Copolymers containing alternating sequences of nucleic acid base pairs. III. Spectroscopic studies

A study was conducted of the complementary base pair interactions between various pairs of electron-donor monomers, electron-acceptor monomers, homopolymers and alternating copolymers selected from the following group: ( 1 ) 9-(2-vinyloxyethyl)adenine; ( 2 ) 1-(2-vinyloxyethyl)thymine; ( 3 ) 1-(2-vinyloxyethyl)cytosine; ( 4 ) 9-(2-maleimidoethyl)adenine; ( 5 ) 6-chloro-9-(2-maleimidoethyl)purine; ( 6 ) 1-(2-maleimidoethyl)thymine; ( 7 ) 1-(2-maleimidoethyl)cytosine; ( 8 ) homopolymer of ( 4 ); ( 9 ) homopolymer of ( 6 ); ( 10 ) alternating copolymer of ( 2 ) and maleic anhydride; ( 11 ) alternating copolymer of ( 2 ) and ( 5 ); and ( 12 ) alternating copolymer of ( 2 ) and ( 4 ). By ¹H-NMR, in CDCL₃, the base pair interactions between ( 1 ) and ( 2 ) were shown to be hydrogen bonding, the extent of which was shown by a calculated binding constant, K = 61.81 L/mol. The nature of this interaction was conformed by IR. Neither monomer pairs ( 1 )/( 2 ) nor ( 4 )/( 6 ) exhibited hydrogen bonding in DMSO-d₆. However, hydrogen bonding interaction was observed for DMSO-d₆ solutions of homopolymers ( 8 ) and ( 9 ) and for alternating copolymer ( 12 ). On the basis of an upfield chemical shift of the 2- and 8-aromatic protons of ademine of ( 1 ) in D₂O, a partial overlap stacking interaction is proposed. No charge-transfer interactions could be observed by UV between donor-acceptor monomer pairs.     

Functional monomers and polymers. CII. Synthesis and properties of oligomer models of polyethyleneimine derivatives containing pendant adenine bases

A series of oligomer model compounds of polyethyleneimine derivatives with pendant adenine bases were prepared by the reaction of a carboxyethyl derivative of adenine with oligomeric amines, using an activated ester method. To evaluate the intramolecular interaction between pendant adenine bases in these compounds, ultraviolet spectra at various pH regions were measured. Ultraviolet hypochromicities and pK_a values depended linearly on the chain length of the oligomers. The results showed that the intramolecular interactions of adenine bases were realized less in their protonated than neutral forms.     

Proton,phosphorus and carbon nuclear magnetic relaxation studies on the interaction of poly(riboadenylic acid) with Cu2+

Interaction between poly(riboadenylic acid) (poly(A)) and Cu²⁺ in neutral aqueous (D₂O) solution has been studied by ¹H, ³¹P, and ¹³C nuclear magnetic resonance. electron-nuclear hyperfine coupling constant and apparent electron-nuclear distances were determined by measurement of T₁ and T₂ values as a function of temperature. The apparent distance from Cu²⁺ to H(2), H(8), H(1′), and phosphorus nuclei were estimated to be 4.1, 3.7, 5.1, and 3.1 Å from these results. Cu²⁺ was found to coordinate directly to the phosphate groups of poly(A) (Type I complex). Simultaneously there are bindings of Cu²⁺ directly to one of the nitrogen atoms of adenine ring, mainly to N(7) (Type II complex) and either N(1) or N(3) (Type III complex).     

Supramolecular hydrogen‐bonded networks in adeninediium hemioxalate chloride and adeninium semioxalate hemi(oxalic acid) monohydrate

