Morpholino spin-labeling for base-pair sequencing of a 3'-terminal RNA stem by proton homonuclear Overhauser enhancements: yeast ribosomal 5S RNA

Lee, Kai Mon; Marshall, Alan G.

doi:10.1021/bi00391a048

Cited by 7 publications

(1 citation statement)

References 40 publications

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“…NMR spectroscopy has been widely used to study the structure of 5S RNA. The majority of these investigations focused on the uridine and guanosine imino resonances, with an emphasis on NOE studies to assign chemical shifts of nearest neighbors (Chan & Marshall, 1986;Chang & Marshall, 1986;Lee & Marshall, 1987). Other factors that influence the specta, such as ionic strength and temperature, were also used to assign resonances (Leontis & Moore, 1986b;Leontis et al, 1986).…”

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confidence: 99%

Nitrogen-15-labeled 5S RNA. Identification of uridine base pairs in Escherichia coli 5S RNA by proton-nitrogen-15 multiple quantum NMR

Davis¹,

Yamaizumi²,

Nishimura³

et al. 1989

Biochemistry

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Escherichia coli 5S RNA labeled with 15N at N3 of the uridines was isolated from the S phi-187 uracil auxotroph grown on a minimal medium supplemented with [3-15N]uracil. 1H-15N multiple quantum filtered and 2D chemical shift correlated spectra gave resonances for the uridine imino 1H-15N units whose protons were exchanging slowly with solvent. Peaks with 1H/15N shifts at 11.6/154.8, 11.7/155.0, 11.8/155.5, 12.1/155.0, and 12.2/155.0 ppm were assigned to GU interactions. Two labile high-field AU resonances at 12.6/156.8 and 12.8/157.3 ppm typical of AU pairs in a shielded environment at the end of a helix were seen. Intense AU signals were also found at 13.4/158.5 and 13.6/159.2 ppm where 1H-15N units in normal Watson-Crick pairs resonate. 1H resonances at 10.6 and 13.8 ppm were too weak, presumably because of exchange with water, to give peaks in chemical shift correlated spectra. 1H chemical shifts suggest that the resonance at 13.8 ppm represents a labile AU pair, while the resonance at 10.6 ppm is typical of a tertiary interaction between U and a tightly bound water or a phosphate residue. The NMR data are consistent with proposed secondary structures for 5S RNA.

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confidence: 99%

Nitrogen-15-labeled 5S RNA. Identification of uridine base pairs in Escherichia coli 5S RNA by proton-nitrogen-15 multiple quantum NMR

Davis¹,

Yamaizumi²,

Nishimura³

et al. 1989

Biochemistry

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Ribosomal RNA

Moore¹

2007

Encyclopedia of Magnetic Resonance

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Structural investigation of helices II, III, and IV of B. megaterium 5S ribosomal RNA by molecular dynamics calculations

Kim

Marshall

1992

Biopolymers

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The structures of the helices II-III region and the helix IV region of B. megaterium 5S rRNA have been examined by means of energy minimization and molecular dynamics calculations. Calculated distances between neighboring hydrogen-bonded imino protons in helices II, III, and IV were between 3.5 and 4.5 A. The overall axis for the helices II-III region is warped rather than straight. Formation of additional Watson-Crick base pairs in loop B and loop C was not evident from the atomic positions calculated by molecular dynamics. Bases in loop C are well stacked, showing no significant change during dynamics. Bulge migration in helix III does not seem to be possible; the helices II-III region prefers one conformation. Helix II is more stable than helix III. Five base pairs in helix IV were sufficiently stable to establish that helix IV is terminated by a hairpin loop of three nucleotides. U87 protrudes from loop D. Structures of the helices II-III segment and the helix IV segment of B. megaterium 5S rRNA obtained by molecular dynamics were generally consistent with the solution structure inferred from high-field proton nmr spectroscopy.

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Morpholino spin-labeling for base-pair sequencing of a 3'-terminal RNA stem by proton homonuclear Overhauser enhancements: yeast ribosomal 5S RNA

Cited by 7 publications

References 40 publications

Nitrogen-15-labeled 5S RNA. Identification of uridine base pairs in Escherichia coli 5S RNA by proton-nitrogen-15 multiple quantum NMR

Nitrogen-15-labeled 5S RNA. Identification of uridine base pairs in Escherichia coli 5S RNA by proton-nitrogen-15 multiple quantum NMR

Ribosomal RNA

Structural investigation of helices II, III, and IV of B. megaterium 5S ribosomal RNA by molecular dynamics calculations

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