2012
DOI: 10.1007/s10858-012-9683-9
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Abstract: The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the 1H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watson–Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 43 possible WC-BP … Show more

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Cited by 51 publications
(65 citation statements)
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“…6H); however, this resonance was not visible in the NOESY spectrum, indicating that it exchanges with water during the 100-ms mixing time. The chemical shift is diagnostic of a U-G wobble pair (34), and the observed exchange broadening during the NOESY mixing time is consistent with tentative assignment of this imino resonance to U6562, which may form a U-G wobble pair with the terminal G6618. SHAPE probing on the PKI RNA showed moderate reactivity for U6562 and G6618 (Fig.…”
Section: Global Structure Of the Iapv Igr Ires Pki Domain By Saxs Anasupporting
confidence: 75%
“…6H); however, this resonance was not visible in the NOESY spectrum, indicating that it exchanges with water during the 100-ms mixing time. The chemical shift is diagnostic of a U-G wobble pair (34), and the observed exchange broadening during the NOESY mixing time is consistent with tentative assignment of this imino resonance to U6562, which may form a U-G wobble pair with the terminal G6618. SHAPE probing on the PKI RNA showed moderate reactivity for U6562 and G6618 (Fig.…”
Section: Global Structure Of the Iapv Igr Ires Pki Domain By Saxs Anasupporting
confidence: 75%
“…Yet, not much has been known about the structure-chemical shift information in nucleic acids. Until recently, several reports have shown that the use of non-exchangeable proton chemical shifts enables the determination of RNA structures [7][8][9]. For DNA, the prediction of chemical shifts can facilitate the laborious resonance assignment based on conventional homonuclear correlation experiments, thus speeding up the structure determination process.…”
Section: Introductionmentioning
confidence: 99%
“…Accurate prediction of chemical shifts can facilitate resonance assignment of biomolecules, recognition of conformational features, and identification of the interactions with drugs, ligands, and other molecules [11][12][13][14][15][16]. Therefore, chemical shift prediction protocols have been established for proteins [17][18][19], RNAs [20][21][22], and DNAs [23][24][25][26][27][28][29][30][31] with specific structures and sequence contexts. For DNA chemical shifts, prediction methods for random coil [27][28][29], complementary B-DNA [23][24][25][26], and B-DNA containing an internal AÁA [30] or TÁT mismatch [31] have been developed.…”
Section: Introductionmentioning
confidence: 99%
“…The structure-based approach for chemical shift prediction has been widely used in RNA [20][21][22] and protein [17][18][19], and the accuracy of a prediction method plays an important role in determining its applicability in relating experimentally determined chemical shifts and derived molecular structure. Since existing structure-based methods like SHIFTS [24] and NUCHEMICS [23] predict the chemical shifts of DNA with accuracies (0.27 and 0.17 ppm, respectively) similar to structure-based methods for RNA (0.16 ppm, [21,22]) and protein (0.12-0.49 ppm, [17][18][19]), structural determination of DNA using chemical shifts should also work well as in the case of RNA and protein [33][34][35][36][37][38].…”
Section: Introductionmentioning
confidence: 99%