aid identification of new regulatory mRNA stem-loops.

Chen Bao
Mingyi Zhu
Dmitri N. Ermolenko
ResearchOpen Access21 Feb 2022
Nature Communications

Volume: 13, P: 1-14
mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances

It was previously suggested that formation of RNA secondary structure tends to bring the 5′ and 3′ ends of RNA into close proximity. Here the authors use experimental and computational approaches to show that mRNAs and lncRNAs have an intrinsic propensity to fold into structures in which the 5′ end and 3′ end are ≤7 nm apart irrespective of length.

Wan-Jung C. Lai
Mohammad Kayedkhordeh
Dmitri N. Ermolenko
ResearchOpen Access18 Oct 2018
Nature Communications

Volume: 9, P: 1-11
An extended U2AF⁶⁵–RNA-binding domain recognizes the 3′ splice site signal

The pre-mRNA splicing factor U2AF65 recognizes 3′ splice sites in human gene transcripts, but the details are not fully understood. Here, the authors report U2AF65 structures and single molecule FRET that reveal mechanistic insights into splice site recognition.

Anant A. Agrawal
Enea Salsi
Clara L. Kielkopf
ResearchOpen Access08 Mar 2016
Nature Communications

Volume: 7, P: 1-14
mRNA translocation occurs during the second step of ribosomal intersubunit rotation

During translation, the messenger RNA undergoes concerted translocation through the ribosome with the tRNA. By FRET labeling the ribosomal subunits, and monitoring fluorescence quenching of a probe on the mRNA, translocation is observed to occur during clockwise but not counterclockwise intersubunit rotational movement, providing direct evidence for a ratchet mechanism.

Dmitri N Ermolenko
Harry F Noller
Research13 Mar 2011
Nature Structural & Molecular Biology

Volume: 18, P: 457-462

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The antibiotic viomycin traps the ribosome in an intermediate state of translocation

Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation

mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances

An extended U2AF65–RNA-binding domain recognizes the 3′ splice site signal

mRNA translocation occurs during the second step of ribosomal intersubunit rotation

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An extended U2AF⁶⁵–RNA-binding domain recognizes the 3′ splice site signal