Effect of the sulphur atom on geometry and spectra of the biomolecule 2-thiouracil and in the WC base pair 2-thiouridine-adenosine. Influence of water in the first hydration shell

The effect of the sulphur atom on 2-thiouracil (2TU) and 2-thiouridine molecules, as compared with uracil and uridine molecules, respectively, was carried out in several environments. The predicted IR spectrum of 2TU in the isolated state was compared with that obtained for uracil molecule and with those reported experimentally in matrix isolation. Its crystal unit cell in the solid state was simulated through a tetramer form using DFT methods for the first time. The calculated Raman spectrum was compared to the experimental ones in the solid state. A linear scaling procedure was used for this task. The first hydration shell was simulated by explicit number of water molecules surrounding 2TU up to 30 and was compared with that obtained in uracil molecule. Water molecules ‘distributed’ around 2TU was preferred over that ‘clustering’, because it can better reproduce the hydration and their effects on different parameters of the molecular structure of 2TU and uracil. The total atomic charges and several calculated thermodynamic parameters were discussed. The effect of the sulphur atom on the Watson-Crick (WC) and reverse WC base pair uridine-adenosine was estimated, and the CP corrected interaction energies were calculated. 2-thiouridine has a weaker WC pair than that with uridine, although its slight higher dipole moment (μ) facilitates the interaction with the water molecules. Several helical parameters were determined.     

Examination by the molecular orbital method of the intrinsic conformation preferences of nucleic acid sequence]

This paper reports a systematic PCILO study of the conformation of the nucleic acid backbone. The authors principally studied the ω′ and ω phosphodiester torsion angles of the disugar triphosphate model as a simultaneous function of (1) the sugar nature, ribose or deoxyribose, (2) the different combinations of the sugar ring puckers C(2′)-endo-C(2′)-endo, C(3′)-endo-C(3′)-endo, C(3′)-endo-C(2′)-endo, and C(2′)-endo-C(3′)-endo, and (3) the different conformations around the ψ(C4′–C5′) exocyclic bond. The dependence of the (ω′,ω) conformational energy maps upon these different factors, is discussed. The results are in very good agreement with the observed structures of ribonucleic (RNA10, RNA11, A′-RNA12, tRNA^Phe) and deoxyribonucleic acids (D-DNA, C-DNA 9.3, B-DNA 10, A-DNA 11). Thus the validity of this model, the disugar triphosphate unit, is ensured. The main conclusions that can be drawn from this systematic study are the following:

• 1 The torsion around P-05′ (angle ω) is, as a general rule, more flexible than the torsion around P-03′ (angle ω′).
• 2 There is no notable difference between the ribose–triphosphate units and the deoxyribose–triphosphate units for the C(3′)-endo–C(3′)-endo and C(3′)-endo–C(2′)-endo sugar puckers.
• 3 The deoxyribose–triphosphate units with C(2′)-endo–C(2′)-endo and C(2′)-endo–C(3′)-endo sugar puckers show much more ω′ flexibility than the ribose–triphosphate units with the same sugar puckers and cis position for the 2′hydroxyl group.
• 4 The preferred values of ω′ are independent of the sugar nature (ribose or deoxyribose) and of ψ values; they are correlated with the sugar pucker of the first sugar-phosphate unit:
  • C(3′)-endo-C(3′)-endo and C(3′)-endo-C(2′)-endo puckers ? ω′ ? 240° (g^? region)
  • C(2′)-endo-C(2′)-endo and C(2′)-endo-C(3′)-endo puckers ? ω′ 180° (t region)
• 5 The preferred values of ω are independent of the nature and the puckering of the sugars; they are correlated with the rotational state of the torsion angle ψ(C4′–C5′): ψ ? 60° (gg) ? ω ? 300° (g^?), ψ ? 180° (gt) or 300° (tg) ? ω ? 60° (g⁺)

     

A vibrational spectroscopic study of the self-association of polyinosinic acid and polyguanylic acid in aqueous solution

We have studied by Raman and ir spectroscopy the structure of self-associated polyinosinic acid and polyguanylic acid in aqueous solution. The results are consistent with the formation of a four-stranded complex, which melts cooperatively near 60°C in the case of poly (I) in the presence of K⁺ ions. The conformation of the ribose in both systems is mixed C2′-endo/C3′-endo, giving a structure that is intermediate between the extremes proposed previously from x-ray diffraction studies. Characteristic Raman bands for the C2′-endo ribose conformation in polyribonucleotides are identified. The four-stranded structure of poly (I) appears to be very flexible, with ≈15% of the tetrameric segments being disrupted and ≈30% of the ribose units adopting a disordered conformation prior to melting. This disordering process increases to ≈75% above the melting transition, with the remaining ≈25% of the ribose units keeping an ordered C2′-endo or C3′-endo conformation. © 1994 John Wiley & Sons, Inc.     

