31P chemical shifts in phosphate diester monoanions. Bond angle and torsional angle effects

Gorenstein, David G.; Kar, Debojyoti

doi:10.1016/s0006-291x(75)80495-5

Cited by 135 publications

(96 citation statements)

References 13 publications

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“…Nevertheless, in a highly crystalline compound, one would still expect to resolve some of the 11 expected signals or observe them as shoulders on other signals, but such resolution is lacking, indicating some disorder of the phosphate sites. Some structural disorder of phosphate sites close to the citrate anion is likely to be imposed by the conformational disorder of the dynamic CH 2 COO(H) branch of the citrate; the 31 P chemical shift is known to correlate strongly with P-O bond length (34) and is sensitive to O-P-O bond angle (35), and a small distribution of both O-P-O-bond angles and P-O-bond lengths would be expected if the neighboring citrate anion has a range of conformations. In turn, a distribution of phosphate structures/orientations close to the citrate anion will have a knockon effect for the phosphate sites more remote from the citrate, leading to some degree of line broadening for all 31 P signals.…”

Section: Resultsmentioning

confidence: 99%

Citrate bridges between mineral platelets in bone

Davies

Müller

Wong

et al. 2014

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

256

246

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We provide evidence that citrate anions bridge between mineral platelets in bone and hypothesize that their presence acts to maintain separate platelets with disordered regions between them rather than gradual transformations into larger, more ordered blocks of mineral. To assess this hypothesis, we take as a model for a citrate bridging between layers of calcium phosphate mineral a double salt octacalcium phosphate citrate (OCPcitrate). We use a combination of multinuclear solid-state NMR spectroscopy, powder X-ray diffraction, and first principles electronic structure calculations to propose a quantitative structure for this material, in which citrate anions reside in a hydrated layer, bridging between apatitic layers. To assess the relevance of such a structure in native bone mineral, we present for the first time, to our knowledge, 17 O NMR data on bone and compare them with 17 O NMR data for OCP-citrate and other calcium phosphate minerals relevant to bone. The proposed structural model that we deduce from this work for bone mineral is a layered structure with thin apatitic platelets sandwiched between OCP-citrate-like hydrated layers. Such a structure can explain a number of known structural features of bone mineral: the thin, plate-like morphology of mature bone mineral crystals, the presence of significant quantities of strongly bound water molecules, and the relatively high concentration of hydrogen phosphate as well as the maintenance of a disordered region between mineral platelets.NMR crystallography | biomineralization B one is a complex organic-inorganic composite material (1), in which calcium phosphate nanoparticles are held within a primarily collagen protein matrix. The mineral component is a poorly crystalline phase, closely related to hydroxyapatite. The currently accepted model of bone mineral is ∼50-to 150-nmthick stacks of very closely packed apatitic platelets, each of order 2.5-4 nm in thickness (1-4), arranged so that their large (100) faces are parallel to each other and their c axes are strongly ordered (parallel to collagen fibrils) (5). NMR studies show that, in addition to the largely ordered but nonstoichiometric apatitic phase, there is a substantial, highly hydrated, disordered phase containing up to 55% of the bone mineral phosphatic ions (6, 7) but in the form of hydrogen phosphate or phosphate strongly hydrogen-bonded to water rather than apatitic orthophosphate (8). This phase has been assigned as a surface phase, but whether the surface in question is that of individual mineral platelets or the surface of the overall structure formed by a stack of such platelets is not yet clear. There is, however, significant experimental evidence that is not explained by this model as it stands. First, there has never been any observation of an isolated mineral platelet in mature bone, even in preparations in which there have been attempts to disperse the mineral structures (9). This feature suggests that the mineral platelets are not independent structures-indeed, their ordered aggregati...

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Section: Resultsmentioning

confidence: 99%

Citrate bridges between mineral platelets in bone

Davies

Müller

Wong

et al. 2014

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

256

246

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“…Porschke and Eigen have reported temperature jump studies on the kinetics of the helix-coil transition of the oligo(ribouridylic acid)-oligo(riboadenylic acid) system (22 (25,26) and drug-nucleic acid complexes (13,27). These studies have demonstrated the wide range of 31P chemical shifts in nucleic acids and their sensitivity to O-P-O bond strain and phosphodiester torsion angles (13,(26)(27)(28) (29)(30)(31)(32)(33).…”

Section: Discussionmentioning

confidence: 99%

Nuclear magnetic resonance studies of the helix-coil transition of poly (dA-dT) in aqueous solution.

