The relationship between hydrogen bonding and base stacking in crystalline 4-thiouridine derivatives

Insights into Cisplatin Binding to Uracil and Thiouracils from IRMPD Spectroscopy and Tandem Mass Spectrometry

The monofunctional primary complexes cis-[PtCl(NH₃)₂(L)]⁺, formed by the reaction of cisplatin, a major chemotherapeutic agent, with four nucleobases L, i.e., uracil (U), 2-thiouracil (2SU), 4-thiouracil (4SU), and 2,4-dithiouracil (24dSU), have been studied by a combination of infrared multiple photon dissociation (IRMPD) action spectroscopy in both the fingerprint (900-1900 cm^-1) and the N-H/O-H stretching (3000-3800 cm^-1) ranges, energy-resolved collision-induced dissociation (CID) mass spectrometry, and density functional calculations at the B3LYP/LACVP/6-311G** level. On the basis of the comparison across the experimental features and the linear IR spectra of conceivable structures, the cisplatin residue is found to promote a monodentate interaction preferentially with the O4(S4) atoms of the canonical forms of U, 4SU, and 24dSU and to the S2 atom of 2SU, yielding the most stable structures. Additional absorptions reveal the presence of minor, alternative tautomers in the sampled ion populations of 2SU and 24dSU, underlying the ability of cisplatin to increase the prospect of (therapeutically beneficial) nucleic acid strand disorder. Implication of these evidence may provide insights into drug mechanism and design.

Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase

Reiterative transcription is a non-canonical form of RNA synthesis by RNA polymerase in which a ribonucleotide specified by a single base in the DNA template is repetitively added to the nascent RNA transcript. We previously determined the X-ray crystal structure of the bacterial RNA polymerase engaged in reiterative transcription from the pyrG promoter, which contains eight poly-G RNA bases synthesized using three C bases in the DNA as a template and extends RNA without displacement of the promoter recognition σ factor from the core enzyme. In this study, we determined a series of transcript initiation complex structures from the pyrG promoter using soak–trigger–freeze X-ray crystallography. We also performed biochemical assays to monitor template DNA translocation during RNA synthesis from the pyrG promoter and in vitro transcription assays to determine the length of poly-G RNA from the pyrG promoter variants. Our study revealed how RNA slips on template DNA and how RNA polymerase and template DNA determine length of reiterative RNA product. Lastly, we determined a structure of a transcript initiation complex at the pyrBI promoter and proposed an alternative mechanism of RNA slippage and extension requiring the σ dissociation from the core enzyme.

Structure and Stability of Chemically Modified DNA Bases: Quantum Chemical Calculations on 16 Isomers of Diphosphocytosine

We studied for the first time 16 tautomers/rotamers of diphosphocytosine by four computational methods. Some of these tautomers/rotamers are isoenergetic although they have different structures. High-level electron correlation MP2 and MP4(SDQ) ab initio methods and density functional methods employing a B3LYP and the new M06-2X functional were used to study the structure and relative stability of 16 tautomers/rotamers of diphosphocytosine. The dienol tautomers of diphosphocytosine are shown to be much more stable than the keto-enol and diketo forms. The tautomers/rotamers stability could be ranked as PC3 = PC12 < PC2 = PC11 < PC1 < PC10 < PC8 < PC9 < PC15 < PC16 < PC6 ~ PC7 < PC13 < PC4 ~ PC14 < PC5. This stability order was discussed in the light of stereo and electronic factors. Solvation effect has been modeled in a high dielectric solvent, water using the polarized continuum model (PCM). Consideration of the solvent causes some reordering of the relative stability of diphosphocytosine tautomers: PC3 ~ PC12 ~ PC2 ~ PC11 < PC1 < PC10 < PC8 < PC9 < PC15 ~ PC16 < PC13 < PC6 ~ PC7 ~ PC14 < PC4 ~ PC5.

