Electron attachment to a hydrated DNA duplex: the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine

The minimal essential section of DNA helices, the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine dimer octahydrate, [dGpdC](2), has been constructed, fully optimized, and analyzed by using quantum chemical methods at the B3LYP/6-31+G(d,p) level of theory. Study of the electrons attached to [dGpdC](2) reveals that DNA double strands are capable of capturing low-energy electrons and forming electronically stable radical anions. The relatively large vertical electron affinity (VEA) predicted for [dGpdC](2) (0.38 eV) indicates that the cytosine bases are good electron captors in DNA double strands. The structure, charge distribution, and molecular orbital analysis for the fully optimized radical anion [dGpdC](2)(·-) suggest that the extra electron tends to be redistributed to one of the cytosine base moieties, in an electronically stable structure (with adiabatic electron affinity (AEA) 1.14 eV and vertical detachment energy (VDE) 2.20 eV). The structural features of the optimized radical anion [dGpdC](2)(·-) also suggest the probability of interstrand proton transfer. The interstrand proton transfer leads to a distonic radical anion [d(G-H)pdC:d(C+H)pdG](·-), which contains one deprotonated guanine anion and one protonated cytosine radical. This distonic radical anion is predicted to be more stable than [dGpdC](2)(·-). Therefore, experimental evidence for electron attachment to the DNA double helices should be related to [d(G-H)pdC:d(C+H)pdG](·-) complexes, for which the VDE might be as high as 2.7 eV (in dry conditions) to 3.3 eV (in fully hydrated conditions). Effects of the polarizable medium have been found to be important for increasing the electron capture ability of the dGpdC dimer. The ultimate AEA value for cytosine in DNA duplexes is predicted to be 2.03 eV in aqueous solution.     

Synthesis and Properties of 2′-Deoxy-1′,2′-seco-D-ribosyl (5′ → 3′)oligonucleotides (= 1′,2′-seco-DNA) containing adenine and thymine

Some 2′-deoxy-1′,2′-seco-D-ribosyl (5′→3′)oligonucleotides (= 1′,2′-seco-DNA), differing from natural DNA only by a bond scission between the centers C(1′) and C(2′), were synthesized and studied in order to compare their structure properties and pairing behavior with those of corresponding natural DNA and homo-DNA oligonucleotides (2′,3′-dideoxy-β-D-glucopyranosyl oligonucleotides). Starting from (?)-D-tartaric acid, 2′-deoxy-1′,2′-secoadenosine derivative 9a and 1′,2′-secothymidine ( 9b ) were obtained in pure crystalline form. Using the phosphoramidite variant of the phosphite-triester method, a dinucleotide monophosphate 1′,2′-seco-d(T₂) was synthesized in solution, while oligonucleotides 1′,2′-seco-d[(AT)₆], 1′,2′-seco-d(A₁₀) and 1′,2′-seco-d(T₁₀) were prepared on solid phase with either automated or manual techniques. Results of UV- and CD-spectroscopic as well as gel-electrophoretic studies indicated that neither adenine-thymine base pairing (as observed in natural DNA and homo-DNA), nor the adenine-adenine base pairing (as observed in homo-DNA) was effective in 1′,2′-seco-DNA, Furthermore, hybrid pairing was observed neither between 1′.2′-seco-DNA and natural DNA nor between 1′,2′-seco-DNA and homo-DNA.     

μ‐2,2′,6,6′‐Tetramethyl‐4,4′‐bipyridine‐κ2N1:N1′‐bis[(diethylenetriamine‐κ3N,N′,N′′)palladium(II)] tetranitrate

The title compound, [Pd₂(C₄H₁₃N₃)₂(C₁₄H₁₆N₂)](NO₃)₄, comprises discrete tetracationic dumbbell‐type dinuclear complex molecules and noncoordinating nitrate anions. Two Pd(dien)²⁺ moieties (dien is diethylenetriamine) are joined by the rigid linear exo‐bidentate bridging 2,2′,6,6′‐tetramethyl‐4,4′‐bipyridine ligand to form the dinuclear complex, which lies across a centre of inversion in the space group P2₁/n, so that the rings in the 2,2′,6,6′‐tetramethyl‐4,4′‐bipyridine bridging ligand are parallel. In the crystal, the primary and secondary amino groups of the dien ligand act as hydrogen‐bond donors towards the nitrate anions to form a three‐dimensional hydrogen‐bond network.     

