Proton Magnetic Resonance Studies of 2′-Deoxythymidine, its 3′- and 5′-Monophosphates and 2′-Deoxythymidylyl-(3′, 5′)-2′ -deoxythymidine in Aqueous Solution

Wood, Donald J.; Hruska, Frank E.; Ogilvie, Kelvin K.

doi:10.1139/v74-495

Cited by 81 publications

(32 citation statements)

References 18 publications

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“…3(a)) are apparent in the sum J(4'5') + J(4'5") (X) ( Table 2). In one group of molecules X varies from 8.7 Hz to 9.9 Hz and is larger than the value for dU (8.5 Hz) (35) and dT (8.6 Hz) (10). At the upper extreme are the X values for 6T1 and 6T2, which are similar to that of m6dU (lo.…”

Section: C4'<5'mentioning

confidence: 79%

“…Data for H3', H4', H5', and H5" are not given since they show smaller variations. Data are also shown for Hl', H2', and H2" of dT and m6du (6-methyl-2'-deoxyuridine), which prefer the anti and syn conformations, respectively, in the crystal and aqueous solution states (10,29,32,33). A striking feature of the diagram is the similarity, for 6T1 and 6T2 on the one hand and for 6T3 and 6T4 on the other hand, in the data for Hl', H2', and H2", the sugar protons of which are expected to sense most strongly the shielding effects of the TAN and base moieties.…”

Section: Geornetry Of the Pyrimidine And Tan Ringsmentioning

confidence: 99%

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A conformational study of the adducts of 2′-deoxythymidine and 2,2,6,6-tetramethyl-1,4-piperidone-N-oxyl by ¹H and ¹³C nuclear magnetic resonance

Hruska¹,

Berger²,

Cadet³

et al. 1985

Can. J. Chem.

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CADET, and MIECZY~LAW REMIN. Can. J. Chem. 63, 15 (1985). y-Irradiation of oxygen-free, aqueous solutions of 2'-deoxythymidine in the presence of the organic nitroxide free radical, 2,2,6,6-tetramethyl-1,4-piperidone-N-oxyl (TAN), leads to a complex mixture of products in which the TAN moiety is linked to the C5 or C6 position of a 5,6-saturated thymine ring. Extensive 'H and '?c nmr data are provided for the eight TAN-dT adducts which are produced in the largest amounts. The results show that the conformational properties of the sugar moiety are dependent on the point of attachment of the TAN group and the configuration of the saturated thymine ring.

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Section: C4'<5'mentioning

confidence: 79%

Section: Geornetry Of the Pyrimidine And Tan Ringsmentioning

confidence: 99%

A conformational study of the adducts of 2′-deoxythymidine and 2,2,6,6-tetramethyl-1,4-piperidone-N-oxyl by ¹H and ¹³C nuclear magnetic resonance

Hruska¹,

Berger²,

Cadet³

et al. 1985

Can. J. Chem.

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“…the peaks due to the base protons and to the H-1' d(-A) signal were assigned by careful comparison with the data on the corresponding dinucleotides : d(T-T) [3] …”

Section: Methodsmentioning

confidence: 99%

“…Arbitrary; when 6,=6, the spectrum is independent of J,,,. (cis with respect to the base) and 2" protons followed from coupling constant considerations [3,14]. An expanded version of the computer program LAME was then used to simulate and to plot the 360-MHz ribose spectra, assumed to consist of three independent eight-spin systems (nine for the central d(-T-) part), to yield self-consistent parameters, intensities and line shapes matching those observed (Fig.…”

Section: 'mentioning

confidence: 99%

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Conformational Analysis of a DNA Triplet in Aqueous Solution

Altona¹,

Boom²,

Haasnoot³

1976

European Journal of Biochemistry

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The proton signals of a 50 mM solution of thymidylyl‐(3′‐5′)‐thymidylyl‐(3′‐5′)‐2′‐deoxyadenosine, d(T‐T‐A), in 2H2O at 65 °C and p2H = 7.4, were detected by nuclear magnetic resonance at 360 MHz. Complete assignment of the 21 ribose proton signals was achieved by extensive decoupling experiments and computer simulations. The coupling constant data show that the ribose rings prefer to adopt the S (2′‐endo) conformation. The presence of a substantial amount of a right handed helical structure of the d(‐T‐A) fragment is indicated from chemical shift considerations. The molecule displays a high degree of conformational purity along the sugar‐phosphate backbone.

