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Non-Protein Coding RNAs pp 317–333Cite as

Biophysical Analyses of IRES RNAs from the Dicistroviridae: Linking Architecture to Function

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Part of the book series: Springer Series in Biophysics ((BIOPHYSICS,volume 13))

Abstract

Internal ribosome entry sites (IRES) are non-protein coding RNAs that can drive translation initiation using RNA in place of protein factors and the modified nucleotide cap. IRESs are critical for successful infection by many viruses and may be an important means of regulating gene expression in healthy cells, yet our understanding of their structure-based mechanism of action remains incomplete. A critical part of understanding their function is knowledge of the biophysical properties of the free IRES RNA itself, as the architecture of the unbound RNA is likely to be a key functional determinant. This chapter presents the application of several biophysical methods to the study of an IRES RNA. Comparing the results of these studies to those performed on a different IRES RNA suggests the biophysical properties of these two IRES RNAs both reflect and predict their mode of interacting with the ribosome

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Abbreviations

IRES:

internal ribosome entry site

UTR:

untranslated region

ORF:

open reading frame

IGR:

intergenic region

HCV:

hepatitis C virus

eIF:

eukaryotic initiation factor

mRNA:

messenger RNA

ITAF:

IRES trans-activating factors

EMCV:

encephalomyocarditis virus

HAV:

hepatitis A virus

FMDV:

footand-mouth disease virus

HIV-1:

human immunodeficiency virus-1

DMS:

dimethysulfate

Kethoxyl:

β-ethoxy-a-ketobutyraldehyde

CMCT:

1-cyclohexyl-3-(morpholinoethyl)-carbodiimide metho-p-toluene sulfonate

RNase:

ribonuclease

SHAPE:

selective 2′-hydroxyl acylation analyzed by primer extension

ENU:

ethylnitrosourea

tRNA:

transfer RNA

cryo-EM:

cryo-electron microscopy

SV/AUC:

sedimentation velocity analytical ultracentrifugation

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Genetics, Denver School of Medicine, University of Colorado, 12801 East 17th Ave, Rm L18-9110, Aurora, CO, 80045, USA

    Jeffrey S. Kief

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  1. Jeffrey S. Kief
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Correspondence to Jeffrey S. Kief .

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Editors and Affiliations

  1. Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI, 48109-1055, USA

    Nils G. Walter (Associate Professor of Chemistry) (Associate Professor of Chemistry)

  2. Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA

    Sarah A. Woodson (Professor of Biophysics) (Professor of Biophysics)

  3. Department of Chemistry and Biochemistry, University of Colorado at Boulder, Box 215, Boulder, CO, 80309-0215, USA

    Robert T. Batey (Associate Professor of Chemistry and Biochemistry) (Associate Professor of Chemistry and Biochemistry)

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Kief, J.S. (2009). Biophysical Analyses of IRES RNAs from the Dicistroviridae: Linking Architecture to Function. In: Walter, N.G., Woodson, S.A., Batey, R.T. (eds) Non-Protein Coding RNAs. Springer Series in Biophysics, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-70840-7_16

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