Carbocyclic 5′‐norcytidine (5′‐norcarbodine)

A preparation of (1′R,2′S,3′R,4′S)‐1‐(2′,3′,4′‐trihydroxycyclopent‐1′‐yl)‐lH‐cytosine (5′‐norcarbodine, 3 ) has formally been achieved in 2 steps from (+)‐(1R,4S)‐4‐hydroxy‐2‐cyclopenten‐1‐yl acetate ( 4 ) and cytosine. The L‐like enantiomer of 3 (that is, 6 ) is also reported using the enantiomer of 4 (that is, 7 ). In evalu ating 3 and 6 for antiviral potential against a number of viruses, compound 3 was found to have activity towards Epstein‐Barr virus (EBV).     

Structural and electronic property responses to the arsenic/phosphorus exchange in GC‐related DNA of the B‐form

The suggestion that phosphorus/arsenic replacement in DNA can play a role in living things has generated great controversy (Wolfe‐Simon et al., Science 2011, 332, 1163). Examined here theoretically are substitution effects on Watson–Crick base pairing and base stacking patterns in realistic DNA subunits. Using duplex DNA models deoxyguanylyl‐3′,5′‐deoxycytidine ([dGpdC]₂) and deoxycytidyly‐3′,5′‐deoxyguanosine ([dCpdG)]₂), this research reveals that the geometric variations caused by the As/P exchange are small and are limited to the phosphate/arsenate groups. As/P replacement leads to alterations of ～0.15 Å in P/As? O bond lengths and less than 1.5° variations in O? P/As? O angles. The Watson–Crick base pairing and base stacking patterns are independent of the As/P replacement. The vertical electron detachment energies are also largely unaffected. However, the electron capture ability of the DNA units is improved by the As substitution. The arsenate is found to be the main electron acceptor in As‐DNA. The results are relevant to the possible existence of viable As‐DNAs, at least in the guanine and cytosine (GC)‐related B‐form DNA. © 2012 Wiley Periodicals, Inc. J Comput Chem, 2012     

Synthetic approaches to 4,8‐dimethyl‐5′‐(N‐pyridiniummethyl)‐ 4′,5′‐dihydropsoralens and 4,8‐dimethyl‐5′‐ (N‐aminomethyl)‐ 4′,5′‐dihydropsoralens

New synthetic approaches to 4,8‐dimethyl‐5′‐(N‐pyridiniummethyl)‐4′,5′‐dihydropsoralens and 4,8‐dimemyl‐5′‐(N‐aminomethyl)‐4′,5′‐dihydropsoralens are described. The 5′‐halomethyl‐4′,5′‐dihydro‐psoralen precursors are formed by electrophilic ring closures of 4,8‐dimethyl‐6‐allyl‐7‐hydroxycoumarin. The ring‐closure reactions may also be applied to the synthesis of 5′‐halomethyl‐4‐methyl‐4′,5′‐dihydroangelicins. The compounds are potential therapeutic agents for improved psoralen ultraviolet A radiation treatment.     

Flip‐type disorder in 3‐substituted 2,2′:5′,2′′‐terthiophenes

In the crystal structures of four thiophene derivatives, (E)‐3′‐[2‐(anthracen‐9‐yl)ethenyl]‐2,2′:5′,2′′‐terthiophene, C₂₈H₁₈S₃, (E)‐3′‐[2‐(1‐pyrenyl)ethenyl]‐2,2′:5′,2′′‐terthiophene, C₃₀H₁₈S₃, (E)‐3′‐[2‐(3,4‐dimethoxyphenyl)ethenyl]‐2,2′:5′,2′′‐terthiophene, C₂₂H₁₈O₂S₃, and (E,E)‐1,4‐bis[2‐(2,2′:5′,2′′‐terthiophen‐3′‐yl)ethenyl]‐2,5‐dimethoxybenzene, C₃₆H₂₆O₂S₆, at least one of the terminal thiophene rings is disordered and the disorder is of the flip type. The terthiophene fragments are far from being coplanar, contrary to terthiophene itself. The central C—C=C—C fragments are almost planar but the bond lengths suggest slight delocalization within this fragment. The crystal packing is determined by van der Waals interactions and some weak, relatively short, C—H...S and C—H...π directional contacts.     

Synthetic approaches to 3‐substituted‐5′‐(N‐pyridiniummethyl)‐4′,5′‐dihydropsoralen

New synthetic approaches to 3‐substituted‐5′‐(N‐pyridiniummethyl)‐4′,5′‐dihydropsoralens are described. The novel pathways presented utilize appropriately substituted coumarins and 4′,5′‐dihydropsoralens. The compounds proposed represent potential therapeutic agents for psoralen uv radiation treatment.     

