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Nucleobases
Selected AbstractsA Tale of Two Targets: Differential RNA Selectivity of Nucleobase,Aminoglycoside ConjugatesCHEMBIOCHEM, Issue 10 2006Kenneth F. Blount Dr. Aminoglycoside antibiotics are RNA-binding polyamines that can bind with similar affinities to structurally diverse RNA targets. To design new semisynthetic aminoglycosides with improved target selectivity, it is important to understand the energetic and structural basis by which diverse RNA targets recognize similar ligands. It is also imperative to discover how novel aminoglycosides could be rationally designed to have enhanced selectivity for a given target. Two RNA drug targets, the prokaryotic ribosomal A-site and the HIV-1 TAR, provide an excellent model system in which to dissect the issue of target selectivity, in that they each have distinctive interactions with aminoglycosides. We report herein the design, synthesis, and binding activity of novel nucleobase,aminoglycoside conjugates that were engineered to be more selective for the A-site binding pocket. Contrary to the structural design, the conjugates bind the A-site more weakly than does the parent compound and bind the TAR more tightly than the parent compound. This result implies that the two RNA targets differ in their ability to adapt to structurally diverse ligands and thus have inherently different selectivities. This work emphasizes the importance of considering the inherent selectivity traits of the RNA target when engineering new ligands. [source] Straightforward Pyrimidine Ring Construction: A Versatile Tool for the Synthesis of Nucleobase and Nucleoside Analogues.CHEMINFORM, Issue 21 2006Aelig Robin Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source] Coordination Modes of 9-Methyladenine in cis -Platinum(II) Complexes with Dimethyl(phenyl)phosphanes as Ancillary Ligands , Synthesis and Characterization of cis -[PtL2(9-MeAd)2](NO3)2, cis -[PtL2{9-MeAd(,H)}]3(NO3)3, and cis -[L2Pt{9-MeAd(,H)}PtL2](NO3)3EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 1 2003Bruno Longato Abstract Treatment of 9-methyladenine (9-MeAd) with cis -[PtL2(NO3)2] (1) (L = PMe2Ph) in a 2:1 molar ratio generated the bis(adduct) cis -[PtL2(9-MeAd)2](NO3)2 (2), which was isolated and fully characterized by multinuclear (1H, 31P, 13C, 195Pt and 15N) NMR analysis, which showed that the two nucleobases are selectively coordinated through the N1 atom. Small amounts of a mono(adduct) cis -[PtL2(S)(9-MeAd)]2+ (3) (S = solvent) and of a diplatinated species cis -[L2Pt(S){9-MeAd(,H)}PtL2]3+ (4) are formed in DMSO solution when 9-MeAd is present in smaller quantities than 1. Complex 3 is platinated at N1, with a solvent molecule representing the fourth ligand around the metal center. Complex 4 contains an adenine molecule deprotonated and platinated at N1,N6,N7, with two cis -L2Pt units bonded to nitrogen atom N1 and to nitrogen atoms N6 and N7, respectively. With increasing relative concentration of the nucleobase, both complexes 3 and 4 progressively convert into the bis(adduct) 2, the only species detectable in solution when the Ad/Pt molar ratio is 2:1. The trinuclear compound cis -[L2Pt{9-MeAd(,H)}]3(NO3)3 (5) (L = PMe2Ph), containing an NH2 -deprotonated nucleobase bridging the metal centers through the N1 and N6 atoms, is quantitatively formed when the dinuclear hydroxo complex cis -[Pt(,-OH)L2]2(NO3)2 (6) reacts with 9-MeAd in CH3CN solution. The isolated complex was fully characterized by multinuclear NMR spectroscopy and mass spectrometry. It appears to be stable in solution in CH3CN and chlorinated solvents, whereas in DMSO it partially converts into a new species, probably the dinuclear analog cis -[PtL2{9-MeAd(,H)}]2(NO3)2, in which the adenine maintains its coordination mode. At equilibrium the trinuclear/dinuclear species molar ratio is 20:1. Through the addition of a stoichiometric amount of nitrate 1 to a DMSO solution of 5 we were able to generate the diplatinated compound 4 in high yield. Complex 4 displays a new coordination mode for the adeninate ion, with N1 bonded to one platinum atom whereas N6 and N7 are chelated to a second one. