Assignment of the <sup>31</sup>P and <sup>1</sup>H resonances in oligonucleotides by two‐dimensional NMR spectroscopy

Sklenář, Vladimı́r; Miyashiro, Hirotsugu; Zon, Gerald; Miles, H. Todd; Bax, Ad

doi:10.1016/0014-5793(86)81539-3

Cited by 359 publications

(218 citation statements)

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“…Comparison of the one-dimensional spectra of the t 6 A 37 -modified and unmodified hairpin indicated a major rearrangement of the loop uridines with the introduction of t 6 A 37 . In the one-and two-dimensional spectra of the unmodified ASL Lys3 UUU , a base-paired imino resonance at 13.55 ppm was assigned to U 33 . This was the only imino proton unaccounted for by standard and 15 N-labeling procedures.…”

Section: Resultsmentioning

confidence: 99%

“…Sequential aromatic-H1′ connectivities could be traced from the 5′ terminus of the stem to the first residue of the loop, C 32 ( Figure 3). At that point there was a break in the sequential connectivity that included the invariant U 33 . Though NOEs were observed between U 35 and U 36 , sequential aromatic to H1′ connectivities began again at t 6 A 37 and continued to the 3′-terminal C 43 (Figure 3).…”

Section: Resultsmentioning

confidence: 99%

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Functional Anticodon Architecture of Human tRNA^Lys3 Includes Disruption of Intraloop Hydrogen Bonding by the Naturally Occurring Amino Acid Modification, t⁶A

et al. 2000

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The structure of the human tRNA Lys3 anticodon stem and loop domain (ASL Lys3 ) provides evidence of the physicochemical contributions of N6-threonylcarbamoyladenosine (t 6 A 37 ) to tRNA Lys3 functions. The t 6 A 37 -modified anticodon stem and loop domain of tRNA Lys3 UUU (ASL Lys3 UUU -t 6 A 37 ) with a UUU anticodon is bound by the appropriately programmed ribosomes, but the unmodified ASL Lys3 UUU is not [Yarian, C., Marszalek, M., Sochacka, E., Malkiewicz, A., Guenther, R., Miskiewicz, A., and Agris, P. F., Biochemistry 39, 13390-13395]. The structure, determined to an average rmsd of 1.57 ( 0.33 Å (relative to the mean structure) by NMR spectroscopy and restrained molecular dynamics, is the first reported of an RNA in which a naturally occurring hypermodified nucleoside was introduced by automated chemical synthesis. The ASL Lys3 UUU -t 6 A 37 loop is significantly different than that of the unmodified ASL Lys3 UUU , although the five canonical base pairs of both ASL Lys3 UUU stems are in the standard A-form of helical RNA. t 6 A 37 , 3′-adjacent to the anticodon, adopts the form of a tricyclic nucleoside with an intraresidue H-bond and enhances base stacking on the 3′-side of the anticodon loop. Critically important to ribosome binding, incorporation of the modification negates formation of an intraloop U 33 ‚A 37 base pair that is observed in the unmodified ASL Lys3 UUU . The anticodon wobble position U 34 nucleobase in ASL Lys3 UUU -t 6 A 37 is significantly displaced from its position in the unmodified ASL and directed away from the codon-binding face of the loop resulting in only two anticodon bases for codon binding. This conformation is one explanation for ASL Lys3 UUU tendency to prematurely terminate translation and -1 frame shift. At the pH 5.6 conditions of our structure determination, A 38 is protonated and positively charged in ASL Lys3 UUU -t 6 A 37 and the unmodified ASL Lys3 UUU . The ionized carboxylic acid moiety of t 6 A 37 possibly neutralizes the positive charge of A + 38 . The protonated A + 38 can base pair with C 32 , but t 6 A 37 may weaken the interaction through steric interference. From these results, we conclude that ribosome binding cannot simply be an induced fit of the anticodon stem and loop, otherwise the unmodified ASL Lys3 UUU would bind as well as ASL Lys3 UUU -t 6 A 37 . t 6 A 37 and other position 37 modifications produce the open, structured loop required for ribosomal binding.Lysine tRNAs with UUU anticodons have a conventional role in ribosome-mediated protein synthesis. In addition, tRNA Lys UUU species facilitate -1 frameshifts for correct translation of the E. coli DNA polymerase γ subunit (1) and retroviral polymerases (2). Also, tRNA Lys UUU often misreads asparagine codons (3, 4) and peptidyl-tRNA Lys prematurely terminates translation more often than other tRNAs (5). In addition, reverse transcription of the HIV-1 genomic RNA is primed by the human tRNA Lys3 UUU . Formation of the viral replication initiation complex is enhanced in vitro by the pr...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Functional Anticodon Architecture of Human tRNA^Lys3 Includes Disruption of Intraloop Hydrogen Bonding by the Naturally Occurring Amino Acid Modification, t⁶A