Reactions of 2,2′,5′,2′-terfuran

Formylation of 2,2′,5′,2′-terfuran ( 1 ) with N-methylformanilide and phosphorus oxychloride gave 5-formyl-2,2′,5′,2′-terfuran ( 2 ) and 5,5′-diformyl-2,2′5′,2′-terfuran ( 3 ). Reduction of 2 and 3 afforded 5-hydroxymethyl-2,2′,5′,2′-terfuran ( 4 ) and 5,5′ dihydroxymethyl-2,2′,5′,2′-terfuran ( 5 ), respectively. Terfuran 1 reacted with phenylmagnesium bromide to give 5-(phenylhydroxymethyl)-2,2′,5′,2′-terfuran ( 6 ), and was carbonated to 5-carboxy 2,2′,5′,2′-terfuran ( 7 ) and 5,5′-dicarboxy-2,2′,5′,2′-terfuran ( 8 ). Bromination of 1 with N-bromosuccinimide gave 5,5′-dibromo 2,2′,5′,2′-terfuran ( 9 ).     

Synthesis of 1,2′,3,3′,5′,6′-hexahydro-3-phenylspiro[isobenzofuran-1,4′-thiopyrans] and 1,2′,3,3′,5′,6′-hexahydro-3-phenylspiro-[isobenzofuran-1,4′-pyrans]

The 1,2′,3,3′,5′,6′-hexahydro-3-phenylspiro[isobenzofuran-1,4′-thiopyran] ring system ( 2a ) has been prepared from o-bromobenzoic acid. The 1,2′,3,3′,5′,6′-hexahydro-3-phenylspiro[isobenzofuran-1,4′-pyran] ring system ( 3a ) has been prepared from 2-bromobenzhydrol methyl ether. Several 3-(dimethylaminoalkyl) derivatives of both 2a and 3a were prepared by lithiation followed by alkylation.     

Enzymatic Synthesis of 7′,5′‐Bicyclo‐DNA Oligonucleotides

The selection of artificial genetic polymers with tailor‐made properties for their application in synthetic biology requires the exploration of new nucleosidic scaffolds that can be used in selection experiments. Herein, we describe the synthesis of a bicyclo‐DNA triphosphate (i.e., 7′,5′‐bc‐TTP) and show its potential to serve for the generation of new xenonucleic acids (XNAs) based on this scaffold. 7′,5′‐bc‐TTP is a good substrate for Therminator DNA polymerase, and up to seven modified units can be incorporated into a growing DNA chain. In addition, this scaffold sustains XNA‐dependent DNA synthesis and potentially also XNA‐dependent XNA synthesis. However, DNA‐dependent XNA synthesis on longer templates is hampered by competitive misincorporation of deoxyadenosine triphosphate (dATP) caused by the slow rate of incorporation of 7′,5′‐bc‐TTP.     

Synthesis of a DNA Promoter Segment Containing All Four Epigenetic Nucleosides: 5‐Methyl‐, 5‐Hydroxymethyl‐, 5‐Formyl‐, and 5‐Carboxy‐2′‐Deoxycytidine

A 5‐formyl‐2′‐deoxycytidine (fdC) phosphoramidite building block that enables the synthesis of fdC‐containing DNA with excellent purity and yield has been developed. In combination with phosphoramidites for 5‐methyl‐dC, 5‐hydroxymethyl‐dC, and carboxy‐dC, it was possible to prepare a segment of the OCT‐4 promoter that contains all four epigenetic bases. Because of the enormous interest in these new epigenetic bases, the ability to insert all four of them into DNA should be of great value for the scientific community.     

Energetic Derivatives of 4, 4′,5, 5′‐Tetranitro‐2, 2′‐bisimidazole (TNBI)