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] A Practical and Efficient Approach to PNA Monomers Compatible with Fmoc-Mediated Solid-Phase Synthesis Protocols,EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 34 2008Andrea Porcheddu Abstract A straightforward synthesis of orthogonally protected PNA monomers is described. Protected aminoethylglycine (Aeg) monomers were efficiently prepared by reductive amination of N -Fmoc-glycinaldehyde with glycine methyl ester and the subsequent acylation of the free amine with N -bis-Boc-protected nucleobase acetic acids. The exocyclic amine group of the nucleobases, including the notoriously difficult-to-protect guanine nucleobase, was protected with a bis-Boc carbamate group; this increased the solubility of the nucleobases in the most common organic solvents. The current protocol allows all Aeg monomers to be prepared on both the micro- and macroscale, which avoids or minimizes the use of toxic reagents or solvents, and moreover, cheap starting materials are used. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Oligonucleotides Containing 7-Deaza-2,-deoxyinosine as Universal Nucleoside: Synthesis of 7-Halogenated and 7-Alkynylated Derivatives, Ambiguous Base Pairing, and Dye Functionalization by the Alkyne,Azide ,Click' ReactionHELVETICA CHIMICA ACTA, Issue 7 2008Frank Seela Abstract Oligonucleotides containing 7-deaza-2,-deoxyinosine derivatives bearing 7-halogen substituents or 7-alkynyl groups were prepared. For this, the phosphoramidites 2b,2g containing 7-substituted 7-deaza-2,-deoxyinosine analogues 1b,1g were synthesized (Scheme,2). Hybridization experiments with modified oligonucleotides demonstrate that all 2,-deoxyinosine derivatives show ambiguous base pairing, as 2,-deoxyinosine does. The duplex stability decreases in the order Cd>Ad>Td>Gd when 2b,2g pair with these canonical nucleosides (Table,6). The self-complementary duplexes 5,-d(F7c7I-C)6, d(Br7c7I-C)6, and d(I7c7I-C)6 are more stable than the parent duplex d(c7I-C)6 (Table,7). An oligonucleotide containing the octa-1,7-diyn-1-yl derivative 1g, i.e., 27, was functionalized with the nonfluorescent 3-azido-7-hydroxycoumarin (28) by the Huisgen,Sharpless,Meldal cycloaddition ,click' reaction to afford the highly fluorescent oligonucleotide conjugate 29 (Scheme,3). Consequently, oligonucleotides incorporating the derivative 1g bearing a terminal CC bond show a number of favorable properties: i) it is possible to activate them by labeling with reporter molecules employing the ,click' chemistry. ii) Space demanding residues introduced in the 7-position of the 7-deazapurine base does not interfere with duplex structure and stability (Table,8). iii) The ambiguous pairing character of the nucleobase makes them universal probes for numerous applications in oligonucleotide chemistry, molecular biology, and nanobiotechnology. [source] Synthesis of the Cyclopentyl Nucleoside (,)-Neplanocin A from D -Glucose via Zirconocene-Mediated Ring ContractionHELVETICA CHIMICA ACTA, Issue 6 2005Two approaches for the conversion of d- glucose to (,) -neplanocin A (2), both based on the zirconocene-promoted ring contraction of a vinyl-substituted pyranoside, are herein evaluated (Scheme,1). In the first pathway (Scheme,2), the substrate possesses the , - d- allo configuration (see 6) such that ultimate introduction of the nucleobase would require only an inversion of configuration. However, this precursor proved unresponsive to Cp2Zr (=[ZrCl2(Cp)2]), an end result believed to be a consequence of substantive nonbonded steric effects operating in a key intermediate (Scheme,5). In contrast, the C(2) epimer (see 7) experienced the desired metal-promoted conversion to an enantiomerically pure polyfunctional cyclopentane (see 5 in Scheme,3). The substituents in this product are arrayed in a manner such that conversion to the target nucleoside can be conveniently achieved by a double-inversion sequence (Scheme,4). Recourse to palladium(0)-catalyzed allylic alkylation did not provide an alternate means of generating 2. [source] Synthesis of 9-Halogenated 9-Deazaguanine N7 -(2,-Deoxyribonucleosides)HELVETICA CHIMICA ACTA, Issue 