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At least 19 recordsLinked to original sources
PubMed2000

[Synthesis and properties of photolabile caged phosphotriester derivatives of dinucleoside phosphates].

Dinucleoside phosphates that harbor phosphate groups transiently blocked (caged) by o-nitrobenzyl or o-nitroveratryl residues were synthesized. It was shown that the conditions of the UV-induced deprotection largely depend on the nature of the protective group. The phosphotriesters obtained were resistant toward snake venom phosphodiesterase and nucleases of the cellular extract. The synthesis of the dinucleoside phosphates containing a photolabile group preceded the incorporation of the modified blocks into extended oligonucleotides by the phosphoramidite method.

Dinucleoside Phosphates↗
PubMed1977

Studies of the conformation of modified dinucleoside phosphates containing 1,N6-ethenoadenosine and 2'-O-methylcytidine by 360-MHz 1H nuclear magnetic resonance spectroscopy. Investigation of the solution conformations of dinucleoside phosphates.

Seven dinucleoside monophosphates containing epsilonA (1,N6-ethenoadenosine) and 2'-O-methylcytidine were studied by 360-MHz proton magnetic resonance and compared with unmodified dimers and component monomers at 4, 20, 45, and 75 degrees C. These studies show that the dimers exhibit preference for the gg and g'g' conformations for the C-4'-C-5' and C-5'-O-5' bonds, respectively, and that dimerization induces an increase of the population and inflexibility of the 3'-endo conformations for the ribose ring. Three stacked (or stable) conformations for dimers, I, II, and III, in equilibrium with an unstacked (or open) form in solution, are suggested by dimerization shifts of ribose protons. Conformation I exhibits anti, gg, 3'-endo, phi' = 203 to approximately 211 degrees, omega' = 300 degrees, omega = 290 degrees, g'g', gg, 3'-endo, and anti conformation from the 5' end to the 3' end of the dimer. Conformation II shows anti, gg, 3'-endo, phi' = 203-211 degrees, omega = 30 degrees, omega = 100 degrees, g'g', gg, 3'-endo, and anti conformation. Conformation III is anti, gg, 2'-endo, phi' = 260 degrees, omega' = 50 degrees, omega = 220 degrees g'g', gg, 3'-endo, and anti (x approximately 100 degrees) conformation. The dimers, PupPu and PupPy, prefer conformations I and II, while PypPu and PypPy prefer conformation II. Introduction of epsilonA for the base of -pN induces an increase of conformations II and III, while the epsilonA substitution for the Np- residue induces an increase of conformation I. 2'-O-methylation of the Cp- residue of CpC decreases conformation I and increases conformation II. Based on the stable solution conformations of these dimers, a possible conformation of the anticodon loop is proposed, which is an alternative to the one observed in the crystal of tRNAPhe.

Adenosine↗
PubMed1979

Conformations of dinucleoside phosphates in aqueous solution.

The conformations of dinucleoside phosphates have been reexamined by semiempirical potential energy calculations. Conformations I, II, and III, proposed by Lee & Tinoco [Lee, C. H., & Tinoco, I., Jr. (1977) Biochemistry 16, 5403], are possible species after refinement of their structures by potential energy minimization. These three conformers can represent three types of dinucleoside phosphate species in solution. Dhingra et al. [Dhingra, M. M., Sarma, R. H., Giessner-Prettre, C., & Pullman, B. (1978) Biochemistry 17, 5815] had concluded that conformations of type II and III were unlikely or impossible. They favored conformations g-g- (equivalent to I), g+g+,g+t, and tg+; the last three conformations have little stacking and are calculated to be energetically less favorable by more than 5 kcal/mol. Common structures of the types I, II, and III are found for dinucleoside phosphates with different purine-pyrimidine sequences. The sequence dependence of the potential energy of these three conformers has been calculated. The experimental nuclear magnetic resonance data of dinucleoside phosphates are consistent with these three conformations.

Calorimetry↗
PubMed1985

Stereoelectronic effects in RNase-catalysed reactions of dinucleoside phosphate cleavage.

The rate at which dinucleoside phosphates are cleaved by RNases is supposed to be determined by the mole fraction of enzyme-substrate complexes in which the phosphodiester moiety of a dinucleoside phosphate has a highly reactive conformation. The mole fraction of such complexes for a particular RNase depends on the nature of a nucleoside at the O5'-end of the phosphodiester bond. Experimental data are presented to support this hypothesis.