Synthesis of 4′-C-Methylnucleosides

Several 4′-C-methylnucleosides were prepared. ¹H-NMR studies on these nucleosides showed that they have the 3′-exo furanose ring conformation different from the 3′-endo conformation of natural nucleosides.     

FT-IR and 1H NMR spectroscopic evidence of sugar ring conformational change in NH4GpG on complexation to form cis-[Pt(NH3)2(GpG)]+

The conformational change of the ribose ring in NH₄GpG and cis-[Pt(NH₃)₂(GpG)]⁺ was confirmed by FT-IR spectroscopic evidence as being C2′-endo, C3′-endo, anti, gg sugar ring pucker in the solid state. These results were compared with ¹H NMR spectral data in aqueous solution. The FT-IR spectrum of NH₄GpG shows marker bands at 802 cm^?1 and 797 cm^?1 which are assigned to the C3′-endo, anti, gg sugar-phosphate vibrations of ribose (?pG) and ribose (Gp?), respectively. The FT-IR spectrum of cis-[Pt(NH₃)₂(GpG)]⁺ (with N7N7 chelation in the GpG sequence) shows a marker band at 800 cm^?1 which is assigned to the C3′-endo, and a new shoulder band at 820 cm^?1 related to a C2′-endo ring pucker. The ribose conformation of (?pG) moiety in NH₄-GpG, C3′-endo, anti, gg changes into C2′-endo, anti, gg when a platinum atom is chelated to N7N7 in the GpG sequence.     

REACTION OF N3-BENZOYL-3′,5′-O-(DI-TERT-BUTYLSILANEDIYL)URIDINE WITH HINDERED ELECTROPHILES: INTERMOLECULAR N3 To 2′-O PROTECTING GROUP TRANSFER

ABSTRACT

The compound N³-benzoyl-3′,5′-O-(di-tert-butylsilanediyl)uridine 2 was alkylated with various alkyl iodides in CH₃CN in the presence of base. Normal 2′-O-alkylated products were obtained with methyl or benzyl iodide. if hindered alkyl iodides with β-branching such as 2-ethylbutyl iodide were used as electrophiles under the same conditions, N³-alkyl-2′-O-benzoyl uridine derivatives were produced. This unexpected transformation is usually dormant with reactive alkylating agents, but expressed with sterically hindered, less reactive electrophiles. This unwanted reaction gives isomeric products whose spectra differ in only subtle ways from target compounds.     

Polarized Raman scattering from oriented single microcrystals of d(A5T5)2 and d(pTpT)

Polarized Raman spectra have been obtained from single microcrystals of the duplex of the decamer d(A₅T₅)₂ using a Raman microscope. This is the first report of Raman spectra from a crystal of a deoxyoligomer that contains only long, nonalternating sequences of adenine and thymine. Sequences containing d(A)_n and d(T)_n are of interest in view of recent suggestions that they induce bends in DNA and that they might exist in a nonstandard B-conformation. Polarized Raman spectra of a crystal of d(pTpT) have also been obtained. Both crystals display Raman bands whose intensities are very sensitive to the orientation of the crystal with respect to the direction of polarization of the incident laser beam. These spectra indicate that the helical axes of the oligonucleotides are parallel to the long axes of the crystals and that the d(A₅T₅)₂ is not appreciably bent in the crystal. The Raman spectrum from the d(pTpT) crystal indicates that all of the furanose ring puckers are in a C2′-endo configuration since only the C2′-endo marker band at 835 ± 5 cm^?1 is present. Crystals of d(A₅T₅)₂ show measurable Raman intensities in both the 838- and 816-cm^?1 bands. This indicates the presence of both the C2′-endo and C3′-endo, or possibly other non-C2′-endo, furanose conformations. The 816-cm^?1 band is weak so that only a small fraction of the residues are estimated to be in the non-C2′-endo conformation. In both the d(pTpT) and d(A₅T₅)₂ crystals the intensity of the bands due to vibrations of the backbone show only a small dependence on orientation of the crystals. This result is explained by the low symmetry of the puckered sugar rings. It is concluded that Raman spectra obtained from oligonucleotide crystals in which the orientation of the crystal axes to the laser polarization is not carefully controlled may contain intensity artifacts that are due to polarization effects.     