et al. 2000

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“…For the phase-sensitive 'H-"P-RCSC (Sklenir et al, 1986) on T4, a 1024x128 data-point matrix with 160 scans for each t, block was collected. The data were zero filled to 2048 in both dimensions and processed using exponential multiplication and a Gaussian-Lorentzian window (t, dimension) and a 30" shifted sine bell window function ( t , dimension).…”

Section: Methodsmentioning

confidence: 99%

Similar Conformations of Hairpins with TTT and TTTT Sequences NMR and Molecular Modeling Evidence for T · T base pairs in the TTTT hairpin

Kuklenyik

Yao

Marzillï

1996

European Journal of Biochemistry

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"P signals of the two hairpins have been nearly completely assigned by means of two-dimensional NMR spectroscopy in D,O (NOESY (two-dimensional nuclear Overhauser effect and exchange spectroscopy) at mixing times of 5, 50, 100, 300 and 500 ms, double-quantum-filtered correlation spectroscopy (DQF-COSY) and 'H-"P reverse chemical shift correlation (RCSC), and one-dime,nsional NOE spectra in 90% H,O. Conformational analysis using distance geometry (DG), molecular mechanics (MM) and molecular dynamics (MD) gave model conformations, which were evaluated by comparison of experimental and simulated 2D NOESY spectra. For the T, sequence in T4, both NMR data and modeling indicated a T(a) . (5) of T3] has a gauche', gauche' <,a conformation with a trans y angle for the second residue in both. These or similar features appear to be present in most of the few other hairpins studied previously by conformational methods. Thus, we believe that the conformations of the loops in T, and T, hairpins have greater similarities than previously recognized.

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“…14) and 1 H-31 P Hetero-TOCSY with a mixing time of 30 ms were recorded at 297 K. Two-dimensional NOESY spectra with mixing times of 80, 150, and 250 ms were obtained at 294 K, and the residual HDO resonance was suppressed by using low-power presaturation. Two-dimensional 1 H- 13 J H1Ј,H2Ј in DQF-COSY spectra.…”

Section: Rna Sample Preparationmentioning

confidence: 99%

Structural features of an influenza virus promoter and their implications for viral RNA synthesis