10 2004Frank Seela The syntheses of N7 -glycosylated 9-deazaguanine 1a as well as of its 9-bromo and 9-iodo derivatives 1b,c are described. The regioselective 9-halogenation with N -bromosuccinimide (NBS) and N -iodosuccinimide (NIS) was accomplished at the protected nucleobase 4a (2-{[(dimethylamino)methylidene]amino}-3,5-dihydro-3-[(pivaloyloxy)methyl]-4H -pyrrolo[3,2- d]pyrimidin-4-one). Nucleobase-anion glycosylation of 4a,c with 2-deoxy-3,5-di- O -(p -toluoyl)-,- D - erythro -pentofuranosyl chloride (5) furnished the fully protected intermediates 6a,c (Scheme,2). They were deprotected with 0.01M NaOMe yielding the sugar-deprotected derivatives 8a,c (Scheme,3). At higher concentrations (0.1M NaOMe), also the pivaloyloxymethyl group was removed to give 7a,c, while conc. aq. NH3 solution furnished the nucleosides 1a,c. In D2O, the sugar conformation was always biased towards S (67,61%). [source] Synthesis and Enzymic Hydrolysis of Oligoribonucleotides Incorporating 3-Deazaguanosine: The Importance of the Nitrogen-3 Atom of Single Conserved Guanosine Residues on the Catalytic Activity of the Hammerhead RibozymeHELVETICA CHIMICA ACTA, Issue 8 2003Frank Seela Four base-modified hammerhead ribozyme/substrate complexes were constructed in which single guanosine (1) residues were replaced by 3-deazaguanosine (2) in the positions G5, G8, GL2.1, and G12. The base-modified ribozyme complexes were prepared by solid-phase synthesis of oligoribonucleotides employing the novel phosphoramidite 3 derived from 2. Phosphoramidite 3 carried a phenoxyacetyl group at the amino function and a diphenylcarbamoyl residue at the oxo group of the nucleobase. The 2,-hydroxy group was blocked with a triisopropylsilyl residue. Kinetic analysis of the phosphodiester hydrolysis showed a moderate decrease of the ribozyme catalytic activity when the residues G5 or G8 were replaced by 3-deazaguanosine and a 200-fold decrease when G12 was substituted. A 6-fold catalytic increase occurred when 3-deazaguanosine was replacing GL2.1 in the loop region. The data indicate that the N(3) atom of compound 2, in particular at position G12 is critical for the ribozyme activity. [source] Organization of nucleobase-functionalized ,-peptides investigated by soft electrospray ionization mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2009Nicola Diezemann Abstract The development and validation of analytical methods is a key to succeed in investigating noncovalent interactions between biomolecules or between small molecules and biomolecules. Electrospray ionization mass spectrometry (ESI-MS) was applied with a Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS) as well as a quadrupole/time-of-flight tandem mass spectrometer (QqToF-MS) for a systematic investigation of noncovalent complexes based on nucleobase pairing in an artificial and noncharged backbone topology. Synthetical ,-peptide helices covalently modified with nucleobases were organized by recognition of a sequence of four nucleobases. Specific duplexes of ,-peptide helices were obtained on the basis of hydrogen bonding base pair complementarity. Oligomer interactions were detected with defined stoichiometry and sensitivity for the respective duplex stability. FTICR-MS and QqToF-MS were used equally well to indicate double strand stabilities in agreement with the dissociation data determined by UV spectroscopy. Furthermore, the dissociation energies of gas phase ions of the noncovalent complexes were analyzed with collision induced dissociation (CID)-MS/MS and infrared multiphoton dissociation (IRMPD)-MS/MS. The CID conditions turned out to be too harsh for a differentiation of the duplex stabilities, whereas IRMPD might be developed as a technique to detect even small interaction energy differences. Copyright © 2009 John Wiley & Sons, Ltd. [source] Synthesis, characterization and hybridization studies of new nucleo-,-peptides based on diaminobutyric acidJOURNAL OF PEPTIDE SCIENCE, Issue 12 2006G. N. Roviello Abstract In the present work, we report the synthesis and the characterization of a new chiral nucleoaminoacid, in which a diaminobutyric moiety is connected to the DNA nucleobase by