4, 4′,5, 5′‐Tetranitro‐2, 2′‐bisimidazole (TNBI) was synthesized by nitration of bisimidazole (BI) and recrystallized from acetone to form a crystalline acetone adduct. Its ammonium salt ( 1 ) was obtained by the reaction with gaseous ammonia. In order to explore new explosives or propellants several energetic nitrogen‐rich 2:1 salts such as the hydroxylammonium ( 3 ), guanidinium ( 4 ), aminoguanidinium ( 5 ), diaminoguanidinium ( 6 ) and triaminoguanidinium 7 4, 4′,5, 5′‐tetranitro‐2, 2′‐bisimidazolate were prepared by facile metathesis reactions. In addition, methylated 1, 1′‐dimethyl‐4, 4′,5, 5′‐tetranitro‐2, 2′‐bisimidazole (Me₂TNBI, 8 ) was synthesized by the reaction of 2 and dimethyl sulfate. Metal salts of TNBI can also be easily synthesized by using the corresponding metal bases. This was proven by the synthesis of pyrotechnically relevant dipotassium 4, 4′,5, 5′‐tetranitro‐2, 2′‐bisimidazolate ( 2 ), which is a brilliant burning component e.g. in near‐infrared flares. All compounds were characterized by single crystal X‐ray diffraction, NMR and vibrational spectroscopy, elemental analysis and DSC. The sensitivities were determined by BAM methods (drophammer and friction tester). The heats of formation were calculated using CBS‐4M electronic enthalpies and the atomization method. With these values and mostly the X‐ray densities different detonation parameters were computed by the EXPLO5 computer code. Due to the great thermal stability and calculated energetic properties, especially guanidinium salt 4 could be served as a HNS replacement.     

3′,4′-Diethynl-2′,3′,5′-trideoxy-5′-noruridine: A new self-polymerizable 2′-deoxyribonucleoside analogue

In 10 steps, 3′,4′-diethynyl-2′,3′,5′-trideoxy-5′-noruridine ( 14 ) was synthesized in 5% overall yield from commercial uridine, using conventional methods of nucleoside chemistry. As two functional groups capable to react with each other are present in the same molecule, the synthetic compound is able to form polymers, similar to the polynucleotides, by an acetylene coupling reaction.     

Synthesis,Crystal Structure and Hydrolysis of a Novel Anhydrogalactosucrose: 2′‐Methoxyl‐O‐1′,4′:3′,6′‐dianhydro‐β‐D‐fructofuranosyl 3,6‐anhydro‐4‐chloro‐4‐deoxy‐α‐D‐galactopyranoside

A novel anhydrogalactosucrose derivative 2′‐methoxyl‐O‐1′,4′:3′,6′‐dianhydro‐β‐D‐fructofuranosyl 3,6‐anhydro‐4‐chloro‐4‐deoxy‐α‐D‐galactopyranoside ( 4 ) was prepared from 3,6:1′,4′:3′,6′‐trianhydro‐4‐chloro‐4‐deoxy‐galactosucrose ( 3 ) via a facile method and characterized by ¹H NMR, ¹³C NMR and 2D NMR spectra. The single crystal X‐ray diffraction analysis shows that the title molecule forms a two thee‐dimensional network structure by two kinds of hydrogen bond interactions [O(2) H(2)···O(7), O(5) H(5)···O(8)]. Its stability was investigated by acid hydrolysis reaction treated with sulfuric acid, together with the formation of 1,6‐Di‐O‐methoxy‐4‐chloro‐4‐deoxy‐β‐D‐galactopyranose ( 5 ) and 2,2‐Di‐C‐methoxy‐1,4:3,6‐dianhydromannitol ( 6 ). According to the result, the relative stability of the ether bonds in the structure is in the order: C(1) O C(5)≈C(3′) O C(6′)≈C(1′) O C(4′)>C(3) O C(6)≈C(1) O C(2′)>C(2′) O C(5′).     

Synthesis of 3′,5′‐Cyclic Phosphate and Thiophosphate Esters of 2′‐C‐Methyl Ribonucleosides

2′‐C‐Methylnucleosides are known to exhibit antiviral activity against Hepatitis C virus. Since the inhibitory activity depends on their intracellular conversion to 5′‐triphosphates, dosing as appropriately protected 5′‐phosphates or 5′‐phosphorothioates appears attractive. For this purpose, four potential pro‐drugs of 2′‐C‐methylguanosine, i.e., 3′,5′‐cyclic phosphorothioate of 2′‐C‐methylguanosine and 2′‐C,O⁶‐dimethylguanosine, 1 and 2 , respectively, the S‐[(pivaloyloxy)methyl] ester of 2′‐C,O⁶‐dimethylguanosine 3′,5′‐cyclic phosphorothioate and the O‐methyl ester of 2′‐C,O⁶‐dimethylguanosine 3′,5′‐cyclic phosphate, 3 and 4 , respectively, have been prepared.     

New heterocyclic derivatives of 1′- and 3′-amino-5′,6′,7′,8′-tetrahydro-2′-acetonaphthones

The preparation of 1′-and 3′-amino-5′,6′,7′,8′-tetrahydro-2′-acetonaphthones (IIIa and IIIb) is described, by reduction of the low temperature nitration products of 5′,6′,7′,8′-tetrahydro-2′-acetonaphtone (I). The structures of the nitro isomers (IIa and IIb), and the reduction products, IIIa and IIIb, were elucidated spectroscopically. By known reactions, a series of new heterocyclic compounds prepared from the o-aminoketones, IIIa and IIIb, resulted in two series of new heterocyclic compounds.     