In 9H‐adenine‐1,7‐diium hemioxalate chloride, C₅H₇N₅²⁺·0.5C₂O₄²⁻·Cl⁻, (I), adenine is doubly protonated, while in 7H‐adenin‐1‐ium semioxalate hemi(oxalic acid) monohydrate, C₅H₆N₅⁺·C₂HO₄⁻·0.5C₂H₂O₄·H₂O, (II), adenine and one oxalate anion are both monoprotonated. In (I), the adeninium cation forms R₂²(8) and R₁²(5) hydrogen‐bonding motifs with the centrosymmetric oxalate anion, while in (II), the cation forms R₂¹(6) and R₁²(5) motifs with the centrosymmetric oxalic acid molecule and R₁²(5)and R₂²(9) motifs with the monoprotonated oxalate anion. Linear hydrogen‐bonded trimers are observed in (I) and (II). In both structures, the hydrogen bonds lead to the formation of two‐dimensional supramolecular hydrogen‐bonded sheets in the crystal packing. The significance of this study lies in the analysis of the interactions occurring via hydrogen bonds and the diversity seen in the supramolecular hydrogen‐bonded networks as a result of such interactions.     

Application of Elimination Voltammetry to the Resolution of Adenine and Cytosine Signals in Oligonucleotides. I. Homo‐oligodeoxynucleotides dA9 and dC9

Elimination voltammetry with linear scan (EVLS) has been applied to the resolution of reduction signals of adenine and cytosine in short synthetic homo‐oligodeoxynucleotides (dA₉ and dC₉). In comparison with the common electrochemical methods (linear sweep, differential pulse, and square‐wave voltammetry) EVLS enables one to resolve the overlapped signals by using the function which eliminates the charging and kinetic currents (I_c, I_k) and conserves the diffusion current (I_d). For the adsorbed electroactive substance, this elimination function gives a good readable peak‐counterpeak which has successfully been utilized to the analysis of overlapped reduction signals of adenine and cytosine on hanging mercury drop electrode (HMDE). The height and potential of signals studied were affected by the dC₉/dA₉ ratio, the time of accumulation, the stirring speed during the adsorption, and pH. Our results showed that EVLS in connection with the adsorption procedure is a useful tool for qualitative and quantitative studies of short oligonucleotides.     

Voltammetric and Differential Pulse Stripping Study of Adenine on a Sol‐gel Derived Carbon Composite Electrode

This communication reports on the electrochemical investigation of adenine on a sol‐gel carbon composite electrode (CCE). Cyclic voltammetric (CV) technique is used to characterize the redox behavior of adenine at CCE. The peak current and peak potentials are dependent on the pH of the buffer solution. From the scan rate and peak current study, there is evidence of adsorption of adenine on the CCE. The parameters affecting the differential pulse stripping adsorption peak were systematically optimized. Under optimum conditions of E_acc=?0.10 and t_acc=60 s, a linear calibration plot was obtained, 2×10^?7–1×10^?6 M. This CCE is useful for the simultaneous analysis of adenine and guanine from denatured DNA.     

The adenine ring influences the adenosine 5′-triphosphate hydrolysis

DFT calculations (ωB97X-D) of the adenosine 5′-triphosphate (ATP) hydrolysis were carried out. Four reactions (A), (B), (C), and (D) were investigated. Reaction (A) is of the acid catalysis and (B) is of the Mg²⁺ one with (H₂O) _n, n = 5, 11, and 17. (C) is of the myosin-model catalysis, and (D) is of the F₁-ATPase one. Transition states were determined precisely. For reaction (A), the experimental activation energy was reproduced well by the n = 11 and 17 models. For the Mg²⁺-containing hydrolysis, (B), 2 reactions (a) [without the Mg²⁺-adenine linkage] and (b) [with the connection] were examined and were compared. The reaction (b) was found to be more likely than (a) in both total and activation energies. The adenine ring works to enhance the polarity of transition states. For the myosin catalyzed (C) and in F₁-ATPase (D) hydrolyses, again, the reaction (b) is much more likely than (a). The proton transfer from the lytic water molecule leads to the protonation of the carboxylate of Glu459 in (C). The adenine ring was suggested to influence and promote the ATP hydrolysis.     

