Structural insights into the effects of 2′-5′ linkages on the RNA duplex

Jia Sheng, Li Li, Aaron E. Engelhart, Jianhua Gan, Jiawei Wang, Jack W. Szostak

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

The mixture of 2′-5′ and 3′-5′ linkages generated during the non-enzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world. However, we recently observed that both a ribozyme and an RNA aptamer retain considerable functionality in the presence of prebiotically plausible levels of linkage heterogeneity. To better understand the RNA structure and function in the presence of backbone linkage heterogeneity, we obtained high-resolution X-ray crystal structures of a native 10-mer RNA duplex (1.32 Å) and two variants: one containing one 2′-5′ linkage per strand (1.55 Å) and one containing three such linkages per strand (1.20 Å). We found that RNA duplexes adjust their local structures to accommodate the perturbation caused by 2′-5′ linkages, with the flanking nucleotides buffering the disruptive effects of the isomeric linkage and resulting in a minimally altered global structure. Although most 2′-linked sugars were in the expected 2′-endo conformation, some were partially or fully in the 3′-endo conformation, suggesting that the energy difference between these conformations was relatively small. Our structural and molecular dynamic studies also provide insight into the diminished thermal and chemical stability of the duplex state associated with the presence of 2′-5′ linkages. Our results contribute to the view that a low level of 2′-5′ substitution would not have been fatal in an early RNA world and may in contrast have been helpful for both the emergence of nonenzymatic RNA replication and the early evolution of functional RNAs.

Original languageEnglish (US)
Pages (from-to)3050-3055
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume111
Issue number8
DOIs
StatePublished - Feb 25 2014

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RNA
Nucleotide Aptamers
Catalytic RNA
Molecular Dynamics Simulation
Nucleotides
Hot Temperature
X-Rays

Keywords

  • Backbone heterogeneity
  • Origin of life
  • X-ray crystallography

Cite this

Structural insights into the effects of 2′-5′ linkages on the RNA duplex. / Sheng, Jia; Li, Li; Engelhart, Aaron E.; Gan, Jianhua; Wang, Jiawei; Szostak, Jack W.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 111, No. 8, 25.02.2014, p. 3050-3055.

Research output: Contribution to journalArticle

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