Dinucleoside Phosphates↗
PubMed1981

A molecular mechanical study of complexes formed between 4-nitroquinoline-N-oxide and dinucleoside phosphates.

Molecular mechanical calculations were done on complexes of 4-nitroquinoline-N-oxide (NQO) with various dinucleoside phosphates [(ApT)2, (CpG)2, (GpC)2, and (TpA)2]. Models built using proflavine (uniform C3' endo sugar puckers) and acridine orange (mixed C3' endo (3'-5') C2' endo sugar puckers) dinucleoside phosphate X-ray structures were used in the calculations. Relative binding energies, complex geometries, and various intercalator orientations in the complexes were studied. The results suggest qualitatively different geometries for pyr-(3'-5')-pur and pur-(3'-5')-pyr sequences. Specifically, we find marked distortion in some of the complexes (i.e. there is not a parallel coplanar relationship between the base pairs and intercalator), distortion of the NQO nitro group from planarity in the complexes and mobility of NQO in the intercalation site. We suggest that experimental studies of NQO-dinucleoside phosphate complexes may reveal intercalation complexes which deviate substantially more from a nearly parallel coplanar arrangement of bases and intercalator than has been previously observed.

4-Nitroquinoline-1-oxide↗
PubMed1993

Computer modeling studies on the binding of 2',5'-linked dinucleoside phosphates to ribonuclease T1-influence of subsite interactions on the substrate specificity.

The modes of binding of Gp(2',5')A, Gp(2',5')C, Gp(2',5')G and Gp(2',5')U to RNase T1 have been determined by computer modelling studies. All these dinucleoside phosphates assume extended conformations in the active site leading to better interactions with the enzyme. The 5'-terminal guanine of all these ligands is placed in the primary base binding site of the enzyme in an orientation similar to that of 2'-GMP in the RNase T1-2'-GMP complex. The 2'-terminal purines are placed close to the hydrophobic pocket formed by the residues Gly71, Ser72, Pro73 and Gly74 which occur in a loop region. However, the orientation of the 2'-terminal pyrimidines is different from that of 2'-terminal purines. This perhaps explains the higher binding affinity of the 2',5'-linked guanine dinucleoside phosphates with 2'-terminal purines than those with 2'-terminal pyrimidines. A comparison of the binding of the guanine dinucleoside phosphates with 2',5'- and 3',5'-linkages suggests significant differences in the ribose pucker and hydrogen bonding interactions between the catalytic residues and the bound nucleoside phosphate implying that 2',5'-linked dinucleoside phosphates may not be the ideal ligands to probe the role of the catalytic amino acid residues. A change in the amino acid sequence in the surface loop region formed by the residues Gly71 to Gly74 drastically affects the conformation of the base binding subsite, and this may account for the inactivity of the enzyme with altered sequence i.e., with Pro, Gly and Ser at positions 71 to 73 respectively. These results thus suggest that in addition to recognition and catalytic sites, interactions at the loop regions which constitute the subsite for base binding are also crucial in determining the substrate specificity.

Binding Sites↗
PubMedDate not supplied

[Oligonucleotides and their analogs. II. Spectra of the circular dichroism of dinucleoside phosphate analogs containing 4-thiouracil].

The dinucleoside phosphates analogues APpSU, SUPpA and UPpSU have been synthesised by direct thionation of DNP analogues, containing cytosine. The structure of compounds prepared was proved by UV- and PMR-spectra. The CD spectra of the DNP analogues were examined. It has been demonstrated that the "induced" dichroism contribution in the Cotton-effect of DNP was substantial in the case of stacking conformations and negligible for unstacking conformations.

Chemical Phenomena↗
PubMedDate not supplied

[Study of the flexibility of complementary dinucleoside phosphates by the Monte-Carlo method].