an amidic bond, and its oligomerization to give the corresponding nucleo-,-peptide. The ability of this synthetic polymer to bind complementary DNA was studied in order to explore its possible use in antigene/antisense or diagnostic applications. Our interest in the presented DNA analogue was also supported by the importance of ,-aminoacid-containing compounds in natural products of biological activity and by the known stability of ,-peptides to enzymatic degradation. Furthermore, our work could contribute to the study of the role of nucleopeptides as prebiotic material in a PNA world that could successively lead to the actual DNA/RNA/protein world, as recently assumed. Copyright © 2006 European Peptide Society and John Wiley & Sons, Ltd. [source] New permanently charged phenanthridinium,nucleobase conjugates.JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 12 2003Interactions with nucleotides, polynucleotides, recognition of ds-polyAH+ Abstract N -Methyl-8-aminophenathridinium,uracil and ,adenine conjugates possessing a nucleobase attached at the phenanthridinium 8-amino group by a trimethylene spacer were prepared in the form of water-soluble hydrogensulfate salts. Spectroscopic characteristics of the conjugates reveal the formation of folded conformations in water characterized by intramolecular aromatic stacking between the phenanthridinium unit and the tethered nucleobase. The conjugates form 1:1 complexes in water with either complementary or non-complementary nucleotides, giving log Ks values between 1 and 2 and showing a lack of any base recognition. Also, the binding studies with single-stranded polynucleotides showed no preference of conjugates to polynucleotides containing complementary nucleobases. At pH 5, the N -methylphenanthridinium,adenine conjugate exhibited preferred binding to double-stranded (ds-) polyAH+, whereas its protonated analogue bound preferably to polyU. The results reveal that the presence of protonated or permanently charged intercalator units in the conjugates dramatically changes their binding preferences for polynucleotides. Copyright © 2003 John Wiley & Sons, Ltd. [source] Can radical cations of the constituents of nucleic acids be formed in the gas phase using ternary transition metal complexes?,RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 13 2005Sheena Wee Electrospray ionization (ESI) tandem mass spectrometry (MS/MS) of ternary transition metal complexes of [M(L3)(N)]2+ (where M,=,copper(II) or platinum(II); L3,=,diethylenetriamine (dien) or 2,2,:6,,2,-terpyridine (tpy); N,=,the nucleobases: adenine, guanine, thymine and cytosine; the nucleosides: 2,deoxyadenosine, 2,deoxyguanosine, 2,deoxythymine, 2,deoxycytidine; the nucleotides: 2,deoxyadenosine 5,-monophosphate, 2,deoxyguanosine 5,-monophosphate, 2,deoxythymine 5,-monophosphate, 2,deoxycytidine 5,-monophosphate) was examined as a means of forming radical cations of the constituents of nucleic acids in the gas phase. In general, sufficient quantities of the ternary complexes [M(L3)(N)]2+ could be formed for MS/MS studies by subjecting methanolic solutions of mixtures of a metal salt [M(L3)X2] (where M,=,Cu(II) or Pt(II); L3,=,dien or tpy; X,=,Cl or NO3) and N to ESI. The only exceptions were thymine and its derivatives, which failed to form sufficient abundances of [M(L3)(N)]2+ ions when: (a) M,=,Pt(II) and L3,=,dien or tpy; (b) M,=,Cu(II) and L3,=,dien. In some instances higher oligomeric complexes were formed; e.g., [Pt(tpy)(dG)n]2+ (n,=,1,13). Each of the ternary complexes [M(L3)(N)]2+ was mass-selected and then subjected to collision-induced dissociation (CID) in a quadrupole ion trap. The types of fragmentation reactions observed for these complexes depend on the nature of all three components (metal, auxiliary ligand and nucleic acid constituent) and can be classified into: (i) a redox reaction which results in the formation of the radical cation of the nucleic acid constituent, N+.; (ii) loss of the nucleic acid constituent in its protonated form; and (iii) fragmentation of the nucleic acid constituent. Only the copper complexes yielded radical cations of the nucleic acid constituent, with [Cu(tpy)(N)]2+ being the preferred complex due to suppression, in this case, of the loss of the nucleobase in its protonated form. The yields of the radical cations of the nucleobases from the copper complexes follow the order of their ionization potentials (IPs): G (lowest IP),>,A,>,C,>,T (highest IP). Sufficient yields of the radical cations of each of the nucleobases allowed their CID reactions (in MS3 experiments) to be compared to their even-electron counterparts. Copyright © 2005 John Wiley & Sons, Ltd. [source] Metal-stabilized rare tautomers: N4 metalated cytosine (M = Li+, Na+, K+, Rb+ and Cs+), theoretical viewsAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 8 2003Majid Monajjemi Abstract Ab initio calculations indicate that metalation of the exocyclic amino group of cytosine by the elements of Group IA (Li, Na, K, Rb and Cs) induces protonation of a nucleobase ring nitrogen atom, and hence causes a proton shift from an exocyclic to an endocyclic nitrogen atom. Thus, this metal-assisted process leads to the generation of rare nucleobase tautomers. The calculations suggest that this kind of metalation increases the protonation energies of the aromatic ring of the nucleobase. The present study reports the quantum chemistry analysis of the metal-assisted tautomerization. The calculations clearly demonstrate that metalation of the exocyclic amino group of the nucleobase significantly increases the protonation energy of the aromatic rings of the nucleobase. Also, absolute anisotropy shift, molecular orbital and natural bond orbital calculations are compatible with these results. Copyright © 2003 John Wiley & Sons, Ltd. [source] Inhibitor design for ribonuclease A: the binding of two 5,-phosphate uridine analoguesACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2009Vicky G. Tsirkone In the quest for the rational design of selective and potent inhibitors for members of the pancreatic ribonuclease A (RNase A) family of biomedical interest, the binding of uridine 5,-phosphate (U5P) and uridine 5,-diphosphate (UDP) to RNase A have been investigated using kinetic studies and X-ray crystallography. Both nucleotides are competitive inhibitors of the enzyme, with Ki values of 4.0 and 0.65,mM, respectively. They bind to the active site of the enzyme by anchoring two molecules connected to each other by hydrogen bonds and van der Waals interactions. While the first of the inhibitor molecules binds with its nucleobase in the pyrimidinyl-binding subsite, the second is bound at the purine-preferring subsite. The unexpected binding of a pyrimidine at the purine-binding subsite has added new important elements to the rational design approach for the discovery of new potent inhibitors of the RNase A superfamily. [source] Crystallization of the hydantoin transporter Mhp1 from Microbacterium liquefaciensACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2008Tatsuro Shimamura The integral membrane protein Mhp1 from Microbacterium liquefaciens transports hydantoins and belongs to the nucleobase:cation symporter 1 family. Mhp1 was successfully purified and crystallized. Initial crystals were obtained using the hanging-drop vapour-diffusion method but diffracted poorly. Optimization of the crystallization conditions resulted in the generation of orthorhombic crystals (space group P212121, unit-cell parameters a = 79.7, b = 101.1, c = 113.8,Å). A complete data set has been collected from a single crystal to a resolution of 2.85,Å with 64,741 independent observations (94% complete) and an Rmerge of 0.12. Further experimental phasing methods are under way. [source] A Tale of Two Targets: Differential RNA Selectivity of Nucleobase,Aminoglycoside ConjugatesCHEMBIOCHEM, Issue 10 2006Kenneth F. Blount Dr. Aminoglycoside antibiotics are RNA-binding polyamines that can bind with similar affinities to structurally diverse RNA targets. To design new semisynthetic aminoglycosides with improved target selectivity, it is important to understand the energetic and structural basis by which diverse RNA targets recognize similar ligands. It is also imperative to discover how novel aminoglycosides could be rationally designed to have enhanced