Carbocyclic Analogs of Nucleosides. Part 3. Synthesis of a new sulfone analog of cyclic adenosine 3′,5′-monophosphate

The novel uncharged analog 2 of adenosine 3′,5′ -monophosphate (1) was prepared in its racemic form. To increase membrane permeability, the phosphate diester monoanion group of 1 was replaced by a dimethylene sulfone unit ( = methanosulfonylmethano group), and the 2′-OH group was removed. To decrease lability against acid-catalyzed depurination, the ring O-atom was replaced by a CH₂ group. All three modifications are also expected to increase the stability of analog 2 towards enzymatic degradation. The carbocyclic skeleton of 2 was constructed from trinorbornenecarbaldehyde 3 (see Scheme 1–3), and the adenine precursor 6-chloropurine was introduced in the carbocyclic unit via an S_N2 reaction based on Mitsunobu chemistry (Schemes 4 and 5).     

Functional monomers and polymers. XIX. Copolymerization of vinyl monomers containing nucleic acid bases

Taking into account the specific base–base interaction existing between nucleic acid molecules, we studied the free-radical copolymerization of N-β-methacryloyloxyethyl derivative of uracil with that of adenine at 60°C in various solvents. N-β-Methacryloyloxyethyltheophylline as well as methyl methacrylate were used also as comonomers. From the data on the rates in different comonomer feed ratios and the r₁ and r₂ values obtained, copolymerizability was discussed in some detail. The results suggest that the interaction between uracil and adenine bases plays a role in the copolymerization behavior.     

N7-DNA: Synthesis and Base Pairing of Oligonucleotides containing 7-(2-Deoxy-β -D-erythro-pentofuranosyl)adenine (N7Ad)

The synthesis of oligonucleotides containing 7-(2-deoxy-β -D -erythro-pentofuranosyl)adenine (N⁷A_d; 1 ) is described. Compound 1 was obtained from the precursor 4-amino-1H -imidazole-5-carbonitrile 2-deoxyribonucleoside 6 and was found to be much more labile than A_d. The N⁶-benzoyl protecting group (see 8 ) destabilized the N-glycosylic bond further and was difficult to remove by NH₃-catalyzed hydrolysis. Therefore, a (dimethyl-amino)methylidene residue was introduced (→ 9 ). Amidine 9 was blocked at OH? C(5′) with the dimethoxytrityl residue ((MeO)₂Tr), and phosphonate 4 as well as phosphoramidite 5 were prepared under standard conditions. Phosphonate 4 was employed in solid-phase oligonucleotide synthesis. Homooligonucleotides as well as self-complementary oligonucleotides were prepared. The oligomer d[(N⁷A)₁₁-A] ( 11 ) formed a duplex with d(T₁₂) ( 13 ). Antiparallel chain polarity and reverse Watson-Crick base pairing was deduced from duplex formation of the self-complementary d[(N⁷A)₈-T₈] ( 14 ).     

Sensitive determination of adenine on poly(amidosulfonic acid)-modified glassy carbon electrode

A novel and reliable direct electrochemical method was established for the detection of adenine, based on the differential pulse anodic stripping response at a poly(amidosulfonic acid) (poly-ASA)-modified glassy carbon electrode (GCE) fabricated by electropolymerization. The characterization of electrochemically synthesized poly-ASA film was investigated by atomic force microscopy, electrochemical impedance spectroscopy, and voltammetric methods. This poly-ASA-modified GCE could greatly enhance the detection sensitivity of adenine. At optimum conditions, the anodic peak exhibits a good linear concentration dependence in the range from 3.0 × 10⁻⁸ to 1.0 × 10⁻⁶ M (r = 0.9994). The detection limit is 8.0 × 10⁻⁹ M (S/N = 3). The proposed method could be used to determinate the adenine in tablets of vitamin B₄ with satisfactory results.     

<Superscript>13</Superscript>C-n.m.r. studies of the binding of 1,3-diazinane-2-selenone and 1,3-diazipine-2-selenone to gold(I) drugs

The interaction of gold(I) thiomalate, Myocrisin [(Autm)_n] with 1,3-diazinane-2-selenone (DiazSe) and 1,3-diazipine-2-selenone (DiapSe) has been studied in aqueous solution using ¹³C-n.m.r. spectroscopy. It is observed that ternary complexes, (DiazSe–Au–tm and DiapSe–Au–tm, respectively) are formed on coordination of these ligands to (Autm)_n. The ¹³C-n.m.r. data suggest that DiapSe binds more strongly to (Autm)_n than does DiazSe, which binds more strongly compared to its analogous thione, 1,3-diazinane-2-thione (Diaz). A similar observation was made for the gold(I) thioglucose (Autg) reaction with DiazSe.     

