Dipyrido[3,2-a:2′,3′-c]phenazine-Tethered Oligo-DNA: Synthesis and Thermal Stability of Their DNA⋅DNA and DNA⋅RNA Duplexes and DNA⋅DNA⋅DNA Triplexes

Dipyrido[3,2-a:2′,3′-c]phenazine (dppz) derivatives were conjugated to 9-mer and 18-mer DNA (ODN) at a site without nucleobase, either at the 5′- or 3′-end or at a internucleotide position, via linkers of 7, 12, or 18 atoms lengths. These dppz-linked ODNs were synthesized using novel backbone glycerol phosphoramidites: Glycerol, serving as artificial nucleoside without nucleobase, was modified to amines 10 , 23 , and 24 , which were suitable for the subsequent key reaction with dppz-carboxylic acid 3 (Schemes 2 and 3). The products of these reactions (see 5 – 7 ) were then transformed to the standard phosphoramidite derivatives (see 27 , 29 , and 30 ) or used for loading on a CPG support (see 28 , 31 , and 32 ). The dppz-modified ODNs were subsequently assembled in the usual manner using automated solid-phase DNA synthesis. The 9-mer ODN-dppz conjugates 35 – 43 were tested for their ability to form stable duplexes with target DNA or RNA strands (D11 ( 60 ) or R11 ( 61 )), while the 18-mer ODN-dppz conjugates 48 – 56 were tested for their ability to form stable triplexes with a DNA target duplex D24⋅D24 ( 62 ) (see Tables 1 and 2). The presence of the conjugated dppz derivative increases the stability of DNA⋅DNA and DNA⋅RNA duplexes, typically by a ΔT_m of 7.3 – 10.9° and 4.5 – 7.4°, respectively, when the dppz is tethered at the 5′- or 3′-terminal (Table 2). The dppz derivatives also stabilize triplexes when attached to the 5′- or 3′-end, with a ΔT_m varying from 3.8 – 11.1° (Table 3). The insertion of a dppz building block at the center of a 9-mer results in a considerably poorer stability of the corresponding DNA⋅DNA duplexes (ΔT_m=0.5 to 4.2°) and DNA⋅RNA duplexes (ΔT_m=−1.5 to 0.9°), while the replacement of one interior nucleotide by a dppz building unit in the corresponding 8-mer ODN does not reveal the formation of any duplex at all. Different types of modifications in the middle of the 18-mer ODN, in general, do not lead to any triplex formation, except when the dppz derivative is tethered to the ODN through a 12-atom-long linker (Entry 9 in Table 3).     

Nucleotides. Part XLV. Synthesis of new (2′–5′)adenylate trimers,containing 5′-amino-5′-deoxyadenosine residues at the 5′-end of the oligoadenylate chain,and of its analogues,carrying a 9-[(2-hydroxyethoxy)methyl]adenine residue at the 2′-terminus

The 5′-amino-5′-deoxy-2′,3′-O-isopropylideneadenosine ( 4 ) was obtained in pure form from 2′,3′-O-isopropylideneadenosine ( 1 ), without isolation of intermediates 2 and 3 . The 2-(4-nitrophenyl)ethoxycarbonyl group was used for protection of the NH₂ functions of 4 (→7) . The selective introduction of the palmitoyl (= hexadecanoyl) group into the 5′-N-position of 4 was achieved by its treatment with palmitoyl chloride in MeCN in the presence of Et₃N (→ 5 ). The 3′-O-silyl derivatives 11 and 14 were isolated by column chromatography after treatment of the 2′,3′-O-deprotected compounds 8 and 9 , respectively, with (tert-butyl)dimethylsilyl chloride and 1H-imidazole in pyridine. The corresponding phosphoramidites 16 and 17 were synthesized from nucleosides 11 and 14 , respectively, and (cyanoethoxy)bis(diisopropylamino)phosphane in CH₂Cl₂. The trimeric (2′–5′)-linked adenylates 25 and 26 having the 5′-amino-5′-deoxyadenosine and 5′-deoxy-5′-(palmitoylamino)adenosine residue, respectively, at the 5′-end were prepared by the phosphoramidite method. Similarly, the corresponding 5′-amino derivatives 27 and 28 carrying the 9-[(2-hydroxyethoxy)methyl]adenine residue at the 2′-terminus, were obtained. The newly synthesized compounds were characterized by physical means. The synthesized trimers 25–28 were 3-, 15-, 25-, and 34-fold, respectively, more stable towards phosphodiesterase from Crotalus durissus than the trimer (2′–5′)ApApA.     