selectivity for a given target. Two RNA drug targets, the prokaryotic ribosomal A-site and the HIV-1 TAR, provide an excellent model system in which to dissect the issue of target selectivity, in that they each have distinctive interactions with aminoglycosides. We report herein the design, synthesis, and binding activity of novel nucleobase,aminoglycoside conjugates that were engineered to be more selective for the A-site binding pocket. Contrary to the structural design, the conjugates bind the A-site more weakly than does the parent compound and bind the TAR more tightly than the parent compound. This result implies that the two RNA targets differ in their ability to adapt to structurally diverse ligands and thus have inherently different selectivities. This work emphasizes the importance of considering the inherent selectivity traits of the RNA target when engineering new ligands. [source] Reaction of Cytidine Nucleotides with Cyanoacetylene: Support for the Intermediacy of Nucleoside-2,,3,-cyclic Phosphates in the Prebiotic Synthesis of RNACHEMBIOCHEM, Issue 6 2006Michael A. Crowe Abstract A robust and prebiotically plausible synthesis of RNA is a key requirement of the "RNA World" hypothesis, but, to date, no such synthesis has been demonstrated. Monomer synthesis strategies involving attachment of preformed nucleobases to sugars have failed, and, even if activated 5,-nucleotides could be made, the hydrolysis of these intermediates in water makes their efficient oligomerisation appear unlikely. We recently reported a synthesis of cytidine-2,,3,-cyclic phosphate 1 (C>p) in which the nucleobase was assembled in stages on a sugar-phosphate template. However, 2,,3,-cyclic nucleotides (N>p's) also undergo hydrolysis, in this case giving a mixture of the 2,- and 3,-monophosphates. This hydrolysis has previously been seen as making the, otherwise promising, oligomerisation of N>p's seem as unlikely as that of the 5,-activated nucleotides. We now find that cyanoacetylene, the reagent used for the second stage of nucleobase assembly in the synthesis of C>p, also reverses the effect of the hydrolysis by driving efficient cyclisation of C2,p and C3,p back to C>p. Excess cyanoacetylene also derivatises the nucleobase, but this modification is reversible at neutral pH. These findings significantly strengthen the case for N>p's in a prebiotic synthesis of RNA. [source] Fluorescent 5-Alkynyl-2,-Deoxyuridines: High Emission Efficiency of a Conjugated Perylene Nucleoside in a DNA DuplexCHEMBIOCHEM, Issue 5 2006Mikhail V. Skorobogatyi Abstract Four fluorescent 5-alkynyl-2,-deoxyuridines were studied in DNA oligonucleotides and their duplexes. The fluorescence response to hybridization differs dramatically for nucleosides containing a perylene fluorochrome either conjugated or not conjugated to the nucleobase. The conjugated nucleoside, 5-(perylen-3-ylethynyl)-2,-deoxyuridine, shows enhanced long-wavelength emission in the DNA duplex, in contrast to the blue fluorescence of perylene on a flexible linker (in 5-[(perylen-3-yl)methoxyprop-1-ynyl]-2,-deoxyuridine), which is quenched upon duplex formation. [source] Remarkable Stabilization of Duplex DNA Containing an Abasic Site by Non-Nucleosidic Phenanthroline and Pyrene Building BlocksCHEMBIOCHEM, Issue 5 2005Simon M. Langenegger Dipl.-Chem. Filling the gap. Abasic sites represent a frequently occurring lesion in DNA. If not repaired, such lesions can lead to mutations or cell death. Stabilization of DNA containing abasic sites is investigated as a therapeutic approach for the treatment of cancer. Non-nucleosidic phenanthroline and pyrene derivatives were found to have a profound stabilizing effect (,Tm=8,°C) on DNA missing a nucleobase. [source] Synthesis of the First Tellurium-Derivatized Oligonucleotides for Structural and Functional StudiesCHEMISTRY - A EUROPEAN JOURNAL, Issue 39 2009Jia Sheng Dr. Abstract We report here the first synthesis of Te-nucleoside phosphoramidites and Te-modified oligonucleotides. We protected the 2,-tellurium functionality by alkylation and found that the Te functionality is compatible with solid-phase synthesis and that the Te oligonucleotides are stable