Deoxy-nitrosugars. 17th communication. Synthesis of ketose-derived nucleosides from 1-deoxy-1-nitroribose

A new approach to ketose-derived nucteosides is described. It is based upon a chain elongation of 1-deoxy-1-nitroaldoses, followed by activation of the nitro group as a leaving group, and introduction of a pyrimidine or purine base. Thus, the nitroaldose 7 was prepared from 3 by pivaloylation (→ 4 ), synthesis of the anomeric nitrones 5/6 , and ozonolysis of 6 (Scheme 1). Partial hydrolysis of 4 yielded 8/9 , which were characterized as the acetates 10/11 and transformed into the nitrones 12/13 . Ozonolysis of 12/13 gave 14/15 , which were acetylated to 16/17 . Henry reaction of 7 lead to 19 and 20 , which were acetylated to 21 and 22 (Scheme 2). Michael addition of 7 to acrylonitrile and to methyl propynoate yielded the anomers 23/24 and 25/26 , respectively. Similar reactions of 16/17 were prevented by a facile β-elimination. Therefore, the nitrodiol 15 was transformed into the orthoesters 27 and then, by Henry reaction, partial hydrolysis, and acetylation, into 28 and 29 (Scheme 2). The structure of 19 was established by X-ray analysis. It was the major product of the kinetically controlled Henry reaction of 7 . Similarly, the β-D-configurated nitroaldoses 23 and 25 were the major products of the Michael addition. This indicates a preferred ‘endo’-attack on the nitronate anion derived from 7 . AMI calculations for this anion indicate a strong pyramidalization at C(1), in agreement with an ‘endo’-attack. Nucleosidation of 21 by 31 afforded 32 and 33 . Yields depended strongly upon the nature and the amount of the promoter and reached 77% for 33 , which was transformed into 34 , 35 , and the known ‘psicouridine’ ( 36 ; Scheme 3). To probe the mechanism, the trityl-protected 30 was nucleosidated yielding 37 , or 37 and 38 , depending upon the amount of FeCl₃. Nucleosidation of the nitroacetate 28 was more difficult, required SnCl₂ as a promoter, and yielded 39 and 40 . The β-D-anomer 40 was transformed into 36 . Nucleosidation of 23 (SnCl₄) yielded the anomers 41 and 42 , which were transformed into 43 and 44 , and hence into 45 and 46 (Scheme 4). Similarly, nucleosidation of 25 yielded 47 and 48 , which were deprotected to 49 and 50 , respectively. The nucleoside 49 was saponified to 51 . Nucleosidation of 21 by 52 (SnCl₂) afforded the adenine nucleosides 53 and 54 (Scheme 5). The adenine nucleoside 53 was deprotected (→ 55 → 56 ) to ‘psicofuranine’ (1), which was also obtained from 58 , formed along with 57 by nucleosidation of 28 . The structure and particularly the conformation of the nitroaldoses, nitroketoses, and nucleosides are examined.     

Force field for platinum binding to adenine

The antitumor drug cis-diamminedichloroplatinum(II) (cisplatin) binds preferentially to GpG and ApG sequences of DNA, forming N7,N7 intrastrand chelates. Molecular modeling of the intrastrand adducts have been handicapped, so far, by the lack of force-field data describing the Pt–guanine and Pt–adenine binding. We used ab initio calculations with relativistic pseudopotentials to evaluate three important parameters for the platinum–adenine model complex [Pt(NH₃)₃(Ade)]²⁺: (1) the force constant for the Pt? N7 bond bending out of the adenine plane; (2) the energy profile for the torsion about Pt? N7; (3) a set of fractional atomic charges that reproduce the ab initio potential for a number of space points placed around the adduct. A population analysis and comparative study on the tetrammine complex [Pt(NH₃)₄]²⁺ have shown that for platinum adenine is a better σ-donor than NH₃, but its capacity as a π-acceptor is weak. © 1993 John Wiley & Sons, Inc.     