Synthesis of nitrogen-containing heterocycles. 8. Preparation and ring-opening of spiro[cycloalkane-[1′,2′,4′]triazolo[1′,5′-c]pyrimidine] derivatives

Diaminomethylene- and aminomethylthiomethylenehydrazones [2] of cyclic ketones 1–8 readily reacted with ethoxymethylenemalononitrile to give spiro[cycloalkane-1,2′-[1,2′,4′]triazolo[1,5′-c]pyrimidine-8′-carbonitrile] derivatives 12–19 through the electrocyclic reaction of the initially formed condensation products 26 in moderate to high yields. The spiro[cyclopentanetriazolopyrimidine] derivatives underwent ring-opening at the cycloalkane moiety upon heating in solution to give 2-alkyl-5-substituted-[1,2,4]triazolo[1,5-c]pyrimidine-8′-carbonitriles 20–23 . When an alkyl substituent was introduced into the cyclopentane ring, cleavage of the spiro compounds occurred preferentially at the cyclopentane moiety between the spiro carbon and the more branched one. In contrast, the cyclohexane ring, especially of spiro-5-amino-triazolopyrimidines 17 and 18 strongly resisted to ring-opening under similar conditions, but those of 5-methylthiotriazolopyrimidines 14 gave up to 17 percent of cleavage after prolonged heating in hot ethanol. 2-t-Butyl-5-methylthio-2,3-dihydro[1,2,4]triazolo[1,5-c]pyrimidine-8-carbonitrile 25 [R³ = C(CH₃)₃] was highly susceptible to the cleavage even at room temperature and produced the corresponding 2-unsubstituted triazolopyrimidine 24 with loss of the t-butyl group.     

New Fluorinated Rhodamines for Optical Microscopy and Nanoscopy

New photostable rhodamine dyes represented by the compounds 1 a – r and 3 – 5 are proposed as efficient fluorescent markers with unique combination of structural features. Unlike rhodamines with monoalkylated nitrogen atoms, N′,N‐bis(2,2,2‐trifluoroethyl) derivatives 1 e , 1 i , 1 j , 3 ‐H and 5 were found to undergo sulfonation of the xanthene fragment at the positions 4′ and 5′. Two fluorine atoms were introduced into the positions 2′ and 7′ of the 3′,6′‐diaminoxanthene fragment in compounds 1 a – d , 1 i – l and 1 m – r . The new rhodamine dyes may be excited with λ=488 or 514 nm light; most of them emit light at λ=512–554 nm (compounds 1 q and 1r at λ=576 and 589 nm in methanol, respectively) and have high fluorescence quantum yields in solution (up to 98 %), relatively long excited‐state lifetimes (>3 ns) and are resistant against photobleaching, especially at high laser intensities, as is usually applied in confocal microscopy. Sulfonation of the xanthene fragment with 30 % SO₃ in H₂SO₄ is compatible with the secondary amide bond (rhodamine‐CON(Me)CH₂CH₂COOH) formed with MeNHCH₂CH₂COOCH₃ to providing the sterically unhindered carboxylic group required for further (bio)conjugation reactions. After creating the amino reactive sites, the modified derivatives may be used as fluorescent markers and labels for (bio)molecules in optical microscopy and nanoscopy with very‐high light intensities. Further, the new rhodamine dyes are able to pass the plasma membrane of living cells, introducing them as potential labels for recent live‐cell‐tag approaches. We exemplify the excellent performance of the fluorinated rhodamines in optical microscopy by fluorescence correlation spectroscopy (FCS) and stimulated emission depletion (STED) nanoscopy experiments.     

