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Raman and Raman optical activity (ROA) analysis of RNA structural motifs in Domain I of the EMCV IRES.

Hobro AJ, Rouhi M, Blanch EW, Conn GL - Nucleic Acids Res. (2007)

Bottom Line: Specific bands are sensitive to the effect of the mismatch and asymmetric bulge on the structure of the RNA.The ROA spectra are also sensitive to conformational mobility of ribose sugars, and verify a decrease in A-type helix content upon introduction of the pyrimidine-rich bulge.Several Raman and ROA bands also clearly show cooperative effects between the mismatch and pyrimidine-rich bulge motifs on the structure of the RNA.

View Article: PubMed Central - PubMed

Affiliation: Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.

ABSTRACT
Raman and Raman optical activity (ROA) spectra were collected for four RNA oligonucleotides based on the EMCV IRES Domain I to assess the contributions of helix, GNRA tetraloop, U.C mismatch base pair and pyrimidine-rich bulge structures to each. Both Raman and ROA spectra show overall similarities for all oligonucleotides, reflecting the presence of the same base paired helical regions and GNRA tetraloop in each. Specific bands are sensitive to the effect of the mismatch and asymmetric bulge on the structure of the RNA. Raman band changes are observed that reflect the structural contexts of adenine residues, disruption of A-form helical structure, and incorporation of pyrimidine bases in non-helical regions. The ROA spectra are also sensitive to conformational mobility of ribose sugars, and verify a decrease in A-type helix content upon introduction of the pyrimidine-rich bulge. Several Raman and ROA bands also clearly show cooperative effects between the mismatch and pyrimidine-rich bulge motifs on the structure of the RNA. The complementary nature of Raman and ROA spectra provides detailed and highly sensitive information about the local environments of bases, and secondary and tertiary structures, and has the potential to yield spectral signatures for a wide range of RNA structural motifs.

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Raman and ROA spectra for all oligonucleotides. Pairwise comparisons of baseline corrected and normalized Raman (top panel) and ROA (bottom panel) spectra for Hairpin RNA (black) and (A) Mismatch RNA, (B) Bulge RNA and (C) EMCV RNA (red). The letters identifying each peak in the spectra correspond to those given in Table 1.
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Figure 3: Raman and ROA spectra for all oligonucleotides. Pairwise comparisons of baseline corrected and normalized Raman (top panel) and ROA (bottom panel) spectra for Hairpin RNA (black) and (A) Mismatch RNA, (B) Bulge RNA and (C) EMCV RNA (red). The letters identifying each peak in the spectra correspond to those given in Table 1.

Mentions: In order to allow direct comparisons between the spectra measured for different oligonucleotides the spectra were normalized for differences in experimental parameters. Figure 3 shows Raman and ROA spectra for the Hairpin, Mismatch and Bulge RNAs after normalization to the same sample concentration and accumulation time. Differences in spectrometer performance after instrument realignment prevented use of this normalization procedure for the EMCV RNA spectra. However, the Raman band at ∼1098 cm−1 is invariant of base composition (27), allowing the EMCV RNA Raman spectrum to be normalized to the intensity of this band in the Raman spectrum of Bulge RNA, after adjusting for the one additional nucleotide in EMCV RNA. As all ROA spectra were collected simultaneously with their corresponding Raman spectra, the same normalization ratios were applied to directly compare ROA spectra. We have adopted a rigorous set of procedures consistently applied to the analysis of spectra and conservatively estimate that the relative Raman and ROA band intensities presented here are accurate to ±5% for strong and medium bands.Figure 3.


Raman and Raman optical activity (ROA) analysis of RNA structural motifs in Domain I of the EMCV IRES.

Hobro AJ, Rouhi M, Blanch EW, Conn GL - Nucleic Acids Res. (2007)

Raman and ROA spectra for all oligonucleotides. Pairwise comparisons of baseline corrected and normalized Raman (top panel) and ROA (bottom panel) spectra for Hairpin RNA (black) and (A) Mismatch RNA, (B) Bulge RNA and (C) EMCV RNA (red). The letters identifying each peak in the spectra correspond to those given in Table 1.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1851652&req=5

Figure 3: Raman and ROA spectra for all oligonucleotides. Pairwise comparisons of baseline corrected and normalized Raman (top panel) and ROA (bottom panel) spectra for Hairpin RNA (black) and (A) Mismatch RNA, (B) Bulge RNA and (C) EMCV RNA (red). The letters identifying each peak in the spectra correspond to those given in Table 1.
Mentions: In order to allow direct comparisons between the spectra measured for different oligonucleotides the spectra were normalized for differences in experimental parameters. Figure 3 shows Raman and ROA spectra for the Hairpin, Mismatch and Bulge RNAs after normalization to the same sample concentration and accumulation time. Differences in spectrometer performance after instrument realignment prevented use of this normalization procedure for the EMCV RNA spectra. However, the Raman band at ∼1098 cm−1 is invariant of base composition (27), allowing the EMCV RNA Raman spectrum to be normalized to the intensity of this band in the Raman spectrum of Bulge RNA, after adjusting for the one additional nucleotide in EMCV RNA. As all ROA spectra were collected simultaneously with their corresponding Raman spectra, the same normalization ratios were applied to directly compare ROA spectra. We have adopted a rigorous set of procedures consistently applied to the analysis of spectra and conservatively estimate that the relative Raman and ROA band intensities presented here are accurate to ±5% for strong and medium bands.Figure 3.

Bottom Line: Specific bands are sensitive to the effect of the mismatch and asymmetric bulge on the structure of the RNA.The ROA spectra are also sensitive to conformational mobility of ribose sugars, and verify a decrease in A-type helix content upon introduction of the pyrimidine-rich bulge.Several Raman and ROA bands also clearly show cooperative effects between the mismatch and pyrimidine-rich bulge motifs on the structure of the RNA.

View Article: PubMed Central - PubMed

Affiliation: Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.

ABSTRACT
Raman and Raman optical activity (ROA) spectra were collected for four RNA oligonucleotides based on the EMCV IRES Domain I to assess the contributions of helix, GNRA tetraloop, U.C mismatch base pair and pyrimidine-rich bulge structures to each. Both Raman and ROA spectra show overall similarities for all oligonucleotides, reflecting the presence of the same base paired helical regions and GNRA tetraloop in each. Specific bands are sensitive to the effect of the mismatch and asymmetric bulge on the structure of the RNA. Raman band changes are observed that reflect the structural contexts of adenine residues, disruption of A-form helical structure, and incorporation of pyrimidine bases in non-helical regions. The ROA spectra are also sensitive to conformational mobility of ribose sugars, and verify a decrease in A-type helix content upon introduction of the pyrimidine-rich bulge. Several Raman and ROA bands also clearly show cooperative effects between the mismatch and pyrimidine-rich bulge motifs on the structure of the RNA. The complementary nature of Raman and ROA spectra provides detailed and highly sensitive information about the local environments of bases, and secondary and tertiary structures, and has the potential to yield spectral signatures for a wide range of RNA structural motifs.

Show MeSH