NMR Studies on the Self-Association of Uridine and Uridine Analogues

Dunger, Anita; Limbach, Hans−Heinrich; Weisz, Klaus

doi:10.1002/(sici)1521-3765(19980416)4:4<621::aid-chem621>3.0.co;2-w

Cited by 39 publications

(51 citation statements)

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“…The value of d (HÀN(3)) extrapolated to a dinucleoside concentration of 0 mm corresponds to the (not observable) chemical-shift value for HÀN(3) of the monoplex, a value that must be close to the one of the weakly associating monomer (ca. 7.70 ppm [5] [22]). The values of d(HÀN(3)) extrapolated to infinite concentration evidence the type of base pairing, WC-type base pairing resulting in a larger value for d (HÀN(3), c ¼1 ) than H-type base pairing (typically,…”

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confidence: 99%

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Oligonucleotide Analogues with Integrated Bases and Backbone. Part 17

Ritter

Egli

Bernet

et al. 2008

Helvetica Chimica Acta

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The formation of cyclic duplexes (pairing) of known oxymethylene‐linked self‐complementary U*[o]A(*) dinucleosides contrasts with the absence of pairing of the ethylene‐linked U*[ca]A(*) analogues. The origin of this difference, and the expected association of U*[x]A(*) and A*[x]U(*) dinucleosides with x=CH2, O, or S was analysed. According to this analysis, pairing occurs via constitutionally isomeric Watson–Crick, reverse Watson–Crick, Hoogsteen, or reverse Hoogsteen H‐bonded linear duplexes. Each one of them may give rise to three diastereoisomeric cyclic duplexes, and each one of them can adopt three main conformations. The relative stability of all conformers with x=CH2, O, or S were analysed. U*[x]A(*) dinucleosides with x=CH2 do not form stable cyclic duplexes, dinucleosides with x=O may form cyclic duplexes with a gg‐conformation about the C(4′)C(5′) bond, and dinucleosides with x=S may form cyclic duplexes with a gt‐conformation about this bond. The temperature dependence of the chemical shift of HN(3) of the self‐complementary, oxymethylene‐linked U*[o]A(*) dinucleosides 1–6 in CDCl3 in the concentration range of 0.4–50 mM evidences equilibria between the monoplex, mainly linear duplexes, and higher associates for 3, between the monoplex and cyclic duplexes for 6, and between the monoplex, linear, and cyclic duplexes as well as higher associates for 1, 2, 4, and 5. The self‐complementary, thiomethylene‐linked U*[s]A(*) dinucleosides 27–32 and the sequence isomeric A*[s]U(*) analogues 33–38 were prepared by S‐alkylation of the 6‐(mesyloxymethyl)uridine 12 and the 8‐(bromomethyl)adenosine 22. The required thiolates were prepared in situ from the C(5′)‐acetylthio derivatives 9, 15, 19, and 25. The association in CHCl3 of the thiomethylene‐linked dinucleoside analogues was studied by 1H‐NMR and CD spectroscopy, and by vapour‐pressure osmometric determination of the apparent molecular mass. The U*[s]A(*) alcohols 28, 30, and 31 form cyclic duplexes connected by Watson–Crick H‐bonds, while the fully protected dimers 27 and 29 form mainly linear duplexes and higher associates. The diol 32 forms mainly cyclic duplexes in solution and corrugated ribbons in the solid state. The nucleobases of crystalline 32 form reverse Hoogsteen H‐bonds, and the resulting ribbons are cross‐linked by H‐bonds between HOCH2C(8/I) and N(3/I). Among the A*[s]U(*) dimers, only the C(8/I)‐hydroxymethylated 37 forms (mainly) a cyclic duplex, characterized by reverse Hoogsteen base pairing. The dimers 34–36 form mainly linear duplexes and higher associates. Dimers 34 and particularly 38 gelate CHCl3. Temperature‐dependent CD spectra of 28, 30, 31, and 37 evidence π‐stacking in the cyclic duplexes. Base stacking in the particularly strongly associating diol 32 in CHCl3 solution is evidenced by a melting temperature of ca. 2°.