Synthesis of (5R)- and (5S)-5-Methyl-5, 6-dihydrouridine Derivatives

The hydrogenation of 2′, 3′-O-isopropylidene-5-methyluridine (1) in water over 5% Rh/Al₂O₃ gave (5 R)- and (5 S)-5-methyl-5, 6-dihydrouridine (2) , separated as 5′-O-(p-tolylsulfonyl)- (3) and 5′-O-benzoyl- (5) derivatives by preparative TLC. on silica gel and ether/hexane developments. The diastereoisomeric differentiation at the C(5) chiral centre depends upon the reaction media and the nature of the protecting group attached to the ribosyl moiety. The synthesis of iodo derivatives (5 R)- and (5 S)- 4 is also described. The diastereoisomers 4 were converted into (5 R)- and (5 S)-2′, 3′,-O-isopropylidene-5-methyl-2, 5′-anhydro-5, 6-dihydrouridine (7) .     

Synthesis and properties of novel soluble poly(amide‐imide)s with different pendant substituents

Two types of novel fluorinated diimide‐diacid monomers—[2,2′‐(4,4′‐(3′‐methylbiphenyl‐2,5‐diyl)bis(oxy)bis(3‐(trifluoromethyl)‐4,1‐phenylene))bis(1,3‐dioxoisoindoline‐5‐carboxylic acid)] (III) and [2,2′‐(4,4′‐(3′‐(trifluoromethyl)biphenyl‐2,5‐diyl)bis(oxy)bis(3‐(trifluoromethyl)‐4,1‐phenylene))bis(1,3‐dioxoisoindoline‐5‐carboxylic acid)] (IV)—were respectively designed and prepared by the condensation of diamines I and II with two molar equivalents of trimellitic anhydride. From both diimide‐diacids, two series of novel poly(amide‐imide)s (PAIs) (IIIa–IIIe and IVa–IVe) bearing different pendant groups were prepared by direct polymerization with various aromatic diamines (a–e). All the PAIs had a high glass transition temperatures (T_gs, 232–265 °C), excellent thermal stability (exhibiting only 5% weight loss at 493–542 °C under nitrogen) and good solubility in various organic solvents due to the introduction of the bulky pendant groups. The cast films of these PAIs (80–90 μm) had good optical transparency (73–81% at 450 nm, 85–88% at 550 nm and 87–89% at 800 nm) and low dielectric constants (2.65–2.98 at 1 MHz). The spin‐coated films of these PAIs presented a minimum birefringence value as low as 0.0077–0.0143 at 650 nm and low optical absorption at the near‐infrared optical communication wavelengths of 1310 and 1550 nm. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 3243–3252     

Green synthesis and crystal structure of 4,7‐diaryl‐2‐oxo(thio)‐1,2,3,4,5,6,7,8‐octahydroquinazoline‐5‐one derivatives

A green and convenient approach to the synthesis of novel 4,7‐diaryl‐2‐oxo(thio)‐1,2,3,4,5,6,7,8‐octahydroquinazoline‐5‐one derivatives from appropriate aromatic aldehydes and 5‐aryl‐1,3‐cyclohexanedione with urea or thiourea in the presence of dilute HCl as catalyst in water is described. This method provides several advantages such as environmental friendliness, low cost, high yields, and simple workup procedure. The structures of all compounds were characterized by elemental analysis, IR, MS, and ¹H NMR. The crystal and molecular structure of 4‐(4′‐chlorophenyl)‐7‐(4′‐methoxyphenyl)‐1,2,3,4,5,6,7,8‐octahydroquinazoline‐2,5‐dione 5m have been determined by single crystal X‐ray diffraction analysis. The crystal of compound 5m belongs to monoclinic with space group P‐2₁/c, a = 1.4353 (4) nm, b = 1.4011 (4) nm, c = 0.9248 (3) nm, α = 90.00°, β = 101.242 (6)°, γ = 90.00°, Z = 4, V = 1.8241 (9) nm³, R₁ = 0.0448, and wR₂ = 0.1022. J. Heterocyclic Chem., (2011).     