Electron-transfer polymers. XXIX. Copolymerizability of vinylhydroquinone derivatives

Ten vinylhydroquinone and one vinyl resorcinol derivatives are compared, particularly with respect to NMR spectra and copolymerizability with styrene. They are vinylhydroquinone dimethyl ether (I), vinyl-O,O′-bis(1-ethoxyethyl)hydroquinone (II), vinylhydroquinone di(2-pentyl)ether (III), 4-vinyl resorcinol bismethoxymethyl ether (IV), 2-vinyl-5-methylhydroquinone dimethyl ether (V), 2-vinyl-5-methyl-O,O′-bis(1-ethoxyethyl)hydroquinone (VI), 2-vinyl-6-methylhydroquinone dimethyl ether (VII), 2-vinyl-5-tert-butylhydroquinone dimethyl ether (VIII), 2-vinyl-5-chlorohydroquinone dimethyl ether (IX), 2-vinyl-3,6-dimethylhydroquinone dimethyl ether (X), and 2-vinyl-3,5,6-trimethylhydroquinone dimethyl ether (XI). All the vinyl protons have almost the same coupling constants. Though subtle distinctions are found among all the spectra, they can in general be put into two groups on the basis of the chemical shifts. Let the hydrogen on carbon-1 of the vinyl group be A, the hydrogen cis to A be B the hydrogen trans to A be C, then in the first group, (I) through (IX), the chemical shifts (τ) are (A) 3.02 ± 0.08, (C) 4.41 ± 0.05, and (B) 4.87 ± 0.07, and in the second group, (X) and (XI), they are (A) 3.30 ± 0.03, (C) 4.49 ± 0.01, and (B) 4.59 ± 0.03. It is supposed that in (X) and (XI) the vinyl group is out of the plane of the ring, because of the two ortho substituents, and this conformation is reflected in the NMR data. Ultraviolet spectra are consonant with this interpretation, since the λ_max of (X) and (XI) correspond closely with those of nonvinyl reference compounds, while those of (II), (V), and (VIII) are shifted to longer wavelengths. When these compounds are copolymerized separately with styrene, the behaviors are classifiable into the following three groups, where r₁ and r₂ are monomer reactivity ratios with styrene as the first monomer: (i) r₁ < 1 and r₂ < 1 for compounds (II) and (III) and the reference compound O,O′-dibenzoylvinylhydroquinone, (ii) r₁ < 1 and r₂ > 1 for compounds (I), (V), (VII), (VIII), (IX), and (iii) r₁ > 1 and r₂ = 0 for compounds (X) and (XI). These behaviors are correlated with the effect of electronegativity of groups on the stability of the radical at the growing end of the chain and with the simultaneous effects of steric hindrance.     

Density functional theory study on hydrogen‐bonded complexes of adenine with polyformamide molecules

The structures of hydrogen‐bonded complexes A–F_n (n = 2–7) of adenine with polyformamide molecules have been fully optimized at B3LYP/6‐31G(d) basis set level. All the formamide molecules prefer to be N? H proton donor rather than C? H proton donor and are favorably bound to the five‐numbered moiety of adenine. A displacement of formamide molecules to one side of adenine mean plane has happened with an increasing number of formamide molecules. An obvious effect of hydrogen‐bonding cooperativity can be seen during the complex process. The most interesting geometrical change of adenine upon the complex is the shortening of the bond C4? N6 resulting from the strengthening of the conjugation between the π system of the adenine ring and the lone pair of the nitrogen atom. An existence of weak N? H···π bonding interaction between the π system of adenine and N? H bond of F7 is found and further conformed by an natural bond orbital analysis specially carried out on A–F₇. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Functional monomers and polymers. XXXXVI. A copolymerization study of methacryloyl-type monomers containing nucleic acid bases in chloroform solution