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“…606.2724). N 6 -Benzoyl-8-(bromomethyl)-5'-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-2',3'-O-isopropylideneadenosine(22). A soln.…”

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Oligonucleotide Analogues with Integrated Bases and Backbone. Part 17

Ritter

Egli

Bernet

et al. 2008

Helvetica Chimica Acta

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“…28–31 This approach is followed for the A•T base pairs, similar to previous work on the A•U base pair formation of 2′-deoxyadenosine and 2′-deoxyuridine derivatives. 8,9,32 We note here that 1 H chemical shifts of the imino protons in N- H ···N are measured, in contrast to a study of 13 C chemical shifts, 33 where it has been realized 34 that such results are too small and too insensitive to correctly probe hydrogen bonds. In our studies the protons in the hydrogen bonds are measured, providing direct access to the hydrogen bond structure.…”

Section: Equilibrium Structures Of A•t Base Pairs In Solutionmentioning

confidence: 73%

N–H Stretching Excitations in Adenosine-Thymidine Base Pairs in Solution: Pair Geometries, Infrared Line Shapes, and Ultrafast Vibrational Dynamics

et al. 2013

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We explore the N-H stretching vibrations of adenosine-thymidine base pairs in chloroform solution with linear and nonlinear infrared spectroscopy. Based on estimates from NMR measurements and ab initio calculations, we conclude that adenosine and thymidine form hydrogen bonded base pairs in Watson-Crick, reverse Watson-Crick, Hoogsteen and reverse Hoogsteen configurations with similar probability. Steady-state concentration- and temperature dependent linear FT-IR studies, including H/D exchange experiments, reveal that these hydrogen-bonded base pairs have complex N-H/N-D stretching spectra with a multitude of spectral components. Nonlinear 2D-IR spectroscopic results, together with IR-pump-IR-probe measurements, as also corroborated by ab initio calculations, reveal that the number of N-H stretching transitions is larger than the total number of N-H stretching modes. This is explained by couplings to other modes, such as an underdamped low-frequency hydrogen-bond mode, and a Fermi resonance with NH2 bending overtone levels of the adenosine amino-group. Our results demonstrate that modeling based on local N-H stretching vibrations only is not sufficient and call for further refinement of the description of the N-H stretching manifolds of nucleic acid base pairs of adenosine and thymidine, incorporating a multitude of couplings with fingerprint and low-frequency modes.

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“…If, in the duplexes shown in Fig. 2, a, R 1 ¼ R 2 , then U 4 · U 2 and U 2 · U 4 are identical, and a 1 : 1 : 2 mixture is expected, and a 1 : 1 : 1.6 mixture of U 4 · U 4 , U 2 · U 2 , and U 4 · U 2 /U 2 · U 4 was indeed observed for a cold (123 K) solution of a uridine monomer in freon [6] [7]. U*[s]U ( * ) Dimers may form a number of cyclic duplexes.…”

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confidence: 78%

Oligonucleotide Analogues with Integrated Bases and Backbone

Ritter

Bernet

Vasella

2008

Helvetica Chimica Acta

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The thiomethylene-linked U*[s]U ( * ) dimers 9 -14 were synthesized by substitution of the 6-[(mesyloxy)methyl]uridine 6 by the thiolate derived from the uridine-5'-thioacetates 7 and 8 followed by O-deprotection. Similarly, the thiomethylene-linked A*[s]A ( * ) dimers 9 -14 were obtained from the 8-(bromomethyl)adenosine 15 and the adenosine-5'-thioacetates 16 and 17. The concentration dependence of both HÀN(3) of the U*[s]U ( * ) dimers 9 -14 evidences the formation of linear and cyclic duplexes, and of linear higher associates, C(8 or 6)CH 2 OH and/or C(5'/II)OH groups favouring the formation of cyclic duplexes. The concentration dependence of the chemical shift for both H 2 NÀC(6) of the A*[s]A ( * ) dimers 18 -23 evidences the formation of mainly linear associates. The heteroassociation of U*[s]U ( * ) to A*[s]A ( * ) dimers is stronger than the homoassociation of U*[s]U ( * ) dimers, as evidenced by diluting equimolar mixtures of 11/20 and 13/22. A 1 : 1 stoichiometry of the heteroassociation is evidenced by a

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NMR Studies on the Self-Association of Uridine and Uridine Analogues

Cited by 39 publications

References 14 publications

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 17

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 17

N–H Stretching Excitations in Adenosine-Thymidine Base Pairs in Solution: Pair Geometries, Infrared Line Shapes, and Ultrafast Vibrational Dynamics

Oligonucleotide Analogues with Integrated Bases and Backbone

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