NIR‐Absorbing Donor–Acceptor Based 1,1,4,4‐Tetracyanobuta‐1,3‐Diene (TCBD)‐ and Cyclohexa‐2,5‐Diene‐1,4‐Ylidene‐Expanded TCBD‐Substituted Ferrocenyl Phenothiazines

A series of unsymmetrical (D‐A‐D₁, D₁‐π‐D‐A‐D₁, and D₁‐A₁‐D‐A₂‐D₁; A=acceptor, D=donor) and symmetrical (D₁‐A‐D‐A‐D₁) phenothiazines ( 4 b , 4 c , 4 c′ , 5 b , 5 c , 5 d , 5 d′ , 5 e , 5 e′ , 5 f , and 5 f′ ) were designed and synthesized by a [2+2] cycloaddition–electrocyclic ring‐opening reaction of ferrocenyl‐substituted phenothiazines with tetracyanoethylene (TCNE) and 7,7,8,8‐tetracyanoquinodimethane (TCNQ). The photophysical, electrochemical, and computational studies show a strong charge‐transfer (CT) interaction in the phenothiazine derivatives that can be tuned by varying the number of TCNE/TCNQ acceptors. Phenothiazines 4 b , 4 c , 4 c′ , 5 b , 5 c , 5 d , 5 d′ , 5 e , 5 e′ , 5 f and 5 f′ show redshifted absorption in the λ =400 to 900 nm region, as a result of a low HOMO–LUMO gap, which is supported by TD‐DFT calculations. The electrochemical study exhibits reduction waves at low potential due to strong 1,1,4,4‐tetracyanobuta‐1,3‐diene (TCBD) and cyclohexa‐2,5‐diene‐1,4‐ylidene‐expanded TCBD acceptors. The incorporation of cyclohexa‐2,5‐diene‐1,4‐ylidene‐expanded TCBD stabilized the LUMO energy level to a greater extent than TCBD.     

Synthesis,characterization, DNA binding studies and in vitro cytotoxicity of platinum(II)-dihalogenido complexes containing bidentate chelating N-donor ligands

Platinum(II) complexes, [Pt(L_x)X₂] (1–6), where X = Br or I and L_x = 2,2′-bipyridine or 1,10-phenanthroline derivatives (5,5′-dimethyl-2,2′-bipyridine (5-Mebpy), 4,4′-dimethyl-2,2′-bipyridine (4-Mebpy), and 5-amino-1,10-phenanthroline (5-NH₂phen)) were prepared. The complexes were characterized by the elemental analysis, mass spectrometry, infrared, and multinuclear (¹H, ¹³C and ¹⁹⁵Pt) 1-D and 2-D NMR spectroscopies, and by single-crystal X-ray analysis of [Pt(4-Mebpy)I₂] (4). All the platinum(II) complexes (1–6) were evaluated for in vitro cytotoxicity against human cancer cell lines A2780 and A2780R, and against non-malignant MRC5 cell line. All the complexes were nontoxic up to the 50 μM concentration, although they were found to readily bind to calf-thymus DNA (CT-DNA), as determined by spectrophotometric titration (K_b ≈ 10⁷ M^?1) and ethidium bromide displacement assay.     

Fluorescent tricyclic β-azavinamidine–BF2 complexes

Boron trifluoride reacted with dipyrid-2-ylamine 6 , its N-methyl and 6,6′-dimethyl derivatives 8 and 10 , and 3,3′,5,5′-tetraphenyl-6-azapyrromethene 13 to give fluorescent β-azavinamidine (1,3,5-triazapenta-1,3-diene) dyes: 10-azapyridomethene–BF₂ complex 5 (λ_f 422 nm, λ_las 426 nm), its quaternary 10-methyl tetrafluoroborate and 4,6-dimethyl derivatives 9 (λ_f 362 nm) and 11 (λ_f 416 nm), and 1,3,5,7-tetraphenyl-8-azapyrromethene–BF₂ complex 17 (λ_f 696 nm). Treating 3,3′,4,4′-tetraphenyl-5,5′,6-trimethylpyrromethene (prepared in situ from ethyl 3,4-diphenyl-5-methylpyrrole-2-carboxylate in a reaction with acetyl chloride) with boron trifluoride gave 1,2,6,7-tetraphenyl-3,5,8-trimethylpyrromethene–BF₂ complex 21 . Absorption for the vinamidine chromophore differed from that for the β-azavinamidine chromophore by a hypsochromic shift of 86 nm in a comparison of pyridomethene–BF₂ complex 3 with its 10-aza derivative 5 and by a bathochromic shift of 105 nm in a comparison of the pyrromethene–BF₂ complex 20 with the 8-azapyrromethene–BF₂ complex 17 .     

