Nuclear magnetic resonance studies of the secondary structure, proton exchange dynamics, and conformational states of the 5S ribosomal RNA of Escherichia coli

Thesis/Dissertation · Wed Jan 01 04:00:00 EST 1986

OSTI ID:6592832

Leontis, N B

The 5S rRNA from E. coli was studied using proton NMR at 500 MHz. To simplify the spectrum of the whole molecule, two complementary, nuclease-resistant fragments were studied: fragment 1 includes bases 1-11 and 69-120 (helices I, IV, and V in their entirety), and fragment 2, bases 15-35 and 44-65 (helix III and most of helix II). The isolation and characterization of fragment 2 is described for the first time. The NMR results on fragment 2 provide the first direct physical evidence for the existence of helices II and III in the parent molecule. The preparation of fragment 1, intact in the loop at residues 87-89 and in a native conformation, is described. The nuclear Overhauser effect was used to establish base pair types of imino proton resonances and connectivities within helices in fragments 1 and 2. NOE data bearing on assignments of resonances to helix V are presented. Imino resonance assignments are suggested for base-pairs in helices II and III. NMR evidence is presented for conformational flexibility in helix III of fragment 2 and in the intact 5S RNA. The stable conformation in the presence of magnesium appears to be that in which bases G54 and C30 and G51 and C31 are paired, while bases A52 and A53 are bulged out of the helix.

• Research Organization: Yale Univ., New Haven, CT (USA)
• OSTI ID: 6592832
• Country of Publication: United States
• Language: English

Related Subjects

550200* -- Biochemistry
59 BASIC BIOLOGICAL SCIENCES
BACTERIA
BARYONS
CONFIGURATION
ELEMENTARY PARTICLES
ESCHERICHIA COLI
FERMIONS
HADRONS
HELICAL CONFIGURATION
MAGNETIC RESONANCE
MICROORGANISMS
MOLECULAR STRUCTURE
NMR SPECTRA
NUCLEAR MAGNETIC RESONANCE
NUCLEIC ACIDS
NUCLEONS
ORGANIC COMPOUNDS
PROTONS
RESONANCE
RIBOSOMAL RNA
RNA
SPECTRA