Bae

Cheong

Lee

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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The influenza A virus, a severe pandemic pathogen, has a segmented RNA genome consisting of eight single-stranded RNA molecules. The 5 and 3 ends of each RNA segment recognized by the influenza A virus RNA-dependent RNA polymerase direct both transcription and replication of the virus's RNA genome. Promoter binding by the viral RNA polymerase and formation of an active open complex are prerequisites for viral replication and proliferation. Here we describe the solution structure of this promoter as solved by multidimensional, heteronuclear magnetic resonance spectroscopy. Our studies show that the viral promoter has a significant dynamic nature and reveal an unusual displacement of an adenosine that forms a novel (A-A)⅐U motif and a C-A mismatch stacked in a helix. The characterized structural features of the promoter imply that the specificity of polymerase binding results from an internal RNA loop. In addition, an unexpected bending (46 ؎ 10°) near the initiation site suggests the existence of a promoter recognition mechanism similar to that of DNA-dependent RNA polymerase and a possible regulatory function for the terminal structure during open complex formation.T he influenza A virus, a member of the Orthomyxoviridae family, has a genome consisting of eight single-stranded RNA molecules of negative polarity. These eight RNA segments encode ten proteins, including three RNA-dependent RNA polymerase (RdRp) proteins (PA, PB1, PB2) and one nucleoprotein (NP). The transcription and replication of the viral genome are performed in the nucleus of infected cells by a ribonucleoprotein (RNP) complex that is composed of the three polymerase proteins, NP, and the viral RNA (vRNA). Replication of the vRNA produces a full-length copy of positive-sense RNA (cRNA). The cRNA is then used in the formation of another RNP complex, which serves to generate newly synthesized vRNA. Transcription is also performed by the same RNP complex; however, initiation occurs by the pirating of a 7-methyl guanosine cap structure from a host mRNA. Viral transcription produces an mRNA molecule that is 15 to 22 nucleotides (nt) shorter than cRNA and contains a poly(A) tail (1).The influenza A virus RdRp binds specifically to the partial duplex promoter (also referred to as the panhandle RNA), which is made from the 5Ј and 3Ј termini of each RNA genome segment. Within this partial duplex, 13 nt at the 5Ј end and 12 nt at the 3Ј end are highly conserved among most influenza A virus variants (Fig. 1A). All of the necessary signals for replication and genome packaging appear to reside in these terminal sequences (2), and several pieces of evidence imply a regulatory role for the terminal structure in viral transcription initiation (3-6), termination, and polyadenylation (7,8).The RdRps are for the most part virus-encoded polymerases that synthesize RNA from an RNA template without a DNA intermediate. Despite the unique features of RdRps, little has been deciphered about their mechanisms of promoter recognition and RNA synthesis. The promoter of the...

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Assignment of the ³¹P and ¹H resonances in oligonucleotides by two‐dimensional NMR spectroscopy

Cited by 359 publications

References 10 publications

Functional Anticodon Architecture of Human tRNA^Lys3 Includes Disruption of Intraloop Hydrogen Bonding by the Naturally Occurring Amino Acid Modification, t⁶A

Functional Anticodon Architecture of Human tRNA^Lys3 Includes Disruption of Intraloop Hydrogen Bonding by the Naturally Occurring Amino Acid Modification, t⁶A

Similar Conformations of Hairpins with TTT and TTTT Sequences NMR and Molecular Modeling Evidence for T · T base pairs in the TTTT hairpin

Structural features of an influenza virus promoter and their implications for viral RNA synthesis

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Assignment of the 31P and 1H resonances in oligonucleotides by two‐dimensional NMR spectroscopy

Cited by 359 publications

References 10 publications

Functional Anticodon Architecture of Human tRNALys3 Includes Disruption of Intraloop Hydrogen Bonding by the Naturally Occurring Amino Acid Modification, t6A

Functional Anticodon Architecture of Human tRNALys3 Includes Disruption of Intraloop Hydrogen Bonding by the Naturally Occurring Amino Acid Modification, t6A

Similar Conformations of Hairpins with TTT and TTTT Sequences NMR and Molecular Modeling Evidence for T · T base pairs in the TTTT hairpin

Structural features of an influenza virus promoter and their implications for viral RNA synthesis

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Assignment of the ³¹P and ¹H resonances in oligonucleotides by two‐dimensional NMR spectroscopy

Functional Anticodon Architecture of Human tRNA^Lys3 Includes Disruption of Intraloop Hydrogen Bonding by the Naturally Occurring Amino Acid Modification, t⁶A

Functional Anticodon Architecture of Human tRNA^Lys3 Includes Disruption of Intraloop Hydrogen Bonding by the Naturally Occurring Amino Acid Modification, t⁶A