mt-tRNA Components: Synthesis of (2-Thio)Uridines Modified with Blocked Glycine/Taurine Moieties at C-5,1

In this paper, we discuss the usefulness of reductive amination of 5-formyl-2′,3′-O-isopropylidene(-2-thio)uridine with glycine or taurine esters in the presence of sodium triacetoxyborohydride (NaBH(OAc)₃) for the synthesis of the native mitochondrial (mt) tRNA components 5-carboxymethylaminomethyl(-2-thio)uridine (cmnm⁵(s²)U) and 5-taurinomethyl(-2-thio)uridine (τm⁵(s²)U) with a blocked amino acid function. 2-(Trimethylsilyl)ethyl and 2-(p-nitrophenyl)ethyl esters of glycine and 2-(2,4,5-trifluorophenyl)ethyl ester of taurine were selected as protection of carboxylic and sulfonic acid residues, respectively. The first synthesis of 5-formyl-2′,3′-O-isopropylidene-2-thiouridine is also reported.     

Conformational analysis of the 2'-deoxyribofuranose ring from proton-proton coupling constants: analysis of a nucleoside-carcinogen adduct formed from 2-acetylaminofluorene utilizing a three-state model

The conformation of the sugar moiety of 8-(N-fluoren-2-ylamino)-2′-deoxyguanosine in solution has been examined as a function of temperature by ¹H-nmr spectroscopy. Analysis of coupling constants shows that lowering the temperature to ?50°C in methanol shifts the conformational equilibrium of the sugar ring resulting in a C2′-endo conformation at a mole fraction of 0.97. The computed phase angle of pseudorotation and amplitude of pucker are 154° and 36°, respectively, with very little discrepancy between the five calculated coupling constants and coupling constants extrapolated from the temperature profiles. A computer program has been written enabling a three-state best-fit analysis. The three-state analysis indicates an equilibrium between C2′-endo, C3′-endo, and 04′-endo conformations. In aqueous solution, the computed mole fraction of the 04′-endo form is 0.18 at 30°C. The conformation associated with the sugar ring and the C4′? C5′ bond is compared to that of 2′-deoxyguanosine.     

1H-nmr studies on the dinucleoside monophosphates containing 2′-halogeno-2′-deoxypurinenucleosides: Effects of 2′-substitutes on conformation

Seven dinucleoside monophosphates containing 2′-halogeno-2′-deoxypurine nucleoside residue, dAfl-U, dAcl-U, dAbr-U, dAio-U, dGfl-U, and dIfl-C, were chemically synthesized and investigated by ¹H-nmr spectroscopy at 300 MHz. The sugar and backbone conformations of these compounds were analyzed by the spectral pattern of furanose proton resonances; and the extents of base-base interaction were estimated from chemical shifts and their temperature-dependent changes of base-proton resonances. It is found that the population of C_3′-endo conformer and the extent of base-base interaction decrease as the electronegativity of 2′-substituent decreases in dAx-U (x = fl, cl, br, and io) series. The C_3′-endo (³E) population and the base-base interaction in Nfl-U (N = A,G)-type dimers as well as dIfl-C are relatively higher than the corresponding natural ribo-dimers but can be recognized as grossly similar to the conformation of regular RNA dimers.     

Configurational effects on conformational properties of cyclic nucleotides. I. Theoretical calculations of conformer preferences in α-nucleoside 3′,5′ cyclic monophosphates

A comparative study has been made of the configurational effects on the conformational properties of α- and β-anomers of purine and pyrimidine nucleoside 3′,5′,-cyclic monophosphates and their 2′-arabino epimers. Correlation between orientation of the base and the 2′-hydroxyl group have been studied theoretically using the PCILO (Perturbative Configuration Interaction using Localized Orbitals) method. The effect of change in ribose puckering on the base-hydroxyl interaction has also been studied. The result show that steric repulsions and stabilizing effects of intramolecular hydrogen bonding between the base and the 2′-hydroxyl (OH) group are of major importance in determining configurations of α-anomers and 2′-arabino-β-epimers. For example, hydrogen bonding between the 2′-hydroxyl group and polar centers on the base ring is clearly implicated as a determinant of syn-anti preferences of the purine (adenine) or pyrimidine (uracil) bases in α-nucleoside 3′,5′-cyclic monophosphates. Moreover, barrier heights for interconversion between conformers are sensitive to ribose pucker and 2′-OH orientations. The result clearly show that a change in ribose-ring pucker plays an essential role in relieving repulsive interaction between the base and the 2′-hydroxyl group. Thus a C2′-exo-C3′-endo (₂T³) pucker is favored for α-anomers in contrast with the C4′-exo-C3′-endo (₄T³) from found in β-compounds.     