ASSOCIATION OF URACIL WITH Zn2+ AND THE HYDRATED Zn2+: A DFT INVESTIGATION

The association behaviors between Uracil and Zn 2+ in vacuum and in the presence of extra water molecules have been investigated systematically using the density functional theory (DFT). In these systems, the interaction of Zn 2+ with the carbonyl oxygen O 4 is systematically favored relative to O 2. For Uracil- Zn 2+ complexes, the more stable coordination mode among the possible complexes corresponds to the bidentate one, where the monodentate coordination mode is about 37 kcal/mol higher in energy relative to the bidentate case. Correspondingly, the stabilities of these structures are enhanced due to the formations of the four-membered chelate ring in the bidentate coordination processes. In the monodentate coordination complexes, the hydration effects are larger than those in the bidentate coordination complexes. The most basic center in the Uracil remains the same regardless of whether introducing the water molecules to Zn 2+ or not. The calculated Zn 2+ bonding energies in Uracil- Zn 2+( H 2 O ) complexes are reduced in comparison to those of the unhydrated Uracil- Zn 2+ complexes. Moreover, investigations of stepwise hydration of Zn 2+ in the most stable Uracil- Zn 2+ complex suggest that the successive hydration effect on the Zn 2+ site can enhance the strength of C = O bond in the Uracil- Zn 2+ complexes and reduce the association interaction of Uracil with Zn 2+. Additionally, the most acidic site of Uracil has been changed from N 1- to N 3– H group before and after introducing the Zn 2+ and there is a significant increase in the overall acidity of the system.

A theoretical study of hydration effects on the prototropic tautomerism of selenouracils

The prototropic tautomerism of 2-, 4-selenouracil and 2,4-diselenouracil has been studied using density functional theory (DFT) methods, at the B3LYP/6-311 + G(3df,2p)//B3LYP/6-31G(d,p) level. The relative stability order of selenouracil tautomers does not resemble that of uracil tautomers, but it is similar to that of thiouracils, even though the energy gaps between the different tautomers of selenouracils are smaller than for thiouracils. The tautomerism activation barriers are high enough as to conclude that only the oxo-selenone or the diselenone structures should be found in the gas phase. The specific interaction with one water molecule reduces these barriers by a half, but still the oxo-selenone form is always the most stable tautomer. The addition of a second water molecule has a relatively small effect, as well as bulk effects, evaluated by means of a continuum-polarized model. For isolated 2- and 4-selenouracils, the more favorable tautomerization process corresponds to a hydrogen transfer towards the selenium atom, the activation barriers for transfer towards the oxygen atom being much higher. This situation changes when specific and bulk effects are included, and the latter process becomes the more favorable one. For 2,4-diselenouracil the more favorable tautomerization, in the gas phase, corresponds to the H shift from N1 to the Se atom at C2, while solvation effects favor the transfer from N3 to the Se atom at C4.

Association of Cu2+with Uracil and Its Thio Derivatives: A Theoretical Study

The structures and relative stabilities of the complexes between Cu2+ and uracil, 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil were investigated by B3LYP/6-311+G(2df,2p)//B3LYP/6-31G* DFT calculations. In those systems in which both types of basic centers, that is, a carbonyl and a thiocarbonyl group, are present, association of Cu2+ with the oxygen atom is systematically favored, in contrast to what was found for the corresponding Cu+ complexes. This can be understood by considering that association of Cu2+ is immediately followed by oxidation of the base, which accumulates the negative charge at the oxygen atoms. Similarly, for 2,4-dithiouracil the most basic site for Cu+ attachment is the sulfur atom at the 4-position, while for association of Cu2+ it is sulfur at the 2-position. In contrast, differences between uracil-Cu+ and uracil-Cu2+ complexes are very small, and in both cases the oxygen atom at the 4-position is the most basic. Cu2+ binding energies are about 4 and 1.2 times larger than Cu+ binding energies and proton affinities, respectively. Uracil- and thiouracil-Cu2+ complexes are thermodynamically unstable but kinetically stable with respect to their dissociation into uracil*+ + Cu+ or thiouracil*+ + Cu+. The Cu2+ binding energies vary with the difference between the second ionization potential of the metal and the first ionization potential of the base. regardless of the reference acid (H+, Cu+, Cu2+) the basicity trend is 2,4-dithiouracil > 4-thiouracil > 2-thiouracil > uracil.

