Improved NOE-Based Sequential Correlation of Base and 1‘ Proton Resonances in Labeled Nucleic Acids

Nikonowicz, Edward P.; Michnicka, Malgorzata; DeJong, Eric S.

doi:10.1021/ja973961v

Cited by 7 publications

(5 citation statements)

References 26 publications

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“…A major problem in resonance assignment and extraction of structural constraints in RNAs remains the poor spectral resolution of 1 H− 13 C correlation spectra, resulting from short 1 H and 13 C transverse relaxation times and homonuclear 13 C− 13 C scalar couplings. Recently, selective and partial deuteration of RNA molecules were proposed to reduce the proton line widths and to simplify the analysis of 13 C-edited NOESY spectra. , While this approach is very promising, it does not solve the severe overlap problems in the 13 C frequency dimension.…”

Section: Introductionmentioning

confidence: 99%

Improved Sensitivity and Resolution in ¹H−¹³C NMR Experiments of RNA

et al. 1998

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NMR studies of the structure and dynamics in RNA are greatly facilitated by the use of 13C-labeled molecules and 1H−13C correlation experiments. We demonstrate here that spin-state selective 13C frequency editing yields greatly improved sensitivity and resolution in 1H−13C correlation spectra of RNA. A sensitivity enhanced version of the previously introduced TROSY sequence (Pervushin et al., Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 12366−12371) is proposed, which offers a √2 signal enhancement. When compared to a sensitivity enhanced HSQC sequence an up to 3-fold increase in both the sensitivity and resolution is observed for the base carbons in a 15% 13C-labeled 33-mer RNA at a magnetic field strength of 14.1 T. This increase results from the relaxation interference between the 13C chemical shielding anisotropy (CSA) and the 1H−13C dipolar interaction, as well as the simultaneous detection of 1H and 13C steady-state polarizations. Simulations indicate that the enhancement effect is maximal at currently available magnetic field strengths (≤18.8 T). It is further shown that the recording of a pair of complementary TROSY experiments, denoted H(α)- and H(β)-TROSY allows the accurate measurement of 1H−13C one-bond coupling constants from the cross-peak positions in the two spectra. An extension of the TROSY sequence is presented for recording high resolution 3D 13C-edited NOESY spectra.

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Section: Introductionmentioning

confidence: 99%

Improved Sensitivity and Resolution in ¹H−¹³C NMR Experiments of RNA

et al. 1998

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“…This makes the NMR spectral assignment easier for structural studies [44][45][46][47][48][49][50][51] . Base deuterated molecules can also be used in conformational investigations by Raman [52][53][54] or infrared 55 spectroscopy, in biological studies [56][57][58][59][60][61] and studies on hydroxyl radical reactions with nucleosides 62,63 .…”

Section: Deuteration Of the Aglyconementioning

confidence: 99%

“…However, there are other examples where the use of ammonium bisulfite/ 2 H 2 O system at pD 7.7 at 65 ?C for 72 hours exchanges proton to deuteron at C5 in 90 atom% 44,46,47,49 .…”

Section: Deuteration At C5 Of Uracil and Cytosine Derivativesmentioning

confidence: 99%

“…-naphthalinamine and p-phenylazoaniline however do not cause transamination 70 and the use of imidazole buffer has also been published 75 . Nevertheless, successful applications of the bisulfite method that provides 90-98 atom% deuterium exchange at C5 for cytosine have been reported 44,46,47 .…”

Section: Scheme 2 R = H or Ribofuranos-1-ylmentioning

confidence: 99%

“…Escherichia coli has been grown on minimal medium containing 90% 2 H 2 O, 15 N-ammonium sulfate as the sole nitrogen and sodium acetate-13 C 2 as the sole carbon source 46 . Alternatively 47 , uniformly 15 N, 13 C labelled 5'-rNMPs are subjected to deuterium exchange at C5 of pyrimidines with metabisulfite anion as catalyst 44 giving ? 98% completion upon incubating for 102 h at 65…”

Section: Synthesis Of 2 H 15 N 13 C Triple Labelled Nucleotidesmentioning

confidence: 99%

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The Synthesis of Deuterionucleosides

Földesi

Trifonova

Kundu

et al. 2000

Nucleosides, Nucleotides and Nucleic Acids

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Measurement of the deuterium relaxation times in double-labeled (13C/2H) thymidine and 2′-deoxyadenosine and in the selectively labeled DNA duplex5′d(1C2G3A4T5T6A7A8T9C10G)23′

1999

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The T1 and T1ρ of deuterium in 13C/2H double‐labeled 2′(R/S),5′(R/ S)‐2H2 ‐1′,2′,3′,4′,5′‐ 13C5 ‐2′‐deoxyadenosine and the corresponding thymidine derivative as well as in the non‐uniformly labeled (shown in bold and underlined) DNA duplex, d5′(1C2G3A4T5T6A7A8T9C10G)23′, have been determined for the first time. These double‐labelled nucleoside blocks have a special feature in that the geminal 2′–2″ and 5′–5″ proton–proton couplings are eliminated by replacement with diastereomeric deuterium at C‐2′ and C‐5′ centers. This uniquely enables us to perform deuterium relaxation measurement experiments through selective polarization transfer, 1H–13C– 2H–13C–1H at C‐2′ and C‐5′ centers, thereby allowing filtration of all other naturally abundant methylene‐ and methine‐13C as well as enriched methine‐ 13C fragments. Comparison of T1 and T 1ρ of 2H in double‐labeled ( 13C/2H) 2′‐deoxyadenosine and thymidine with that of the non‐uniformly labeled DNA duplex, d5′(1C2G3 A4T5T6A7A8T9C10G)23′, shows that the dynamics of various nucleotide residues are indeed non‐uniform. Copyright © 1999 John Wiley & Sons, Ltd.

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Improved NOE-Based Sequential Correlation of Base and 1‘ Proton Resonances in Labeled Nucleic Acids

Cited by 7 publications

References 26 publications

Improved Sensitivity and Resolution in ¹H−¹³C NMR Experiments of RNA

Improved Sensitivity and Resolution in ¹H−¹³C NMR Experiments of RNA

The Synthesis of Deuterionucleosides

Measurement of the deuterium relaxation times in double-labeled (13C/2H) thymidine and 2′-deoxyadenosine and in the selectively labeled DNA duplex5′d(1C2G3A4T5T6A7A8T9C10G)23′

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Improved NOE-Based Sequential Correlation of Base and 1‘ Proton Resonances in Labeled Nucleic Acids

Cited by 7 publications

References 26 publications

Improved Sensitivity and Resolution in 1H−13C NMR Experiments of RNA

Improved Sensitivity and Resolution in 1H−13C NMR Experiments of RNA

The Synthesis of Deuterionucleosides

Measurement of the deuterium relaxation times in double-labeled (13C/2H) thymidine and 2′-deoxyadenosine and in the selectively labeled DNA duplex5′d(1C2G3A4T5T6A7A8T9C10G)23′

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Improved Sensitivity and Resolution in ¹H−¹³C NMR Experiments of RNA

Improved Sensitivity and Resolution in ¹H−¹³C NMR Experiments of RNA