Synthesis and properties of noncoplanar rigid‐rod aromatic polyhydrazides and poly(1,3,4‐oxadiazole)s containing phenyl or naphthyl substituents

Two new phenyl‐ and naphthyl‐substituted rigid‐rod aromatic dicarboxylic acid monomers, 2,2′‐diphenylbiphenyl‐4,4′‐dicarboxylic acid ( 4 ) and 2,2′‐di(1‐naphthyl)biphenyl‐4,4′‐dicarboxylic acid ( 5 ), were synthesized by the Suzuki coupling reaction of 2,2′‐diiodobiphenyl‐4,4′‐dicarboxylic acid dimethyl ester with benzeneboronic acid and naphthaleneboronic acid, respectively, followed by alkaline hydrolysis of the ester groups. Four new polyhydrazides were prepared from the dicarboxylic acids 4 and 5 with terephthalic dihydrazide (TPH) and isophthalic dihydrazide (IPH), respectively, via the Yamazaki phosphorylation reaction. These polyhydrazides were amorphous and readily soluble in many organic solvents. Differential scanning calorimetry (DSC) indicated that these hydrazide polymers had glass transition temperatures in the range of 187–234 °C and could be thermally cyclodehydrated into the corresponding oxadiazole polymers in the range of 300–400 °C. The resulting poly(1,3,4‐oxadiazole)s exhibited T_g's in the range of 252–283 °C, 10% weight‐loss temperature in excess of 470 °C, and char yield at 800 °C in nitrogen higher than 54%. These organo‐soluble polyhydrazides and poly(1,3,4‐oxadiazole)s exhibited UV–Vis absorption maximum at 262–296 and 264–342 nm in NMP solution, and their photoluminescence spectra showed maximum bands around 414–445 and 404–453 nm, respectively, with quantum yield up to 38%. The electron‐transporting properties were examined by electrochemical methods. Cyclic voltammograms of the poly(1,3,4‐oxadiazole) films cast onto an indium‐tin oxide (ITO)‐coated glass substrate exhibited reversible reduction redox with E_onset at ?1.37 to ?1.57 V versus Ag/AgCl in dry N,N‐dimethylformamide solution. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 6466–6483, 2006     

An efficient synthesis of spiroacridinone derivatives from the facile reaction of isatins,dimedone, and 5-aminoindazole (6-aminoindazole or 5-aminoindole)

We have developed a simple and facil protocol for the synthesis of tetrahydrospiro(indoline-3,11′-pyrazolo[4,3-a]acridine)-2,10′(7′H)-dione, tetrahydrospiro(indoline-3, 11′-pyrazolo[3,4-a]acridine)-2,10′(7′H)-dione, and tetrahydrospiro (indoline-3,11′-pyrrolo[3,2-a]acridine)-2,10′(7′H)-dione via PTSA·H₂O-induced cyclization reaction from isatins, dimedone, and 5-aminoindazole (6-aminoindazole or 5-aminoindole) in mixed solvent (EtOH and CH₃CN). In this research, 5-aminoindazole, 6-aminoindazole, and 5-aminoindole were effectively used to react with isatins and dimedone to give spiroacridinone derivatives. The advantages of this method are mild conditions, convenient manipulation, high yields, and a wide range of substrates.     