The fidelity of replication of the three-base-pair set adenine/thymine, hypoxanthine/cytosine and 6-thiopurine/5-methyl-2-pyrimidinone with T7 DNA polymerase

With the goal of constructing a genetic alphabet consisting of a set of three base pairs, the fidelity of replication of the three base pairs T(H) (5-methyl-2-pyrimidinone)/H(S) (6-thiopurine; thiohypoxanthine), C/H (hypoxanthine) and T/A was evaluated using T7 DNA polymerase, a polymerase with a strong 3'-->5' exonuclease activity. An evaluation of the suitability of a new base pair for replication should include both the contribution of the fidelity of a polymerase activity and the contribution of proofreading by a 3'-->5' exonuclease activity. Using a steady-state kinetics method that included the contribution of the 3'-->5' exonuclease activity, the fidelity of replication was determined. The method determined the ratio of the apparent rate constant for the addition of a deoxynucleotide to the primer across from a template base by the polymerase activity and the rate constant for removal of the added deoxynucleotide from the primer by the 3'-->5' exonuclease activity. This ratio was designated the eni (efficiency of net incorporation). The eni of the base pair C/H was equal to or greater than the eni of T/A. The eni of the base pair T(H)/H(S) was 0.1 times that of A/T for T(H) in the template and 0.01 times that of A/T for H(S) in the template. The ratio of the eni of a mismatched deoxynucleotide to the eni of a matched deoxynucleotide was a measure of the error frequency. The error frequencies were as follows: thymine or T(H) opposite a template hypoxanthine, 2x10(-6); H(S) opposite a template cytosine, <3x10(-4). The remaining 24 mismatched combinations of bases gave no detectable net incorporation. Two mismatches, hypoxanthine opposite a template thymine or a template T(H), showed trace incorporation in the presence of a standard dNTP complementary to the next template base. T7 DNA polymerase extended the primer beyond each of the matched base pairs of the set. The level of fidelity of replication of the three base pairs with T7 DNA polymerase suggests that they are adequate for a three-base-pair alphabet for DNA replication.

Ab initio study on tautomerism of 2-thiouracil in the gas phase and in solution

Ab initio geometry optimizations were carried out at the HF/3-21G and HF/6-31+G** levels for the six tautomeric forms of 2-thiouracil (2TU, 2TU1, 2TU2, 2TU3, 2TU4, 2TU5) in the gas phase and in solution. To obtain a more definitive estimate of the relative stabilities for 2-thiouracil tautomers in the gas phase, single-point MP2/6-31+G** calculations were performed on the HF/6-31+G** optimized geometries. The tautomeric equilibria in 1,4-dioxane (epsilon = 2.21), acetonitrile (epsilon = 38), and in water (epsilon = 78.54) were studied using the self-consistent reaction field (SCRF) theory. The calculated relative free energies indicated that 2TU is the energetically preferred tautomer in the gas phase and in solution. The stability order of 2-thiouracil tautomers depends on the level of theory and the dielectric constant of the solvent. The obtained results are compared with the available experimental data.

On the structure of poly d(A-S4T)

The helical twist of poly d(A-s4T) was determined from the periodicity of the cleavage patterns of the double stranded polydeoxynucleotide adsorbed on calcium phosphate and found to be 14 bp per turn. Both cleavage patterns and 31P NMR spectra indicate a mononucleotide structure rather than an alternating B DNA like poly d(A-T). The failure of nucleosome formation excludes a B type structure. The discrepancy of the mononucleotide structure found in 31P NMR spectra and the dinucleotide structure given by X ray fiber diffraction is explained by an alternating tilt of the planes of the base pairs (base roll) as a consequence of a strong propeller twist. The importance of interstrand stacking interactions of adjacent 4-thiothymidines for the helical stability is discussed.