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Proton and phosphorus nmr studies of d‐CpG(pCpG)_n duplexes in solution. Helix–coil transition and complex formation with actinomycin‐D

Patel¹

1976

Biopolymers

139

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SynopsisThe Watson-Crick imino and amino exchangeable protons, the nonexchangeable base and sugar protons, and the backbone phosphates for d-CpG(pCpG),, n = 1 and 2, have been monitored by high-resolution nmr spectroscopy in aqueous solution over the temperature range Oo-90°C. The temperature dependence of the chemical shifts of the tetramer and hexamer resonances is consistent with the formation of stable duplexes a t low temperature in solution. Comparison of the spectral characteristics of the tetranucleotide with those of the hexanucleotide with temperature permits the differentiation and assignment of the cytosine proton resonances on base pairs located a t the end of the helix from those in an interior position. There is fraying a t the terminal base pairs in the tetranucleotide and hexanucleotide duplexes. The Watson-Crick ring imino protons exchange a t a faster rate than the Watson-Crick side-chain amino protons, with exchange occurring by transient opening of the double helix. The structure of the d-CpG(pCpG), double helices has been probed by proton relaxation time measurements, sugar proton coupling constants, and the proton chemical shift changes associated with the helix-coil transition. The experimental data support a structural model in solution, which incorporates an anti conformation about the glycosyl bonds, C(3) exo sugar ring pucker, and base overlap geometries similar to the B-DNA helix. Rotational correlation times of 1.7 and 0.9 X sec have been computed for the hexanucleotide and tetranucleotide duplexes in 0.1 M salt, D20, pH 6.25 a t 27OC. The well-resolved 31P resonances for the internucleotide phosphates of the tetramer and hexamer sequences a t superconducting fields shift upfield by 0.2-0.5 pprn on helix formation. These shifts reflect a conformational change about the w,w' phosphodiester bonds from gauche-gauche in the duplex structure to a distribution of gauche-trans states in the coil structure. Significant differences are observed in the transition width and midpoint of the chemical shift versus temperature profiles plotted in differentiated form for the various base and sugar proton and internucleotide phosphorous resonances monitoring the d-CpG(pCpG), helix-coil transition. The twofold symmetry of the d-CpGpCpG duplex is removed on complex formation with the antibiotic actinomycin-D. Two phosphorous resonances are shifted downfield by -2.6 ppm and -1.6 pprn on formation of the 1:2 Act-D:d-CpGpCpG complex in solution. Model studies on binding of the antibiotic to dinucleotides of varying sequence indicate that intercalation of the actinomycin-D occurs a t the GpC site in the d-CpGpCpG duplex and that the magnitude of the downfield shifts reflects strain a t the 0-P-0 backbone angles and hydrogen bonding between the phenoxazone and the phosphate oxygens. Actinomycin-D is known to bind to nucleic acids that exhibit a B-DNA conformation; this suggests that the d-CpG(pCpG), duplexes exhibit a B-DNA conformation in solution. 533

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Proton Magnetic Resonance Studies of 2′-Deoxythymidine, its 3′- and 5′-Monophosphates and 2′-Deoxythymidylyl-(3′, 5′)-2′ -deoxythymidine in Aqueous Solution

Cited by 81 publications

References 18 publications

A conformational study of the adducts of 2′-deoxythymidine and 2,2,6,6-tetramethyl-1,4-piperidone-N-oxyl by ¹H and ¹³C nuclear magnetic resonance

A conformational study of the adducts of 2′-deoxythymidine and 2,2,6,6-tetramethyl-1,4-piperidone-N-oxyl by ¹H and ¹³C nuclear magnetic resonance

Conformational Analysis of a DNA Triplet in Aqueous Solution

Proton and phosphorus nmr studies of d‐CpG(pCpG)_n duplexes in solution. Helix–coil transition and complex formation with actinomycin‐D

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Proton Magnetic Resonance Studies of 2′-Deoxythymidine, its 3′- and 5′-Monophosphates and 2′-Deoxythymidylyl-(3′, 5′)-2′ -deoxythymidine in Aqueous Solution

Cited by 81 publications

References 18 publications

A conformational study of the adducts of 2′-deoxythymidine and 2,2,6,6-tetramethyl-1,4-piperidone-N-oxyl by 1H and 13C nuclear magnetic resonance

A conformational study of the adducts of 2′-deoxythymidine and 2,2,6,6-tetramethyl-1,4-piperidone-N-oxyl by 1H and 13C nuclear magnetic resonance

Conformational Analysis of a DNA Triplet in Aqueous Solution

Proton and phosphorus nmr studies of d‐CpG(pCpG)n duplexes in solution. Helix–coil transition and complex formation with actinomycin‐D

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A conformational study of the adducts of 2′-deoxythymidine and 2,2,6,6-tetramethyl-1,4-piperidone-N-oxyl by ¹H and ¹³C nuclear magnetic resonance

A conformational study of the adducts of 2′-deoxythymidine and 2,2,6,6-tetramethyl-1,4-piperidone-N-oxyl by ¹H and ¹³C nuclear magnetic resonance

Proton and phosphorus nmr studies of d‐CpG(pCpG)_n duplexes in solution. Helix–coil transition and complex formation with actinomycin‐D