during deprotection and purification. In addition, the redox properties of the Te functionalities have been explored. We found that the telluride and telluoxide DNAs are interchangeable by redox reactions. At elevated temperature, the Te-DNA can also be site-specifically fragmented oxidatively or reductively when 2,-TePh functionality is present, whereas elimination of the nucleobase is observed in the presence of 2,-TeMe. Moreover, the stability of the DNA duplexes derivatized with the Te functionalities has been investigated. Our Te derivatization of nucleic acids provides a novel approach for investigating DNA damage as well as for structure and function studies of nucleic acids and their protein complexes. [source] G,G Base-Pairing in Nucleobase Adducts of the Anticancer Drug cis -[PtCl2(NH3)(2-picoline)] and Its trans IsomerCHEMISTRY - A EUROPEAN JOURNAL, Issue 15 2005Geraldine McGowan Abstract cis -[PtCl2(NH3)(2-picoline)] (AMD473) is a sterically-hindered anticancer complex with a profile of chemical and biological activity that differs significantly from that of cisplatin. Adducts of AMD473 with neutral 9-ethylguanine (9-EtGH) and anionic (N1-deprotonated) 9-ethylguanine (9-EtG) as perchlorate and nitrate salts, and also a nitrate salt of the trans isomer (AMD443), were prepared and their structures determined by X-ray crystallography: cis -[Pt(NH3)(2-pic)(9-EtGH)2](ClO4)2 (1),2,H2O,Me2CO, cis -[Pt(NH3)(2-pic)(9-EtGH)2](NO3)2 (2),2,H2O, cis -[Pt(NH3)(2-pic)(9-EtGH)(9-EtG)]NO3 (3),3.5,H2O, trans -[Pt(NH3)(2-pic)(9-EtGH)(9-EtG)]NO3 (4),8,H2O. In all cases, platinum coordination is through N7 of neutral (1, 2) and anionic (3, 4) guanine. In each complex, the guanine bases are arranged in the head-to-tail conformation. In complex 1, there is an infinite array of six-molecule cycles, based on both hydrogen bonding and ,,, stacking of the 2-picoline and guanine rings. Platinum(II) coordinated at N7 acidifies the N1 proton of neutral 9-ethylguanine (pKa=9.57) to give pKa1=8.40 and pKa2=8.75 for complex 2, and pKa1=7.77 and pKa2=9.00 for complex 4. In complexes 3 and 4, three intermolecular hydrogen bonds are formed between neutral and deprotonated guanine ligands involving O6, N1 and N2 sites. Unusually, both of the platinated guanine bases of complexes 3 and 4 participate in this triple GG hydrogen bonding. This is the first report of X-ray crystal structures of nucleobase adducts of the promising anticancer drug AMD473. [source] Highly Concise Synthesis of 3'-"Up"-ethynyl-5'-methylbicyclo- [3.1.0]hexyl Purine and Pyrimidine Nucleoside Derivatives Using Rhodium(II) Carbenoid Cycloaddition and Highly Diastereoselective Grignard ReactionCHINESE JOURNAL OF CHEMISTRY, Issue 12 2009Zunhua Yang Abstract Synthesis of north -5'-methylbicyclo[3.1.0]hexyl purine and pyrimidine nucleosides with an ethynyl group at C-3' position has been successfully accomplished by a facile method. Methylbicyclo[3.1.0]hexanone (±)- 5 having three contiguous chiral centers was remarkably simply constructed only by four steps containing a carbenoid insertion reaction in the presence of rhodium(II) acetate dimer and CuSO4, giving a correct relative stereochemistry of the generated three chiral centers. Upon Grignard reaction of (±)- 5 with ethynylmagnesium bromide, exclusive diastereoselectivity was observed. Condensation of glycosyl donor (±)- 9 with purine nucleobase afforded only the desired N9 -alkylated nucleoside, while condensation with pyrimidine, N3 -benzoylated uracil gave the desired N1 -alkylated nucleoside (±)- 13 with the undesired O2 -alkylated nucleoside (±)- 14. Probably, (±)- 14 would be formed due to steric hindrance caused upon approaching for N1 -alkylation. [source] Comparison of DNA-Reactive Metabolites from Nitrosamine and Styrene Using Voltammetric DNA/Microsomes SensorsELECTROANALYSIS, Issue 9 2009Sadagopan Krishnan Abstract Voltammetric sensors made with films of polyions, double-stranded DNA and liver microsomes adsorbed layer-by-layer onto pyrolytic graphite electrodes were evaluated for reactive metabolite screening. This approach features simple, inexpensive screening without enzyme purification for applications