Trityloxyethylamino group for the protection of phosphoryl group in oligonucleotide synthesis

Trityloxyethylamino group was used for the protection of 5′-phosphoryl group of deoxyribonucleoside. This group is not only protecting group of phosphate also the intermediate for the synthesis of d-ppA and d-pppA.     

Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes

The structures and interaction energies of guanine and uracil quartets have been determined by B3LYP hybrid density‐functional calculations. The total interaction energy ΔE^T of the C_4h‐symmetric guanine quartet consisting of Hoogsteen‐type base pairs with two hydrogen bonds between two neighbor bases is −66.07 kcal/mol at the highest level. The uracil quartet with C6 H6O4 interactions between the individual bases has only a small interaction energy of −20.92 kcal mol⁻¹, and the interaction energy of −24.63 kcal/mol for the alternative structure with N3 H3O4 hydrogen bonds is only slightly more negative. Cooperative effects contribute between 10 and 25% to all interaction energies. Complexes of metal ions with G‐quartets can be classified into different structure types. The one with Ca²⁺ in the central cavity adopts a C_4h‐symmetric structure with coplanar bases, whereas the energies of the planar and nonplanar Na⁺ complexes are almost identical. The small ions Li⁺, Be²⁺, Cu⁺, and Zn²⁺ prefer a nonplanar S₄‐symmetric structure. The lack of coplanarity prevents probably a stacking of these base quartets. The central cavity is too small for K⁺ ions and, therefore, this ion favors in contrast to all other investigated ions a C₄‐symmetric complex, which is 4.73 kcal/mol more stable than the C_4h‐symmetric one. The distance 1.665 Å between K⁺ and the root‐mean‐square plane of the guanine bases is approximately half of the distance between two stacked G‐quartets. The total interaction energy of alkaline earth ion complexes exceeds those with alkali ions. Within both groups of ions the interaction energy decreases with an increasing row position in the periodic table. The B3LYP and BLYP methods lead to similar structures and energies. Both methods are suitable for hydrogen‐bonded biological systems. Compared with the before‐mentioned methods, the HCTH functional leads to longer hydrogen bonds and different relative energies for two U‐quartets. Finally, we calculated also structures and relative energies with the MMFF94 forcefield. Contrary to all DFT methods, MMFF94 predicts bifurcated C HO contacts in the uracil quartet. In the G‐quartet, the MMFF94 hydrogen bond distances N2 H22N7 are shorter than the DFT distances, whereas the N1 H1O6 distances are longer. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 109–124, 2001     

A new strategy for the protection of deoxyguanosine during oligonucleotide synthesis

The protection of the 6-oxo group of deoxyguanosine with the 2-trimethylsilylethyl ($\text{2}$), phenylthioethyl ($\text{3}$), 4-nitrophenylthioethyl ($\text{4}$), 4-nintrophenethyl ($\text{5}$), and cyanoethyl ($\text{6}$) groups is described. Each protecting group is introduced in good yield and is cleaved under mild conditions. Compatibility with the various approaches to oligonucleotide synthesis is discussed.     

Maleimide-dimethylfuran exo adducts: effective maleimide protection in the synthesis of oligonucleotide conjugates

The reaction of maleimide-containing compounds with 2,5-dimethylfuran gives a mixture of exo and endo isomers from which the exo cycloadduct can be easily isolated taking advantage of its stability in concentrated aqueous ammonia. Bifunctional compounds incorporating a dimethylfuran-protected maleimide (exo adduct) have been attached to resin-linked oligonucleotide chains. Removal of protecting groups masking oligonucleotide functionalities followed by retro-Diels-Alder maleimide deprotection affords maleimido-oligonucleotides suitable for conjugation, as assessed by their reaction with different thiols.     