Monte-Carlo calculations have revealed a significant flexibility of the double stranded dinucleoside phosphates AA: TT, AT: AT, TA: TA, GG: CC, GC: GC and CG: CG within the limits of the B-family of forms. Fluctuations of the dihedral angles and of the phase angle of pseudorotation, P, have been found to be 5-20 degrees and 10-20 degrees respectively. The r.m.s. deviation of the helical winding angle varies from 3 degrees to 6 degrees for different dimers. The G: C-containing dimers proved to be more rigid that the A: T-containing ones, though the methyl groups of thymines take part in stabilization of AA: TT and AT: AT dimers. The propeller angles in A: T and G: C pairs are of opposite sing. The pyrimidine-(3'-5')-purine dinucleoside phosphates demonstrate the least stability. All the dimers proved to be more flexible when opened into both grooves than in perpendicular directions. Due to the greater value of the glycosidic angle in the 3'-monomer the base pairs are opened into the wide groove. A connection between opening of the base pairs and bending of the double helix for different nucleotide sequences has been discussed. This might be important for the DNA package in nucleosomes.

Base Composition↗
PubMed2005

Phenyl radicals react with dinucleoside phosphates by addition to purine bases and H-atom abstraction from a sugar moiety.

Laser-induced acoustic desorption combined with mass spectrometry has been used to demonstrate that phenyl radicals can attack dinucleoside phosphates at both the sugar and base moieties, that purine bases are more susceptible to the attack than pyrimidine bases, and that the more electrophilic the radical, the more efficient the damage to dinucleoside phosphates.

Benzene Derivatives↗
PubMed1992

Dissection of the ribonuclease T1 subsite. The transesterification kinetics of Asn36Ala and Asn98Ala ribonuclease T1 for minimal dinucleoside phosphates.

Ribonuclease T1 contains a subsite which by interacting with the leaving nucleoside N of GpN dinucleoside phosphate substrates, contributes to catalysis [Steyaert, J., Wyns, L. & Stanssens, P. (1991) Biochemistry 30, 8661-8665]. The Asn36Ala and Asn98Ala mutations reduce the transesterification rates of GpA, GpC and GpU considerably whereas they have virtually no effect on the transesterification kinetics of the synthetic substrate guanosine 3'-(methyl phosphate) (GpMe) (in which the leaving nucleoside is replaced by methanol), indicating that the Asn36 and Asn98 side chains are part of the RNase T1 subsite [Steyaert, J., Haikal, A. F., Wyns, L. & Stanssens, P. (1991) Biochemistry 30, 8666-8670]. The kinetics of the Asn36Ala, Asn98Ala and wild-type catalyzed transesterification of guanosine 3'-(5'-D-ribosyl phosphate) (GpRib), another GpN analog in which the leaving groups is replaced by D-ribose, enables the mapping of the subsite interactions provided by Asn36 and Asn98. We find that the Asn36 amide function contributes 4.6 kJ/mol to catalysis through interactions with the ribose moiety of the leaving nucleoside. Asn98 is at least in part responsible for the subsite preference for cytidine; the Asn98 side chain preferentially binds cytosine as the leaving nucleoside base.

Alanine↗
PubMedDate not supplied

[The circular dichroism spectrum of dinucleoside phosphate analogs].

Circular dichroism spectra of 11 analogues of the dinucleoside phosphate containing achiral 3'-terminal monomers have been measured at several pH values, various temperatures and various concentrations of ethanol. The conformation of analogues studied has been shown to by very similar to that of natural compounds. Comparison of the results obtained with the circular dichroism spectra of the corresponding natural compounds indicates that Cotton effect arises from monomeric circular dichroism, at least in main features. The exciton interaction is relatively small.

Chemical Phenomena↗
PubMed1978

5-Substituents in the uridine moiety and their effect on the conformation of ApU-type dinucleoside phosphates.

The ApU analogues ApT, Apcl5U, Apbr5U, Apa5U and Apno5(2)U were synthesized with the aid of ribonuclease U2 starting from 2',3'-cyclic Ap and the respective uridine derivatives. For these compounds the ultraviolet data, the difference spectra, the hypochromism and the temperature dependence of the CD spectra are reported. The dimerisation shifts of the pyrimidine protons which were obtained from the 100 MHz PMR spectra confirm the optical results. The influence of the substituents in the 5 position of the uracil ring on base-base interaction and the conformation of the dinucleoside phosphates is discussed with respect to the van der Waals radii and the electronic effects of these groups. As calculated from the hypochromism the dinucleoside phosphates can be arranged according to decreasing base-base interaction: Apno5(2)U greater than Apbr5U approximately ApT greater than Apcl5U greater than ApU greater than Apa5U.