Behavior of the free radical copolymerization of N-β-methacryloyloxyethyl derivatives of adenine with that of thymine was studied in chloroform solution, taking account of the specific base-base interaction of these monomers. Hydrogen bonding interaction between such monomers was observed by NMR spectroscopy. The acceleration of copolymerization was found to be greater either at lower monomer concentration or at lower polymerization temperature. When N-β-methacryloyloxyethylcarbazole was used as a comonomer, the rate of copolymerization showed a similar trend as in the case of usual free radical copolymerizations. From r₁ and r₂ values obtained, the copolymerization was found to be alternating, particularly in the case of copolymerization between monomers having complementary nucleic acid bases. The results suggest that the hydrogen bonding interaction between adenine and thymine plays a role in the propagation step.     

Multifunctional coupling agents for living cationic polymerization. I. Sodiomalonate anions for vinyl ethers

A series of multifunctional malonate anions, [Na^⊕?C(COOEt)₂CH₂]_mC₆H_6?m(I; m = 2–4), were examined as polymer coupling agents for the living cationic polymerization of vinyl ethers initiated with the hydrogen iodide/zinc iodide (HI/ZnI₂) initiating system. The bifunctional anion ( 2 ;I, m = 2), 1,4-[Na^⊕?C(COOEt)₂CH₂]₂C₆H₄, terminated living polymers of isobutyl vinyl ether (IBVE) (DP _n = 10) almost quantitatively in toluene at ?15°C to give coupled living polymers with doubled molecular weights in 96% yield; the dianion 2 was dissolved in tetrahydrofuran containing 18-crown-6 for maintaining the solution homogeneous. The yield of the coupled polymers was increased with shorter living chains or in less polar solvents. Also by coupling via 2 , ABA block copolymers were obtained from living AB block polymers of IBVE and an ester-functionalized vinyl ether (CH₂?CHOCH₂CH₂OCOCH₃). Coupling of living poly(IBVE) with the trifunctional anion ( 3 ; I, m = 3) led to tri-armed polymers in 56% yield, whereas with the tetrafunctional version ( 4 ; I, m = 4), only three out of the four anions reacted to give another tri-armed polymer in 85% yield. © 1993 John Wiley & Sons, Inc.     

Reactivity and gelation. II. Substitution effect

The development in Paper I is extended to multifunctional condensations where the functional groups exhibit unequal reactivities induced by substitution effects in the course of the polymerization. A system R(A)₂/R′(B)₃ is examined to determine how the gel point varies with the strength and positive or negative sense of the substitution effect. As in Paper I, intramolecular interactions are not considered.     

Application of Elimination Voltammetry to the Resolution of Adenine and Cytosine Signals in Oligonucleotides II. Hetero‐Oligodeoxynucleotides with Different Sequences of Adenine and Cytosine Nucleotides

Elimination voltammetry with linear scan (EVLS) was applied to the resolution of reduction signals of adenine (A) and cytosine (C) residues in short synthetic hetero‐oligodeoxynucleotides (ODNs) with different sequences of A and C. The EVLS evaluation required linear sweep voltammograms measured on a hanging mercury drop electrode (HMDE) at different scan rates. Compared to linear sweep voltammetry (LSV) and usual voltammetric methods the EVLS is capable of resolving the overlapped A and C signals, specifically by using the elimination function which eliminates the charging and kinetic currents (I_c, I_k) and conserves the diffusion current (I_d). Since for an adsorbed electroactive substance this elimination function yields a well readable peak–counterpeak signal, the adsorptive stripping (AdS) procedure was favorably used. The adsorption of ODNs was carried out at ?0.1 V for accumulation time of 120 s under stirring. It was found that heights and potentials of LSV signals were affected by ODNs concentrations, pH, scan rates, time of accumulation, and stirring speed during the adsorption. While on LSV curves the only one reduction peak of A and C residues was observed in all ODNs, the EVLS yielded two separated peaks in dependence on A, C sequences and pH. Our results showed that the EVLS in connection with the AdS procedure is a useful tool for qualitative and quantitative studies of short ODNs and a promising sensitive method for the development of electrochemical sensor following the ODN sequences.