Lifetimes and reaction pathways of guanine radical cations and neutral guanine radicals in an oligonucleotide in aqueous solutions

The exposure of guanine in the oligonucleotide 5'-d(TCGCT) to one-electron oxidants leads initially to the formation of the guanine radical cation G(?+), its deptotonation product G(-H)(?), and, ultimately, various two- and four-electron oxidation products via pathways that depend on the oxidants and reaction conditions. We utilized single or successive multiple laser pulses (308 nm, 1 Hz rate) to generate the oxidants CO(3)(?-) and SO(4)(?-) (via the photolysis of S(2)O(8)(2-) in aqueous solutions in the presence and absence of bicarbonate, respectively) at concentrations/pulse that were ～20-fold lower than the concentration of 5'-d(TCGCT). Time-resolved absorption spectroscopy measurements following single-pulse excitation show that the G(?+) radical (pK(a) = 3.9) can be observed only at low pH and is hydrated within 3 ms at pH 2.5, thus forming the two-electron oxidation product 8-oxo-7,8-dihydroguanosine (8-oxoG). At neutral pH, and single pulse excitation, the principal reactive intermediate is G(-H)(?), which, at best, reacts only slowly with H(2)O and lives for ～70 ms in the absence of oxidants/other radicals to form base sequence-dependent intrastrand cross-links via the nucleophilic addition of N3-thymidine to C8-guanine (5'-G*CT* and 5'-T*CG*). Alternatively, G(-H)(?) can be oxidized further by reaction with CO(3)(?-), generating the two-electron oxidation products 8-oxoG (C8 addition) and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih, by C5 addition). The four-electron oxidation products, guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), appear only after a second (or more) laser pulse. The levels of all products, except 8-oxoG, which remains at a low constant value, increase with the number of laser pulses.     

Modification of guanine residues in PNA-synthesis by PyBOP

The phosphonium-type coupling reagent PyBOP, when applied to the synthesis of peptide nucleic acid (PNA) oligomers, was found to form O⁴-phosphonium compounds of the nucleobase guanine which can be converted into C⁴-modified guanine-derived PNAs by nucleophiles.     

New synthesis of uracil derivatives

When N,N-dialkylamide dimethylsulfate adducts are reacted with cyanoacetyl urea or carbethoxy acetyl urea, the corresponding dialkylamino alkylidene derivatives are formed which cyclize to substituted uracils in the presence of a strong base. When the adducts of cyclic amides are used, the lactam ring is opened simultaneously on cyclisation.     

Optimized synthesis of LNA uracil nucleosides

A short, very high yielding, and practical synthesis of LNA uracil diol 6 has been developed from the easily accessible glycosyl donor 1. The concluding O3′-debenzylation of 5 resulted in significant reduction of the uracil moiety with many typical debenzylation conditions, while catalytic transfer hydrogenation using Pd(OH)₂/C and formic acid largely suppressed this undesired side reaction. Facile access to 6 will allow full exploration of RNA-based LNA-technology applications, including polymerase-catalyzed synthesis of LNA-modified RNA-strands.     

Facile synthesis of oligonucleotide phosphoroselenoates

Se-(2-cyanoethyl)phthalimide was synthesized from di-(2-cyanoethyl) diselenide. This reagent was found to be an efficient selenium transfer reagent in the synthesis of selenophosphates. Thus, nucleotide H-phosphonate diesters that are formed in situ through the H-phosphonate chemistry undergo quantitative reaction with Se-(2-cyanoethyl)phthalamide. The resulting Se-(2-cyanoethyl) oligonucleotide phosphoroselenoate triesters are subsequently deprotected to give oligonucleotide phosphoroselenoate diesters in excellent yields.     

Pyridyl groups for protection of the imide functions of uridine and guanosine. Exploration of their displacement reactions for site-specific modifications of uracil and guanine bases

For the protection of the O-4 function of uridine and the O-6 of guanosine, 2-, 3- and 4-hydroxypyridines, 2-pyridinethiol, 6-methyl-2-hydroxy- and 6-methyl-3-hydroxypyridines have been employed. These substituted pyridines gave pyridyl-N-and/or pyridyl-O-substituted derivatives, depending both upon the position of the hydroxyl and methyl groups in the pyridine ring, at the C-4 and the C-6 of the uracil and guanine residues, respectively. These groups were found to be good leaving groups for nucleophilic substitution reactions by amines, thiolates and oximate. If needed, the rate of these substitution reactions could be conveniently increased by almost 1000-fold by conversion of the pyridyl moiety to its methiodide.     