The Equally Important Role of Adenine Derivatives to That of Pyrimidine Derivatives in Near‐0 eV Electron‐Induced DNA Lesions

The role of adenine (A) derivatives in DNA damage is scarcely studied due to the low electron affinity of base A. Experimental studies demonstrate that low‐energy electron (LEE) attachment to adenine derivatives complexed with amino acids induces barrier‐free proton transfer producing the neutral N₇‐hydrogenated adenine radicals rather than conventional anionic species. To explore possible DNA lesions at the A sites under physiological conditions, probable bond ruptures in two models—N₇‐hydrogenated 2′‐deoxyadenosine‐3′‐monophosphate (3′‐dA(N7H)MPH) and 2′‐deoxyadenosine‐5′‐monophosphate (5′‐dA(N7H)MPH), without and with LEE attachment—are studied by DFT. In the neutral cases, DNA backbone breakage and base release resulting from C_3′?O_3′ and N₉?C_1′ bond ruptures, respectively, by an intramolecular hydrogen‐transfer mechanism are impossible due to the ultrahigh activation energies. On LEE attachment, the respective C_3′?O_3′ and N₉?C_1′ bond ruptures in [3′‐dA(N7H)MPH]^? and [5′‐dA(N7H)MPH]^? anions via a pathway of intramolecular proton transfer (PT) from the C_2′ site of 2′‐deoxyribose to the C₈ atom of the base moiety become effective, and this indicates that substantial DNA backbone breaks and base release can occur at non‐3′‐end A sites and the 3′‐end A site of a single‐stranded DNA in the physiological environment, respectively. In particular, compared to the results of previous theoretical studies, not only are the electron affinities of 3′‐dA(N7H)MPH and 5′‐dA(N7H)MPH comparable to those of hydrogenated pyrimidine derivatives, but also the lowest energy requirements for the C_3′?O_3′ and N₉‐glycosidic bond ruptures in [3′‐dA(N7H)MPH]^? and [5′‐dA(N7H)MPH]^? anions, respectively, are comparable to those for the C_3′?O_3′ and N₁‐glycosidic bond cleavages in corresponding anionic hydrogenated pyrimidine derivatives. Thus, it can be concluded that the role of adenine derivatives in single‐stranded DNA damage is equally important to that of pyrimidine derivatives in an irradiated cellular environment.     

Synthesis and fluorescent properties of conjugated copolymers containing maleimide and fluorene units at the main chain

Yamamoto or Suzuki–Miyaura coupling polymerizations of 2,3‐diiodo‐N‐cyclohexylmaleimide with fluorene derivatives (2,7‐dibromo‐9,9′‐dihexylfluorene and 9,9′‐dihexylfluorene‐2,7‐diboronic acid) were carried out. The number‐average molecular weights (M_n) of the resulting copolymers were 2600–3500 by gel permeation chromatography analysis. The fluorescence emission of the alternating copolymer showed the emission maxima at 551 nm in THF. On the other hand, the random copolymers showed the bimodal emission peaks at 418–420 and 555–557 nm region, respectively. The fluorescence peaks of the random copolymers on the long wavelength region (555–557 nm) were attributed to the conjugated neighboring N‐cyclohexylmaleimide‐9,9′‐dihexylfluorene units in the polymer main chain. Furthermore, the copolymers exhibited the fluorescence solvatochromism by the difference of the polarity of solvents. The alternating and random copolymers showed the different fluorescence solvatochromism, and the emission colors are distinguishable by the naked eye, respectively. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51, 4945–4956     

Factors Affecting DNA–DNA Interstrand Cross‐Links in the Antiparallel 3′–3′ Sense: A Comparison with the 5′–5′ Directional Isomer