Circular Dichroism↗
PubMedDate not supplied

[Nuclear magnetic resonance study of the conformational situation in an aqueous solution of dinucleoside phosphates].

The strategy of quantitative study of conformational situation in aqueous solutions of dinucleoside phosphates (DNP) has been proposed. It includes the following steps: (1) conformational calculation of stacking conformers (SC) of DNP; (2) measurement of thermodynamic parameters of conformational equililbrium; (3) determination of extensive parameters of stacking state (SS) on the basis of experimental data and thermodynamic parameters; (4) computation of extensive parameters of SC on the basis of the calculated geometry of SC and theoretical concepts of experimental method; (5) comparison of experimental parameters of SS with the calculated ones of SC to establish the SC participating in the equilibrium as well as its relative weights. This strategy was exemplified by ApA, ApC, CpA and CpC. The chemical shifts, spin-spin coupling constants and spin-lattice relaxation rates of DNP protons were used. The predominant SC was found to be related to Pba type with a large twirl angle (45-54 degrees) and almost parallel base planes. For all DNP the presence in equilibrium of left-handed forms was typical. These were Mab forms for ApA, Mbb forms for CpC and CpA, Mbb and Mab forms for ApC. About 10% of SS of ApA and CpA were presented by SC with trans-conformation of C(4')-C(5') bond of oN-part. The SC with C(3')-endo, C(3')-endo combination of ribose conformations were basic for ApA, ApC and CpA, and the only possible for CpC. In case of ApA, ApC and CpA the conformers with C(3')-endo, C(2')-endo sugar combination were presented.

Chemical Phenomena↗
PubMedDate not supplied

[Comparative conformational analysis of dinucleoside phosphate CpA and its analog C(3'NH)pA].

By the method of theoretical conformational analysis, on the examples of CpA and C(3'NH)pA comparison is made of conformational flexibility of dinucleoside phosphates with the natural O-P-O and abnormal N-P-O internucleotide bonds. The conformational flexibility of sugar cycles is accounted for. It is shown that substitution of the phosphodiester bond into amide ester leads to a noticeable limitation of favorable areas in conformational space of molecules and, as consequence, to the increase of the equilibrium ratio of conformers with the Pba and Mbb type of base stacking. The obtained results are used for discussion of the binding experiments of acylamino acid derivatives of CpA and C(3'NH)pA to the donor site of the peptidyl transferase center of ribosomes.

Adenosine↗
PubMedDate not supplied

[Theoretical investigation on the hypochromism of dinucleoside phosphates].

The hypochromism of stacked dimers of the nucleotide bases taken as models of the dinucleoside phosphates and dinucleotides was studied with the use of the configuration interaction and pertubation theory methods. General expression for the hypochromism of the polynucleotides is given in the first order perturbation theory with three different ways for approximation of the matrix elements of the perturbation operator. This expression was used for calculation of the dimer hypochromism in terms of theoretically calculated monomer characteristics. Dependence of the hypochromism on the dimer conformation was investigated. The results obtained so far demonstrate that it is important to take into account the electronic transitions in the vacuum UV region. This approach will enable one to elucidate the contribution of neighbouring bases into the DNA hypochromism.

Binding Sites↗
PubMedDate not supplied

[Conformation of dinucleoside phosphates: the conformation encoding hypothesis].

The temperature dependence of the spin-lattice relaxation rate of nucleic bases protones and HI' of ApA, ApC, CpA and CpC (D2O, pH 7) were measured. The possible closed conformers of these dinucleoside phosphates (DNP) were computed by atom-atom potential method. On the basis of conformational calculation and experimental data the composition of closed state was determined. Besides the right-handed "canonic" conformers, the "non-canonic" right- and left-handed conformers were shown to be present in the solution of all DNP studied. It is important to note that, "canonic" conformers of DNP studied being equally probable, the possibility of the realization of "non-canonic" conformers is determined by the nucleotide sequence. It may be expected that different nucleotide sequences have unique "non-canonic" conformations. That type of dependence of the spatial organization of polynucleotides on its nucleotide sequence we call "the conformational encoding".

Adenosine↗