An efficient synthesis of new fluorinated uracil derivatives

A series of potentially biologically active fluorinated uracil derivatives has been prepared in three steps from oxazolines and fluorinated nitriles with good chemical yields.     

Two-dimensional supramolecular nanopatterns formed by the coadsorption of guanine and uracil at the liquid/solid interface

A novel supramolecular nanostructure formed by the coadsorption of the complementary nucleobases guanine (G) and uracil (U) at the liquid (1-octanol solvent)/solid (graphite) interface is revealed by scanning tunneling microscopy (STM). The GU supramolecular structure is distinctly different from the structures observed by STM when the individual nucleobases (NB) are adsorbed on graphite in the control experiments. Using a systematic methodology and ab initio density functional theory (DFT), an atomistic structural model is proposed for the supramolecular coadsorbed GU structure, which consists of a periodic repetition of cyclic units based on the strongest GU base pairing.     

Active monomeric nucleotide intermediate in the oligonucleotide synthesis

The interaction of 3′ - O - acetylthymidine - 5′ - phosphate (pT-Ac) and p - nitrophenylphosphate (pPhNO₂) with triisopropylbenzenesulphonyl chloride (TPS) in pyridine was studied by the pulsed NMR spectroscopy on ³¹P nuclei. The esters investigated were shown to convert to the corresponding disubstituted pyrophosphates, trisubstituted tripolyphosphates and compounds showing a singlet displaced 5–8 ppm from the original ester. The latter are the main final products of the interaction of nucleotide and pPhNO₂ with TPS. The investigation of the chemical conversion of a pT-Ac derivative with a 5·1 ppm shift showed that this product is a powerful phosphorylating reagent. It was shown that this active derivative contains one P atom in accordance with the structure of monomeric metaphosphoric acid ester proposed by Todd for these compounds. The reaction of monomeric metaphosphate with 5′-O-tritylthymidine results information of a compound, containing stoichiometric amounts of pT-Ac and 5′ - O - tritylthymidilyl - (3′ → 5′) - 3′ - O - acetylthymidine residues. This compound was identified as a trisubstituted P¹ - 5′ - O - trityl - P¹ - P² -bis -(3′ - O - acetylthymidine) - pyrophosph     

The nitrogen inversion in fused isoxazolidinyl derivatives of substituted uracil: synthesis,NMR and computational analysis

A series of fused isoxazolidines have been prepared via 1,3-dipolar cycloaddition reactions of N-protected methylenenitrones with 1,3-dimethyluracil derivatives, and their NMR spectra have been recorded in TFA-d and in CDCl₃ over a wide range of temperatures. The spectra indicate the presence of two invertomers for all isoxazolidines. Barriers to nitrogen inversion in the cycloadduct 6a have been determined using DFT quantochemical calculations. Our estimates have shown that the inversion proceeds at more complex path, involving four structures of local minima and four transition states.

     

The synthesis of new framework structures containing rigidly-linked pyrimidines suitable for uracil and cytosine elaboration

Fused norbornenes and tricyclo[4.2.2.1^2,5]undec-3,7,9-trienes containing 2,4-dichloropyrimidine and 2,4-dimethoxy pyrimidine units are coupled with norbornadiene, benzonorbornadienes and dimethoxynaphthaleno norbornadienes using s-tetrazines or ACE coupling techniques to afford framework structures where different geometrical interrelationships can be attained between the chromophores.     

The benzoylation of uracil and thymine

Uracil and thymine react with benzoyl chloride in acetonitrile-pyridine solution at room temperature to give first their 1-$\text{N}$-benzoyl (2b and 3b) and then their 1-$\text{N}$, 3-$\text{N}$-dibenzoyl derivatives (4a and 4b, respectively); the latter compounds are converted into the corresponding 3-$\text{N}$-benzoyl derivatives (5a and 6a) under mild conditions of basic hydrolysis.