(1'-13C)-2'-deoxyribonucleosides: structural and conformational insights derived from carbon-13-proton spin coupling constants involving C1'

Bandyopadhyay, Tapasree; Wu, Jian; Serianni, Anthony S.

doi:10.1021/jo00072a040

Cited by 20 publications

(24 citation statements)

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“…As shown recently in 2‘-deoxyribonucleosides, 2 J C1,H2 R and 2 J C1,H2 S values in 2-deoxy-β- d -ribofuranosyl rings 2 can differ substantially ( e.g. , 2 J C1 ‘ ,H2 ‘ S = −5.7 Hz and 2 J C1 ‘ ,H2 ‘ R = ±0.4 Hz in 2‘-deoxyadenosine) …”

Section: Resultssupporting

confidence: 55%

“…These predictions are consistent with data in Figure A for the β- d - ribo ring but differ from computed values for N forms of the 2-deoxy-β- d - ribo ring. Interestingly, 2 J C1,H2 R in 2-deoxy-α- d -[1- 13 C]glucopyranose is −3.8 Hz, although the projection rule predicts a value of ∼0 Hz; this situation is similar to that for 2 J C1,H2 S in N forms of 6 . In contrast, 2 J C1,H2 S in 2-deoxy-β- d -[1- 13 C]glucopyranose is −8.3 Hz, in good agreement with the projection rule prediction of ∼ −8 Hz; this situation is similar to that for 2 J C1,H2 S in S forms of 6 .…”

Section: Resultsmentioning

confidence: 73%

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¹³C−¹H and ¹³C−¹³C Spin-Coupling Constants in Methyl β-d-Ribofuranoside and Methyl 2-Deoxy-β-d-erythro- pentofuranoside: Correlations with Molecular Structure and Conformation

1997

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Methyl β-d-ribofuranoside 5 and methyl 2-deoxy-β-d-erythro-pentofuranoside (methyl 2-deoxy-β-d-ribofuranoside) 6 were synthesized with single sites of 13C-enrichment at each carbon, and a complete set of 13C−1H and 13C−13C spin-coupling constants (37 couplings in 5, 41 couplings in 6) in these molecules were obtained by 1D and 2D NMR spectroscopy. 2 J CH coupling signs were determined from the observation of relative cross-peak displacements in 2D TOCSY data. The 13C−1H couplings (one-, two-, and three-bond) were interpreted in structural and conformational terms with assistance from conformational models of 5 and 6 based on conventional two-state pseudorotational analysis of 3 J HH values (PSEUROT) and on theoretical predictions of conformational energies and J CH values obtained from ab initio molecular orbital calculations on the ten envelope and planar conformers of β-d-ribofuranose 4 and 2-deoxy-β-d-erythro-pentofuranose (2-deoxy-β-d-ribofuranose) 3. A comparison of theoretical J CH values in 3 and 4 allowed an assessment of the effect of C2 structure (C2 oxy vs C2 deoxy) on coupling magnitudes and signs. Results show that the behavior of related J CH values in 5 and 6 may differ, especially when C2 is involved as a coupled nucleus. In addition, several 1 J CH, 2 J CH, and 3 J CH values in β-d-ribo and 2-deoxy-β-d-ribo rings were found to be sensitive to furanose ring and hydroxymethyl group conformation; in the deoxyribo ring, the presence of diastereotopic protons at C2 produces paired 13C−1H coupling pathways involving H2R and H2S that are complementary, and differences in the resulting paired J CH values are, in some instances, sensitive to ring conformation. J CC values in β-d-ribo and 2-deoxy-β-d-ribo rings also reflect differences in ring structure and geometry, although fewer (e.g., 2 J C3,C5, 3 J C1,C5, 3 J C2,C5) appear useful as conformational probes. The correlations drawn between ring structure/conformation and J CH/J CC magnitude and sign in 5 and 6 will be useful in anticipated applications of these couplings to assess furanose ring conformation/dynamics in DNA and RNA oligomers and in other biomolecules containing β-d-ribo and 2-deoxy-β-d-ribo rings.