Patel¹,

Canuel²

1976

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

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The well-resolved base and sugar proton resonances in the high resolution proton nuclear magnetic resonance (NMR) spectra of poly (dA-dT) Arnott and coworkers (1) have recently extended the early studies of Davies and Baldwin (2) on the x-ray diffraction patterns from oriented, crystalline fibers of poly(dA-dT). They propose a novel, 8-fold helical structure, with an axial rise per residue of 3.03 A and a C3 exo sugar pucker conformation. Baldwin and coworkers (3-6) have investigated the helix-coil transition of poly(dA-dT) and circular oligo(dAdT). They have characterized the role of hairpin and straight chain helices by monitoring absorbance melting curves as a function of salt, temperature, and pH. The thermodynamic parameters for the helix-coil transition of poly(dA-dT) have been elucidated from differential heat calorimetry (7,8).High resolution nuclear magnetic resonance (NMR) spectroscopy is capable of monitoring many aspects of the helixcoil transition of alternating deoxypurine-deoxypyrimidine oligonucleotides in aqueous solution. These studies include investigations of the exchangeable and nonexchangeable protons in the duplex of the self-complementary hexanucleotide d(A-T-G-C-A-T) (9-12) and the d[C-G(-C-G)n], n = 1,2 duplexes (13) in aqueous solution.The Watson-Crick thymine imino protons in the oligomer duplexes d(pT-A)n, n = 3,4,5, were monitored in our laboratory as a function of temperature by high resolution proton NMR spectroscopy in H20 solution (14). The chemical shifts and line widths of these exchangeable resonances were obAbbreviation: NMR, nuclear magnetic resonance. servable when the double helix was predominantly intact but broadened with increasing coil concentration. An alternate NMR approach monitors the entire helix-coil transition as followed by the nonexchangeable protons and the, phosphates in D20 solution (11)(12)(13)(15)(16)(17).Nuclear magnetic resonance spectral line widths yield kinetic information about the helix-coil transition when the exchange rate is on the order of the chemical shift difference between the helix and coil states. It will be demonstrated that the adenine H2 proton in poly(dA-dT) exhibits an about 1 ppm chemical shift difference between the two states and provides a handle for monitoring the kinetic aspects of the helix-coil transition. EXPERIMENTAL Sample preparationThe alternating copolymer poly(dA-dT) samples for proton NMR studies were purchased from Long Island Biochemical Corp. and were shipped in Tris buffer (chain length: about 300 nucleotides).270 MHz Proton NMR Studies. The purchased sample in Tris buffer was lyophilized and the spectra were recorded on 18.8 mM (with respect to phosphorus) poly (dA-dT)

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“…As discussed in more detail below, two of the most important parameters controlling 31 P chemical shifts in phosphate esters are the P-O torsional angles (in nucleic acids the P-O5′ (α) and P-O3′ (ζ) torsional angles (65,66) and the C-O5′ (β) and C-O3′ (ε) torsional angles) ( 67,68), although the P-O torsional angle may be more important. Using the selective 2D-J resolved long-range correlation experiment, we can measure the three-bond H3′-C3′-O-P coupling constant (listed in table I) for each of the phosphates in the decamer (48,63).…”

Section: Positional and Sequence-specific Variation Of 31 P Chemical mentioning

confidence: 99%

Two-Dimensional¹H and³¹P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys³, MeCys⁷]TANDEM) Drug Duplex Complex

Powers

Olsen

Gorenstein

1989

Journal of Biomolecular Structure and Dynamics

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Assignment of the 1 H and 31 P NMR spectra of a decamer oligodeoxyribonucleotide duplex, d(CCCGATCGGG), and its quinoxaline ([MeCys 3 , MeCys 7 ]TANDEM) drug duplex complex has been made by two-dimensional 1 H-1 H and heteronuclear 31 P-1 H correlated spectroscopy. The 31 P chemical shifts of this 10 base pair oligonucleotide follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the 31 P resonance occurs. While the 31 P chemical shifts show sequence-specific variations, they also do not generally follow the Calladine "rules" previously demonstrated. 31 P NMR also provides a convenient monitor of the phosphate ester backbone conformational changes upon binding of the drug to the duplex. Although the quinoxaline drug, [MeCys 3 , MeCys 7 ]TANDEM, is generally expected to bind to duplex DNA by bis-intercalation, only small 31 P chemical shift changes are observed upon binding the drug to duplex d(CCCGATCGGG). Additionally, only small perturbations in the 1 H NMR and UV spectra are observed upon binding the drug to the decamer, although association of the drug stabilizes the duplex form relative to the other states. These results are consistent with a nonintercalative mode of association of the drug. Modeling and molecular mechanics energy minimization demonstrate that a novel structure in which the two quinoxaline rings of the drug binds in the minor groove of the duplex is possible.

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31P chemical shifts in phosphate diester monoanions. Bond angle and torsional angle effects

Cited by 135 publications

References 13 publications

Citrate bridges between mineral platelets in bone

Citrate bridges between mineral platelets in bone

Nuclear magnetic resonance studies of the helix-coil transition of poly (dA-dT) in aqueous solution.

Two-Dimensional¹H and³¹P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys³, MeCys⁷]TANDEM) Drug Duplex Complex

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31P chemical shifts in phosphate diester monoanions. Bond angle and torsional angle effects

Cited by 135 publications

References 13 publications

Citrate bridges between mineral platelets in bone

Citrate bridges between mineral platelets in bone

Nuclear magnetic resonance studies of the helix-coil transition of poly (dA-dT) in aqueous solution.

Two-Dimensional1H and31P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys3, MeCys7]TANDEM) Drug Duplex Complex

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Product

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Two-Dimensional¹H and³¹P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys³, MeCys⁷]TANDEM) Drug Duplex Complex