Reported herein is a study of the unusual 3′–3′ 1,4‐GG interstrand cross‐link (IXL) formation in duplex DNA by a series of polynuclear platinum anticancer complexes. To examine the effect of possible preassociation through charge and hydrogen‐bonding effects the closely related compounds [{trans‐PtCl(NH₃)₂}₂(μ‐trans‐Pt(NH₃)₂{NH₂(CH₂)₆NH₂}₂)]⁴⁺ (BBR3464, 1 ), [{trans‐PtCl(NH₃)₂}₂(μ‐NH₂(CH₂)₆NH₂)]²⁺ (BBR3005, 2 ), [{trans‐PtCl(NH₃)₂}₂(μ‐H₂N(CH₂)₃NH₂(CH₂)₄)]³⁺ (BBR3571, 3 ) and [{trans‐PtCl(NH₃)₂}₂{μ‐H₂N(CH₂)₃‐N(COCF₃)(CH₂)₄}]²⁺ (BBR3571‐COCF₃, 4 ) were studied. Two different molecular biology approaches were used to investigate the effect of DNA template upon IXL formation in synthetic 20‐base‐pair duplexes. In the “hybridisation directed” method the monofunctionally adducted top strands were hybridised with their complementary 5′‐end labelled strands; after 24 h the efficiency of interstrand cross‐linking in the 5′–5′ direction was slightly higher than in the 3′–3′ direction. The second method involved “postsynthetic modification” of the intact duplex; significantly less cross‐linking was observed, but again a slight preference for the 5′–5′ duplex was present. 2D [¹H, ¹⁵N] HSQC NMR spectroscopy studies of the reaction of [¹⁵N]‐ 1 with the sequence 5′‐d{TATACATGTATA}₂ allowed direct comparison of the stepwise formation of the 3′–3′ IXL with the previously studied 5′–5′ IXL on the analogous sequence 5′‐d(ATATGTACATAT)₂. Whereas the preassociation and aquation steps were similar, differences were evident at the monofunctional binding step. The reaction did not yield a single distinct 3′–3′ 1,4‐GG IXL, but numerous cross‐linked adducts formed. Similar results were found for the reaction with the dinuclear [¹⁵N]‐ 2 . Molecular dynamics simulations for the 3′–3′ IXLs formed by both 1 and 2 showed a highly distorted structure with evident fraying of the end base pairs and considerable widening of the minor groove.     

Synthesis of 5‐[2‐(guanin‐9‐yl)‐ and 5‐[2‐(2‐aminopurin‐9‐yl)ethyl]‐2‐D‐ribo‐(1,2′,3′,4′‐tetrahydroxybutyl)‐1,3‐dioxane

Stereoselective synthesis of 5‐[2‐(guanin‐9‐yl)‐ and 5‐[2‐(2‐aminopurin‐9‐yl)ethyl]‐2‐D‐ribo‐(1′,2′,3′,4′‐tetrahydroxybutyl)‐1,3‐dioxane, 2‐5, as potential prodrugs of penciclovir, has been accomplished in six steps from readily available 2,3,4,5‐tetra‐O‐acetyl‐aldehydo‐D‐ribose ( 6 ) and the 1,3‐diol 7 . It has been demonstrated that the use of boron trifluoride diethyl etherate (BF₃·Et₂O) in dichloromethane along with excess anhydrous copper(II) sulfate was crucial for the efficient formation of cyclic acetal 8 . In addition, the chromatographic separation of cis and trans isomers of the cyclic acetal at the bromide stage 10 was feasible, which was requisite for the successful stereoselective synthesis of the ribosyl derivatives 2–5 .     

Theoretical Study on Second‐order Nonlinear Optical Properties of Substituted Thiazole Derivatives

On the basis of ZINDO program, we have designed a program to calculate the nonlinear second‐order polarizability β_yk and β_μ according to the SOS expression. The second‐order nonlinear optical properties of 4‐nitro‐4′‐dimethylamino‐stilbene and a series of its thiazole derivatives were studied. The calculated results were that: When replacing a benzene ring in 4‐nitro‐4′‐dimethylamino‐stilbene by a thiazole ring, the influence on β values depends on the position of thiazole ring. When the thiazole ring connects with nitro group (acceptor), the β values increase significantly compared with corresponding stilbene derivatives. The β values of 2‐(p‐donor‐β‐styryl)‐5‐nitro‐thiazole derivatives (2–7) are larger than those of 2‐(p‐nitro‐β‐styryl)‐5‐donor‐thiazole derivatives (8–13) and 2‐(p‐donor‐phenyl)‐azo‐5‐nitro‐thiazole derivatives (14–19). The 2‐(p‐donor‐β‐styryl)‐5‐nitro‐thiazole derivatives (2–7) are good candidates as chromophores duo to their high nonlinearities and potential good thermal stability.     