Different nucleobase orientations in two cyclic 2′,3′‐phosphates of purine ribonucleosides: Et3NH(2′,3′‐cAMP) and Et3NH(2′,3′‐cGMP)·H2O

The crystal structures of triethyl­ammonium adenosine cyclic 2′,3′‐phosphate {systematic name: triethyl­ammonium 4‐(6‐amino­purin‐9‐yl)‐6‐hydroxy­methyl‐2‐oxido‐2‐oxoperhydro­furano[3,4‐c][1,3,2]dioxaphosphole}, Et₃NH(2′,3′‐cAMP) or C₆H₁₆N⁺·C₁₀H₁₁N₅O₆P⁻, (I), and guanosine cyclic 2′,3′‐phosphate monohydrate {systematic name: triethyl­ammonium 6‐hydroxy­methyl‐2‐oxido‐2‐oxo‐4‐(6‐oxo‐1,6‐dihydro­purin‐9‐yl)perhydro­furano[3,4‐c][1,3,2]dioxaphosphole monohydrate}, [Et₃NH(2′,3′‐cGMP)]·H₂O or C₆H₁₆N⁺·C₁₀H₁₁N₅O₇P⁻·H₂O, (II), reveal different nucleobase orientations, viz. anti in (I) and syn in (II). These are stabilized by different inter‐ and intra­molecular hydrogen bonds. The structures also exhibit different ribose ring puckering [₄E in (I) and ³T₂ in (II)] and slightly different 1,3,2‐dioxaphospho­lane ring conformations, viz. envelope in (I) and puckered in (II). Infinite ribbons of 2′,3′‐cAMP⁻ and helical chains of 2′,3′‐cGMP⁻ ions, both formed by O—H⋯O, N—H⋯X and C—H⋯X (X = O or N) hydrogen‐bond contacts, characterize (I) and (II), respectively.     

2,2′‐Anhydro‐1‐(3′,5′‐di‐O‐acetyl‐β‐D‐arabinofuranosyl)uracil,a cyclouridine nucleoside with a C4′‐endo furanosyl conformation

2,2′‐Anhydro‐1‐(3′,5′‐di‐O‐acetyl‐β‐D‐arabinofuranosyl)uracil, C₁₃H₁₄N₂O₇, was obtained by refluxing 2′,3′‐O‐(methoxymethylene)uridine in acetic anhydride. The structure exhibits a nearly perfect C4′‐endo (⁴E) conformation. The best four‐atom plane of the five‐membered furanose ring is O—C—C—C, involving the C atoms of the fused five‐membered oxazolidine ring, and the torsion angle is only −0.4 (2)°. The oxazolidine ring is essentially coplanar with the six‐membered uracil ring [r.m.s. deviation = 0.012 (5) Å and dihedral angle = −3.2 (3)°]. The conformation at the exocyclic C—C bond is gauche–trans which is stabilized by various C—H...π and C—O...π interactions.     

Synthesis,structure and some reactions of 4a',5′,6′,7′,8′,8a'‐hexahydro‐4′H‐spiro[cyclohexane‐1,9′‐[1,2,4]triazolo[5,1‐b]‐quinazolines]

2′‐Substituted 5′,6′,7′,8′‐tetrahydro‐4′H‐spiro[cyclohexane‐1,9′‐[1,2,4]triazolo[5,1‐b]quinazolines] 3a‐d were synthesized by condensation of 3‐substituted 5‐amino‐1,2,4‐triazoles 1a‐d with 2‐cyclohexylidene cyclohexanone 2 in DMF. The compounds 3 were hydrogenated with sodium borohydride in ethanol to give 2′‐substituted cis‐4a',5′,6′,7′,8′,8a'‐hexahydro‐4′H‐spiro[cyclohexane‐1,9′‐[1,2,4]triazolo[5,1‐b]quinazolines] 4a‐d in high yields. The reactions of alkylation, acylation and sulfonylation of the compounds 4 were studied. The structure of the synthesized compounds was determined on the basis of NMR measurements including HSQC, HMBC, NOESY techniques and confirmed by the X‐ray analysis of 6 and 11b . The described synthetic protocols provide rapid access to novel and diversely substituted hydrogenated [1,2,4]triazolo[5,1‐b]quinazolines.