Presentation Title

Backbone Probing of CVB3 RNA

Advisor Information

William Tapprich

Location

UNO Criss Library, Room 107

Presentation Type

Oral Presentation

Start Date

7-3-2014 2:00 PM

End Date

7-3-2014 2:15 PM

Abstract

Coxsackievirus B3 (CVB3) is a pathogenic enterovirus of the Picornaviridae family that is responsible for myocarditis and pancreatitis in humans. The positive single-stranded RNA genome consists of 7,400 nucleotides and four regions: a 5’ untranslated region (5’UTR), an open reading frame (ORF), a 3’UTR, and a poly(A) tail. The 5’UTR contains 742 bases and seven secondary structure domains. Because virulence has been associated with the 5’UTR, understanding the structure of this region is essential. Selective 2’hydroxyl acylation analyzed by primer extension (SHAPE) is a method used to investigate the structure of the CVB3 5’UTR. SHAPE involves modification of the RNA backbone with the use of an electrophile, N-methylisatoic anhydride (NMIA). NMIA reacts with the 2’hydroxyl group of the ribose sugar to produce a 2’-O-adduct. Single-stranded and unconstrained nucleotide positions will react more readily with NMIA than positions that are base-paired and constrained. Quantifying the reactivity with NMIA will help determine regions of the genome that are accessible to modification. SHAPE experiments will allow us to comparatively analyze the three-dimensional structure of virulent and non-virulent strains of CVB3 and will reveal regions that are exposed for functional activities such as protein binding. A better understanding of virulence determinants in the RNA genome could lead to the development of effective antivirals.

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COinS
 
Mar 7th, 2:00 PM Mar 7th, 2:15 PM

Backbone Probing of CVB3 RNA

UNO Criss Library, Room 107

Coxsackievirus B3 (CVB3) is a pathogenic enterovirus of the Picornaviridae family that is responsible for myocarditis and pancreatitis in humans. The positive single-stranded RNA genome consists of 7,400 nucleotides and four regions: a 5’ untranslated region (5’UTR), an open reading frame (ORF), a 3’UTR, and a poly(A) tail. The 5’UTR contains 742 bases and seven secondary structure domains. Because virulence has been associated with the 5’UTR, understanding the structure of this region is essential. Selective 2’hydroxyl acylation analyzed by primer extension (SHAPE) is a method used to investigate the structure of the CVB3 5’UTR. SHAPE involves modification of the RNA backbone with the use of an electrophile, N-methylisatoic anhydride (NMIA). NMIA reacts with the 2’hydroxyl group of the ribose sugar to produce a 2’-O-adduct. Single-stranded and unconstrained nucleotide positions will react more readily with NMIA than positions that are base-paired and constrained. Quantifying the reactivity with NMIA will help determine regions of the genome that are accessible to modification. SHAPE experiments will allow us to comparatively analyze the three-dimensional structure of virulent and non-virulent strains of CVB3 and will reveal regions that are exposed for functional activities such as protein binding. A better understanding of virulence determinants in the RNA genome could lead to the development of effective antivirals.