Synthesis of (5′S)‐5′‐C‐Alkyl‐2′‐deoxynucleosides

We describe the synthesis of (5′S)‐5′‐C‐butylthymidine ( 5a ), of the (5′S)‐5′‐C‐butyl‐ and the (5′S)‐5′‐C‐isopentyl derivatives 16a and 16b of 2′‐deoxy‐5‐methylcytidine, as well as of the corresponding cyanoethyl phosphoramidites 9a , b and 14a , b , respectively. Starting from thymidin‐5′‐al 1 , the alkyl chain at C(5′) is introduced via Wittig chemistry to selectively yield the (Z)‐olefin derivatives 3a and 3b (Scheme 2). The secondary OH function at C(5′) is then introduced by epoxidation followed by regioselective reduction of the epoxy derivatives 4a and 4b with diisobutylaluminium hydride. In the latter step, a kinetic resolution of the diastereoisomer mixture 4a and 4b occurs, yielding the alkylated nucleoside 2a and 2b , respectively, with (5′S)‐configuration in high diastereoisomer purity (de=94%). The corresponding 2′‐deoxy‐5‐methylcytidine derivatives are obtained from the protected 5′‐alkylated thymidine derivatives 7a and 7b via known base interconversion processes in excellent yields (Scheme 3). Application of the same strategy to the purine nucleoside 2′‐deoxyadenine to obtain 5′‐C‐butyl‐2′‐deoxyadenosine 25 proved to be difficult due to the sensitivity of the purine base to hydride‐based reducing agents (Scheme 4).     

Interactions of binuclear copper(II) complexes with S-substituted thiosalicylate derivatives with some relevant biomolecules

Abstract

Interactions of copper(II) complexes which contain S-alkyl derivatives of thiosalicylic acid (alkyl?=?methyl, ethyl, propyl and butyl; aryl?=?benzyl), marked as 1–5, with guanosine-5′-monophosphate (5′-GMP) and calf thymus DNA (CT-DNA) were studied. Kinetics of substitution reactions of 1–5 with 5′-GMP and CT-DNA were investigated under pseudo-first-order conditions at 310 K and pH = 7.2 in 25?mM Hepes buffer using stopped-flow method. All complexes have high affinity toward studied bio-molecules. Additionally, interactions with CT-DNA were followed by absorption spectroscopy and fluorescence quenching measurements. The results indicate that complexes bind to DNA exhibiting high binding constants (K_b = 10⁴ M^?1). During the examination of competitive reactions with ethidium bromide (EB), results showed that complexes can replace EB-bound DNA. In addition, a new crystal structure of the binuclear Cu(II) complex with S-substituted thiosalicylate derivative has been reported. In the present series of Cu(II) complexes the crystal structure is the first example of a complex comprising an S-aryl derivative of thiosalicylate ligand. Through comparative study of structural properties of six molecules from four crystal structures we examined the structural variations, potentially important for biological activity of these complexes.     

3′-Amino-Modified Nucleotides Useful as Potent Chain Terminators for current DNA sequencing methods

We describe the synthesis of modified nucleoside triphosphates of the four DNA bases containing a 3′-amino group which were prepared from the corresponding 3′-azido derivatives. Introduction of the triphosphate and subsequent reduction of the N₃ to the NH₂ group led directly to the target molecules 6a–d . Furthermore, 3′-amino-2′,3′-dideoxynucleoside 5′-triphosphates proved to be potent inhibitors of the enzymatic synthesis of DNA catalyzed by the standard sequencing enzymes T7 DNA polymerase, sequenase version 2.0, Thermus aquaticus DNA polymerase, and Thermus thermophilus DNA polymerase. Both radioactive and fluorescent sequencing methods were applied successfully to the 3′-amino-modified terminators. Investigations in view of using these chain terminators according to Sanger's sequencing method for fluorescence labeling were done.