Determination of the molecular conformation of beta-D-O2,2'-cyclouridine in aqueous solution by proton magnetic resonance spectroscopy

The solution conformation of β-D -O²,2′-cyclouridine has been determined at 27 and 88°C in D₂O by proton magnetic resonance spectroscopy. The conformation is described in terms of a fixed syn-like sugar-base torsional angle, a type S furanose ring conformation (similar to 2′-endo), and a temperature-dependent exocyclic C(4)′–C(5′) rotamer population containing approximately 50% of the gauche-gauche form at 27°C. β-D -O²,2′-Cyclouridine 5′-phosphate likewise possesses a type S furanose ring conformation.     

Molecular mechanical studies on left- and right-handed B-DNA

Molecular mechanical simulations on base-paired deoxyhexanucleoside phosphates, (dAdT)₃ · (dAdT)₃, (dTdA)₃ · (dTdA)₃, (dGdC)₃ · (dGdC)₃, and (dCdG)₃ · (dCdG)₃, have been carried out to assess their energetic stabilities in left- and right-handed forms. These hexamers have also been simulated with alternating sugar-puckering profiles with the combinations (purine : C2′-endo–pyrimidine : C3′-endo) and (purine : C3′-endo–pyrimidine C2′-endo). The right-handed models have been found to be the energetically most stable structures and the left-handed structures are significantly destabilized. This instability has been rationalized in terms of competition between stabilizing stacking interactions on one hand, and distortions in the bond angles and torsion angles in the sugar-phosphate backbone on the other.     

NMR and FT-IR conformational studies of 8-substituted guanine nucleosides and nucleotides and their metal adducts and cancer

NMR and FT-IR Studies of the conformational changes of guanosine and guanosine-5′-monophosphate upon substitution of the H8 of guanine by a heavy, large atom, such as bromine, are presented. The conformational forms, syn, anti, C2′-endo and C3′-endo and gg, gt and tg rotamers of the above molecules are compared to those of their metal (Mg²⁺ and P^t2+) adducts, where the metal is fixed to the N7 nitrogen atom of guanine. The antitumor activity of cisplatin is discussed with relation to the conformational form and the effect of cisplatin is compared to the effects of the Mg²⁺ ion and carcinogens.     

Synthesis of (2′S)-1-(2-C-Azidomethyl-2-deoxy and 2-C-Cyanomethyl-2-deoxy-β-D-arabinofuranosyl)cytosines

Abstract

2′-C-Cyanomethyl-2′-deoxy-arabinosylcytosine 3 and 2′-C-azidomethyl-2′-deoxy-arabinosylcytosine 4 were synthesized from uridine. The antineoplastic activities of these compounds were evaluated.     

Structure and Conformation of 5′-Chlorocyclocytidine,a Potent Inhibitor of Nucleic Acid Synthesis: X-Ray, 1H and 13C NMR Analyses

Abstract

The structure of the hydrochloride of 5′-chlorocyclocytidine, a potent inhibitor of DNA synthesis, was determined by X-ray crystallography. The nucleoside crystallizes in the orthorhombic space group P2₁2₁2₁ with cell dimensions a = 10.413(4), b = 13.236(5), c = 17.064(6) Å and with two independent molecules in the asymmetric unit (Z = 8). Atomic parameters were refined by full-matrix least squares to a final value of R = 0.053 for 2490 observed reflections. In both molecules the furanose ring has a C4′ endo/04′ exo (⁴ T ₀) pucker. In molecule A the orientation of the -CH₂Cl side chain is gauche. In molecule B the side chain is disordered: in 70% of these molecules the orientation is trans and in 30% it is gauche ⁺. ¹H NMR spectra indicate a conformational equilibrium between C4′ exo/04′ endo (₄ T ⁰) and C4′ endo/C3′ exo (⁴ ₃ T) with a population ratio of 38:62. All three side chain rotamers occur in solution, the trans orientation contributing most. ¹J(C, H) values for C1′ and C2′ are significantly higher than normal and can therefore be used as a diagnostic tool for the assignment of bridgehead carbon atoms in cyclonucleosides.     

