4NFO

Crystal Structure Analysis of the 16mer GCAGACUUAAGUCUGC

Summary for 4NFO

• Entry DOI: 10.2210/pdb4nfo/pdb
• Related: 4NFP 4NFQ
• Descriptor: GCAGACUUAAGUCUGC, SPERMINE (3 entities in total)
• Functional Keywords: rna 16mer oligo, rna
• Total number of polymer chains: 3
• Total formula weight: 15496.58

Authors

Beal, P.A.,Fisher, A.J.,Phelps, K.J.,Ibarra-Soza, J.M.,Zheng, Y. (deposition date: 2013-10-31, release date: 2014-07-02, Last modification date: 2024-02-28)

Primary citation

Phelps, K.J.,Ibarra-Soza, J.M.,Tran, K.,Fisher, A.J.,Beal, P.A.
Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-aza-7-deazaadenosine in RNA.
Acs Chem.Biol., 9:1780-1787, 2014

PubMed Abstract: Ribonucleoside analogues bearing terminal alkynes, including 7-ethynyl-8-aza-7-deazaadenosine (7-EAA), are useful for RNA modification applications. However, although alkyne- and triazole-bearing ribonucleosides are in widespread use, very little information is available on the impact of these modifications on RNA structure. By solving crystal structures for RNA duplexes containing these analogues, we show that, like adenosine, 7-EAA and a triazole derived from 7-EAA base pair with uridine and are well-accommodated within an A-form helix. We show that copper-catalyzed azide/alkyne cycloaddition (CuAAC) reactions with 7-EAA are sensitive to the RNA secondary structure context, with single-stranded sites reacting faster than duplex sites. 7-EAA and its triazole products are recognized in RNA template strands as adenosine by avian myoblastosis virus reverse transcriptase. In addition, 7-EAA in RNA is a substrate for an active site mutant of the RNA editing adenosine deaminase, ADAR2. These studies extend our understanding of the impact of these novel nucleobase analogues and set the stage for their use in probing RNA structure and metabolism.

PubMed: 24896732
DOI: 10.1021/cb500270x

Experimental method

X-RAY DIFFRACTION (1.96 Å)