Z‐RNA: The solution NMR structure of r(CGCGCG)

Davis, Peter W.; Adamiak, Ryszard W.; Tinoco, Ignacio

doi:10.1002/bip.360290116

Cited by 57 publications

(41 citation statements)

References 48 publications

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“…The work of Davis et al, [18] and Popenda et al, [19] on the high salt structure of a left-handed RNA double helix is well-known. It was found that for the natural ribohexanucleotide r(C P G P C P G P C P G) at 1M concentration a duplex is formed with an A-conformation.…”

Section: Comparison With a Self-complementary Natural Rna And Its 2ꞌ-mentioning

confidence: 99%

Modified RNA with a Phosphate-Methylated Backbone. A Serious Omission in Our (Retracted) Study at HIV-1 RNA Loops and Integrated DNA. Specific Properties of the (Modified) RNA and DNA Dimers

Buck¹

2016

JBPC

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After the recent publication in the Journal of Biophysical Chemistry entitled "Retracted HIV Study Provides New Information about the Status of the in Vitro Inhibition of DNA Replication by Backbone Methylation", it is of importance to review the results of Buck's group on the synthesis and conformation analyses of phosphate-methylated RNAs in order to afford information on the absence of a further investigation with regard to this de facto acceptable approach. In fact these compounds belong to the very first group of RNAs with a modified neutral backbone by phosphatemethylation. In contrast to the corresponding phosphate-methylated DNAs with a frozen Bconformation, the phosphate-methylated RNAs show an A-conformation. The latter is a prerequisite for duplex formation with (complementary) (natural) RNA. A number of experiments support this fundamental statement. After the HIV study was retracted, the overall results concerning the phosphate-methylated RNAs were published without mentioning Buck's initial proof of concept and his contributions. Generally, the (modified) dimer RNAs and DNAs possess a number of specific biophysical properties. A novel explanation is given for conflicting structural determinations.

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Section: Comparison With a Self-complementary Natural Rna And Its 2ꞌ-mentioning

confidence: 99%

Modified RNA with a Phosphate-Methylated Backbone. A Serious Omission in Our (Retracted) Study at HIV-1 RNA Loops and Integrated DNA. Specific Properties of the (Modified) RNA and DNA Dimers

Buck¹

2016

JBPC

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“…The crystal structures of nucleosides and nucleotides 23 and solution phase NMR studies [24][25][26][27][28][29] suggest that the conformation of the sugar ring can be adequately described by two conformations such as the C3′-endo-C2′-exo (North sugar) and C2′-endo- Values are for radicals formed via photoexcitation at 143 K in the frozen aqueous (7.5 M LiCl D2O) glassy solution with native pH (ca. 5).…”

Section: Detection Of Sugar Radical Components In Glassy Samples Of Gmentioning

confidence: 99%

Formation of Sugar Radicals in RNA Model Systems and Oligomers via Excitation of Guanine Cation Radical

et al. 2008

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In previous work, we have shown that photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of DNA and its model compounds at 143 K results in the formation of neutral sugar radicals with substantial yield. In this report, we present electron spin resonance (ESR) and theoretical (DFT) evidence regarding the formation of sugar radicals after photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of one-electron-oxidized RNA model compounds (nucleosides, nucleotides and oligomers) at 143 K. Specific sugar radicals C5'*, C3'* and C1'* were identified employing derivatives of Guo deuterated at specific sites in the sugar moiety, namely, C1'-, C2'-, C3'- and C5'-. These results suggest C2'* is not formed upon photoexcitation of G*+ in one-electron-oxidized Guo and deuterated Guo derivatives. Phosphate substitution at C5'- (i.e., in 5-GMP) hinders formation of C5'* via photoexcitation at 143 K but not at 77 K. For the RNA-oligomers studied, we observe on photoexcitation of oligomer-G*+ the formation of mainly C1'* and an unidentified radical with a ca. 28 G doublet. The hyperfine coupling constants of each of the possible sugar radicals were calculated employing the DFT B3LYP/6-31G* approach for comparison to experiment. This work shows that formation of specific neutral sugar radicals occurs via photoexcitation of guanine cation radical (G*+) in RNA systems but not by photoexcitation of its N1 deprotonated species (G(-H)*). Thus, our mechanism regarding neutral sugar formation via photoexcitation of base cation radicals in DNA appears to be valid for RNA systems as well.

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“…C3'-endo) conformations. Coupling constants listed in Table 2 were used to determine relative populations of S-and N-type sugars from the Hi'-H2' coupling, and the approximate pseudorotation phase angle (P°) from the additional H2'-H3' and H3'-H4' couplings (23,32).…”

Section: Rna Synthesismentioning

confidence: 99%

Structure of a small RNA hairpin

1993

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The hairpin stem-loop form of the RNA oligonucleotide rCGC(UUU)GCG has been studied by NMR spectroscopy. In 10 mM phosphate buffer this RNA molecule forms a unimolecular hairpin with a stem of three base pairs and a loop of three uridines, as judged by both NMR and UV absorbance melting behavior. Distance and torsion angle restraints were determined using homonuclear proton-proton and heteronuclear proton-phosphorus 2-D NMR. These values were used in restrained molecular dynamics to determine the structure of the hairpin. The stem has characteristics of A-form geometry, although distortion from A-form occurs in the 3'-side of the stem, presumably to aid in accommodating the small loop. The loop nucleotides adopt C2'-endo conformations. NOE's strongly suggest stacking of the uracils with the stem, especially the first uracil on the 5'-side of the loop. The reversal of the chain direction in the loop seems to occur between U5 and U6. Loop structures produced by molecular dynamics simulations had a wide range of conformations and did not show stacking of the uracils. A flexible loop with significant dynamics is consistent with all the data.

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Z‐RNA: The solution NMR structure of r(CGCGCG)

Cited by 57 publications

References 48 publications

Modified RNA with a Phosphate-Methylated Backbone. A Serious Omission in Our (Retracted) Study at HIV-1 RNA Loops and Integrated DNA. Specific Properties of the (Modified) RNA and DNA Dimers

Modified RNA with a Phosphate-Methylated Backbone. A Serious Omission in Our (Retracted) Study at HIV-1 RNA Loops and Integrated DNA. Specific Properties of the (Modified) RNA and DNA Dimers

Formation of Sugar Radicals in RNA Model Systems and Oligomers via Excitation of Guanine Cation Radical

Structure of a small RNA hairpin

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