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Section: Resultssupporting

confidence: 55%

Section: Resultsmentioning

confidence: 73%

¹³C−¹H and ¹³C−¹³C Spin-Coupling Constants in Methyl β-d-Ribofuranoside and Methyl 2-Deoxy-β-d-erythro- pentofuranoside: Correlations with Molecular Structure and Conformation

1997

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“…Labeled ribonucleosides may be converted chemically to 2' -deoxyribonucleosides (37,38), and the latter converted to their corresponding phosphoramidites for use in solid-phase DNA synthesis (39). 13 C-Labeled 2-deoxy-D-ribose (2-deoxy-D-erythropentose) may also be generated from labeled D-ribose (37).…”

Section: Routes To Specific Isotopomersmentioning

confidence: 99%

¹³C-Labeled D-Ribose: Chemi-Enzymic Synthesis of Various Isotopomers

Serianni

Bondo²

1994

Journal of Biomolecular Structure and Dynamics

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Current interest in the use of heteronuclear multidimensional NMR methods to assess the structures, conformations and/or dynamics of oligonucleotides in solution has created an immediate need for nucleosides and their derivatives labeled in various ways with stable isotopes (13C, 2H, 15N and/or 17,18O). This short review focuses exclusively on chemienzymic methods to introduce one or more 13C labels into D-ribose, a precursor to ribo- and 2'-deoxyribonucleosides. It will be demonstrated that five convenient reactions, applied in specific sequences, provide access to 26 of the 32 13C-labeled isotopomers of D-ribose in acceptable yields. While not explicitly discussed herein, these same reactions, appropriately modified, can also be used to insert one or more 2H and/or 17,18O isotopes into this aldopentose.

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“…The other acylated thymidines 1Oa-c have also large J(H-C( 1'),Hpr0.s-C(2')) (9.0, 9.1, and 9.6 Hz, resp. ), thus strongly preferring the southern conformation, whereas thymidine exists as a 2: 1 mixture of the southern and northern conformation [17]. The structure of the a-L-threo derivative 14b was assigned by X-ray analysis (4E envelope, pseudorotation phase angle P = 52", The configuration of 1Oc could be assigned by a 'H-NOESY experiment as well as by comparison with the NMR data of the compound obtained after desilylation of 9c (+ 1Oc).…”

mentioning

confidence: 99%

“…Flash chromatography (FC): Merck silica gel 60 (0.040-0.063 nim). MPLC: Buchi chromatograph; Mucherey-Nugel silica-gel column (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25). HPLC: Kontron chromatograph with UV detector (254 nm); anal.…”

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confidence: 99%

Synthesis of 4′‐C‐Acylated Thymidines

Marx

Erdmann

Senn

et al. 1996

Helvetica Chimica Acta

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Two synthetic pathways towards 4′‐C‐acylthymidines are presented. These modified mononucleosides are precursors of the 2′‐deoxyribonucleotide 4′‐C‐radical. They were converted into their corresponding 3′‐O‐[(2‐cyanoethyl) N,N‐diisopropylphosphoramidites] 3a–c and incorporated in oligonucleotides by solid‐phase synthesis. The structure of some modified nucleosides was revealed by X‐ray crystal‐structure analysis.

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(1'-13C)-2'-deoxyribonucleosides: structural and conformational insights derived from carbon-13-proton spin coupling constants involving C1'

Cited by 20 publications

References 0 publications

¹³C−¹H and ¹³C−¹³C Spin-Coupling Constants in Methyl β-d-Ribofuranoside and Methyl 2-Deoxy-β-d-erythro- pentofuranoside: Correlations with Molecular Structure and Conformation

¹³C−¹H and ¹³C−¹³C Spin-Coupling Constants in Methyl β-d-Ribofuranoside and Methyl 2-Deoxy-β-d-erythro- pentofuranoside: Correlations with Molecular Structure and Conformation

¹³C-Labeled D-Ribose: Chemi-Enzymic Synthesis of Various Isotopomers

Synthesis of 4′‐C‐Acylated Thymidines

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(1'-13C)-2'-deoxyribonucleosides: structural and conformational insights derived from carbon-13-proton spin coupling constants involving C1'

Cited by 20 publications

References 0 publications

13C−1H and 13C−13C Spin-Coupling Constants in Methyl β-d-Ribofuranoside and Methyl 2-Deoxy-β-d-erythro- pentofuranoside: Correlations with Molecular Structure and Conformation

13C−1H and 13C−13C Spin-Coupling Constants in Methyl β-d-Ribofuranoside and Methyl 2-Deoxy-β-d-erythro- pentofuranoside: Correlations with Molecular Structure and Conformation

13C-Labeled D-Ribose: Chemi-Enzymic Synthesis of Various Isotopomers

Synthesis of 4′‐C‐Acylated Thymidines

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Product

Resources

About

¹³C−¹H and ¹³C−¹³C Spin-Coupling Constants in Methyl β-d-Ribofuranoside and Methyl 2-Deoxy-β-d-erythro- pentofuranoside: Correlations with Molecular Structure and Conformation

¹³C−¹H and ¹³C−¹³C Spin-Coupling Constants in Methyl β-d-Ribofuranoside and Methyl 2-Deoxy-β-d-erythro- pentofuranoside: Correlations with Molecular Structure and Conformation

¹³C-Labeled D-Ribose: Chemi-Enzymic Synthesis of Various Isotopomers