5NQI

E.coli 16S rRNA Sarcin-Ricin Loop containing a 5-hydroxymethylcytosine modification

Summary for 5NQI

• Entry DOI: 10.2210/pdb5nqi/pdb
• Related: 3DVZ
• Descriptor: E.Coli 27-mer SRL RNA (2 entities in total)
• Functional Keywords: rna, modification
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 8774.28

Authors

Ennifar, E.,Micura, R. (deposition date: 2017-04-20, release date: 2017-07-26, Last modification date: 2024-05-08)

Primary citation

Riml, C.,Lusser, A.,Ennifar, E.,Micura, R.
Synthesis, Thermodynamic Properties, and Crystal Structure of RNA Oligonucleotides Containing 5-Hydroxymethylcytosine.
J. Org. Chem., 82:7939-7945, 2017

PubMed Abstract: 5-Hydroxymethylcytosine (hmC) is an RNA modification that has attracted significant interest because of the finding that RNA hydroxymethylation can favor mRNA translation. For insight into the mechanistic details of hmC function to be obtained, the availability of RNAs containing this modification at defined positions that can be used for in vitro studies is highly desirable. In this work, we present an eight-step route to 5-hydroxymethylcytidine (hmrC) phosphoramidite for solid-phase synthesis of modified RNA oligonucleotides. Furthermore, we examined the effects of hmrC on RNA duplex stability and its impact on structure formation using the sarcin-ricin loop (SRL) motif. Thermal denaturation experiments revealed that hmrC increases RNA duplex stability. By contrast, when cytosine within an UNCG tetraloop motif was replaced by hmrC, the thermodynamic stability of the corresponding hairpin fold was attenuated. Importantly, incorporation of hmrC into the SRL motif resulted in an RNA crystal structure at 0.85 Å resolution. Besides changes in the hydration pattern at the site of modification, a slight opening of the hmrC-G pair compared to the unmodified C-G in the native structure was revealed.

PubMed: 28707898
DOI: 10.1021/acs.joc.7b01171

Experimental method

X-RAY DIFFRACTION (0.851 Å)