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Major alteration in coxsackievirus B3 genomic RNA structure distinguishes a virulent strain from an avirulent strain.

Prusa J, Missak J, Kittrell J, Evans JJ, Tapprich WE - Nucleic Acids Res. (2014)

Bottom Line: Comparative sequence analysis of 170 closely related enteroviruses revealed that the SLII region lacks conservation.Neither the parent SLII nor the remaining domains of the background 5'UTR were structurally altered by the exchange, supporting an independent mechanism of folding and function.We show that the attenuated 5'UTR lacks structure in the SLII cardiovirulence determinant.

View Article: PubMed Central - PubMed

Affiliation: Biology Department, University of Nebraska at Omaha, Omaha, NE 68182, USA.

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Related in: MedlinePlus

Chemical probing results for CV-B3/28 and CV-B3/GA SLII. For all sequencing gels, arrows indicate modified positions and vertical lines between two nucleotide positions indicate that all positions between and including the positions shown are modified. Sequencing tracks indicating the nucleotide positions are labelled A, C, G and U. Tracks with chemically modified RNA are labelled (+) and tracks with unmodified RNA are labelled (−). (A) 12% sequencing gel shows CV-B3/28 SLII region–positions 80–140. (B) 12% sequencing gel shows CV-B3/GA SLII region–positions 80–140. (C) 12% sequencing gel shows CV-B3/28 SLII region–positions 110–190. (D) Chemical probing of CV-B3/GA SLII region–positions 110–200.
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Figure 1: Chemical probing results for CV-B3/28 and CV-B3/GA SLII. For all sequencing gels, arrows indicate modified positions and vertical lines between two nucleotide positions indicate that all positions between and including the positions shown are modified. Sequencing tracks indicating the nucleotide positions are labelled A, C, G and U. Tracks with chemically modified RNA are labelled (+) and tracks with unmodified RNA are labelled (−). (A) 12% sequencing gel shows CV-B3/28 SLII region–positions 80–140. (B) 12% sequencing gel shows CV-B3/GA SLII region–positions 80–140. (C) 12% sequencing gel shows CV-B3/28 SLII region–positions 110–190. (D) Chemical probing of CV-B3/GA SLII region–positions 110–200.

Mentions: The structure of the SLII region was analysed with chemical probing analysis (Figure 1). A summary of the modification results at each position is displayed on models of SLII in Figure 2. The C-rich region ranging from positions 90–100 is shown at the top of Figure 1A and B. A strong stop at positions 99–100 partially obscures the results for the 90–100 region in Figure 1A and B. Despite the strong stop, a lack of reactivity is observed in the DMS lane for both CV-B3/28 and CV-B3/GA between positions 90 - 100, indicating that this C-rich region is not accessible to solvent. The A-U rich region spanning positions 100—110 is partially protected in both CV-B3/28 and CV-B3/GA (Figure 1A and B). Positions 102G, 103A, 104U, 105G and 106U are modified in CV-B3/GA. Likewise, for CV-B3/28, positions 101A, 102A, 103C, 104U, 105G and 106U are accessible.


Major alteration in coxsackievirus B3 genomic RNA structure distinguishes a virulent strain from an avirulent strain.

Prusa J, Missak J, Kittrell J, Evans JJ, Tapprich WE - Nucleic Acids Res. (2014)

Chemical probing results for CV-B3/28 and CV-B3/GA SLII. For all sequencing gels, arrows indicate modified positions and vertical lines between two nucleotide positions indicate that all positions between and including the positions shown are modified. Sequencing tracks indicating the nucleotide positions are labelled A, C, G and U. Tracks with chemically modified RNA are labelled (+) and tracks with unmodified RNA are labelled (−). (A) 12% sequencing gel shows CV-B3/28 SLII region–positions 80–140. (B) 12% sequencing gel shows CV-B3/GA SLII region–positions 80–140. (C) 12% sequencing gel shows CV-B3/28 SLII region–positions 110–190. (D) Chemical probing of CV-B3/GA SLII region–positions 110–200.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150801&req=5

Figure 1: Chemical probing results for CV-B3/28 and CV-B3/GA SLII. For all sequencing gels, arrows indicate modified positions and vertical lines between two nucleotide positions indicate that all positions between and including the positions shown are modified. Sequencing tracks indicating the nucleotide positions are labelled A, C, G and U. Tracks with chemically modified RNA are labelled (+) and tracks with unmodified RNA are labelled (−). (A) 12% sequencing gel shows CV-B3/28 SLII region–positions 80–140. (B) 12% sequencing gel shows CV-B3/GA SLII region–positions 80–140. (C) 12% sequencing gel shows CV-B3/28 SLII region–positions 110–190. (D) Chemical probing of CV-B3/GA SLII region–positions 110–200.
Mentions: The structure of the SLII region was analysed with chemical probing analysis (Figure 1). A summary of the modification results at each position is displayed on models of SLII in Figure 2. The C-rich region ranging from positions 90–100 is shown at the top of Figure 1A and B. A strong stop at positions 99–100 partially obscures the results for the 90–100 region in Figure 1A and B. Despite the strong stop, a lack of reactivity is observed in the DMS lane for both CV-B3/28 and CV-B3/GA between positions 90 - 100, indicating that this C-rich region is not accessible to solvent. The A-U rich region spanning positions 100—110 is partially protected in both CV-B3/28 and CV-B3/GA (Figure 1A and B). Positions 102G, 103A, 104U, 105G and 106U are modified in CV-B3/GA. Likewise, for CV-B3/28, positions 101A, 102A, 103C, 104U, 105G and 106U are accessible.

Bottom Line: Comparative sequence analysis of 170 closely related enteroviruses revealed that the SLII region lacks conservation.Neither the parent SLII nor the remaining domains of the background 5'UTR were structurally altered by the exchange, supporting an independent mechanism of folding and function.We show that the attenuated 5'UTR lacks structure in the SLII cardiovirulence determinant.

View Article: PubMed Central - PubMed

Affiliation: Biology Department, University of Nebraska at Omaha, Omaha, NE 68182, USA.

Show MeSH
Related in: MedlinePlus