Simultaneous Removal of Benzyl and Benzyloxycarbonyl Protective Groups in 5′-O-(2-Deoxy-α-D-Glucopyranosyl)Uridine by Catalytic Transfer Hydrogenolysis

Synthesis of N ³,2′,3′-O-tris-(benzyloxycarbonyl)uridine and its use in the synthesis of 5′-O-(2-deoxy-α-d-glucopyranosyl)uridine is described. Simultaneous removal of benzyl and benzyloxycarbonyl groups was accomplished by catalytic transfer hydrogenolysis in the presence of Pearlman's catalyst without competing side reactions.     

The X-ray crystal structure of 6-deoxy-α-l-sorbofuranose. Conformational analysis of ketohexofuranosides and their comparison with ribofuranosides and arabinofuranosides

The crystal and molecular structure of 6-deoxy-l-sorbose have been determined by the application of multisolution methods and refined to an R-index of 0.063 for 560 reflections, using three-dimensional intensity data collected on a Picker automatic diffractometer. The compound crystallizes in the space group P2₁2₁2₁ with unit-cell dimensions a = 18.470 (10), b = 7.636 (10), and c = 5.371 (8) Å; Z = 4. The molecule occurs as the α-furanose form, which is also the preponderant tautomer in solution. The puckering of the furanoid ring is C-3′-exo-C-4′-endo (₃T⁴) [equivalent to C-2′-exo-C-3′-endo (₂T³) in the numbering for d-ribose], with P and τ_m angles of -6.5 and 42.7° respectively. Conformational analysis of the known ketofuranosides shows that the ₃T⁴ (₂T³ in d-ribose numbering) puckering mode, which is typical of α-nucleosides, is favored, in contrast to the favored ³T₂ or ²T₃ puckering mode for the β-d-ribonucleosides and β-d-arabinonucleosides. The conformational differences among furanoid rings are mainly influenced by the configuration at the anomeric carbon atom. The favored orientation about the C-2′-C-1′ bond (O-5′-C-2′-C-1′-O-1′)of the ketofuranosidesis — gauche. All four hydroxyl groups are involved in donor-acceptor hydrogen bonding, and O-4′-8 appears to be involved in a bifurcated hydrogen bond to O-2′ and O-3′ of neighboring molecules.     

FT-IR spectroscopic evidence of sugar ring conformational changes in GpC and CpG on platination and intercalation

An FT-IR spectroscopic study concerning changes in the conformation of sugar in the dinucleotides; GpC and CpG, on platination and intercalation is presented. The results are compared with the FT-IR spectral data of 5′-CMP, 5′-GMP, 3′-GMP and their metal adducts. The spectra of free GpC, free CpG, proflavine-GpC, proflavine-CpG, and cis-[Pt(NH₃)₂(GpC)₂]²⁺ exhibit the diagnostic band at 800 cm⁻¹ which was assigned to a sugar phosphate vibrational mode and diagnostic of C3′-endo sugar pucker. In the case of 9-aminoacridine-GpC and cis-[Pt(NH₃)₂(CpG]⁺ the diagnostic bands of the C2′-endo and C3′-endo conformations are observed at 810–820 cm⁻¹ and near 800 cm⁻¹ respectively. The results are in good agreement with X-ray data. The infrared diagnostic bands are important for distinguishing the sugar pucker conformational changes.     

The Discovery of Intramolecular Stereoelectronic Forces That Drive The Sugar Conformation in Nucleosides and Nucleotides

Abstract

This report summarizes our results⁸ on how the determination of the thermodynamics of the two-state North (N, C2′-exo-C3′-endo) ? South (S,C2′-endo-C3′-exo) pseudorotational equilibrium in aqueous solution (pD 0.6 - 12.0) basing on vicinal ³J_HH extracted from ¹H-NMR spectra measured at 500 MHz from 278K to 358K yields an experimental energy inventory of the unique stereoelectronic forces that dictate the conformation of the sugar moiety in β-D-ribonucleosides (rNs), β-D-nucleotides, in the mirror-image β-D- versus β-L-2′-deoxynucleosides (dNs) as well as in α-D- or L- versus β-D- or L-2′-dNs. Our work shows for the first time that the free-energies of the inherent internal flexibilities of β-D- versus β-L-2′-dNs and α-D- versus α-L-2′-dNs are identical, whereas the aglycone promoted tunability of the constituent sugar conformation is grossly affected in the α-nucleosides compared to the β-counterparts.