in drug or environmental chemical development. Cytochrome P450 enzymes (CYPs) in the liver microsomes were activated by an NADPH regenerating system or by electrolysis to metabolize model carcinogenic compounds nitrosamine and styrene. Reactive metabolites formed in the films were trapped as adducts with nucleobases on DNA. The DNA damage was detected by square-wave voltammetry (SWV) using Ru(bpy) as a DNA-oxidation catalyst. These sensors showed a larger rate of increase in signal vs. reaction time for a highly toxic nitrosamine than for the moderately toxic styrene due to more rapid reactive metabolite-DNA adduct formation. Results were consistent with reported in vivo TD50 data for the formation of liver tumors in rats. Analogous polyion/ liver microsome films prepared on 500,nm silica nanoparticles (nanoreactors) and reacted with nitrosamine or styrene, provided LC-MS or GC analyses of metabolite formation rates that correlated well with sensor response. [source] Multi-walled carbon nanotube composites with polyacrylate prepared for open-tubular capillary electrochromatographyELECTROPHORESIS, Issue 19 2010Jian-Lian Chen Abstract A new phase containing immobilized carbon nanotubes (CNTs) was synthesized by in situ polymerization of acid-treated multi-walled CNTs using butylmethacrylate (BMA) as the monomer and ethylene dimethacrylate as the crosslinker on a silanized capillary, forming a porous-layered open-tubular column for CEC. Incorporation of CNT nanomaterials into a polymer matrix could increase the phase ratio and take advantage of the easy preparation of an OT-CEC column. The completed BMA-CNT column was characterized by SEM, ATR-IR, and EOF measurements, varying the pH and the added volume organic modifier. In the multi-walled CNTs structure, carboxylate groups were the major ionizable ligands on the phase surface exerting the EOF having electroosmotic mobility, 4.0×104,cm2,V,1,S,1, in the phosphate buffer at pH 2.8 and RSD values (n=5), 3.2, 4.1, and 4.3%, for three replicate capillaries at pH 7.6. Application of the BMA-CNT column in CEC separations of various samples, including nucleobases, nucleosides, flavonoids, and phenolic acids, proved satisfactory upon optimization of the running buffers. Their optima were found in the borate buffers at pH 9.0/50,mM, pH 9.5/10,mM/50% v/v ACN, and pH 9.5/30,mM/10% v/v methanol, respectively. The separations could also be used to assess the relative contributions of electrophoresis and chromatography to the CEC mechanism by calculating the corresponding velocity and retention factors. Discussions about interactions between the probe solutes and the bonded phase included the ,,, interactions, electrostatic repulsion, and hydrogen bonding. Furthermore, a reversed-phase mode was discovered to be involved in the chromatographic retention. [source] Coordination Modes of 9-Methyladenine in cis -Platinum(II) Complexes with Dimethyl(phenyl)phosphanes as Ancillary Ligands , Synthesis and Characterization of cis -[PtL2(9-MeAd)2](NO3)2, cis -[PtL2{9-MeAd(,H)}]3(NO3)3, and cis -[L2Pt{9-MeAd(,H)}PtL2](NO3)3EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 1 2003Bruno Longato Abstract Treatment of 9-methyladenine (9-MeAd) with cis -[PtL2(NO3)2] (1) (L = PMe2Ph) in a 2:1 molar ratio generated the bis(adduct) cis -[PtL2(9-MeAd)2](NO3)2 (2), which was isolated and fully characterized by multinuclear (1H, 31P, 13C, 195Pt and 15N) NMR analysis, which showed that the two nucleobases are selectively coordinated through the N1 atom. Small amounts of a mono(adduct) cis -[PtL2(S)(9-MeAd)]2+ (3) (S = solvent) and of a diplatinated species cis -[L2Pt(S){9-MeAd(,H)}PtL2]3+ (4) are formed in DMSO solution when 9-MeAd is present in smaller quantities than 1. Complex 3 is platinated at N1, with a solvent molecule representing the fourth ligand around the metal center. Complex 4 contains an adenine molecule deprotonated and platinated at N1,N6,N7, with two cis -L2Pt units bonded to nitrogen atom N1 and to nitrogen atoms N6 and N7, respectively. With increasing relative concentration of the nucleobase, both complexes 3 and 4 progressively convert into the bis(adduct) 2, the only species detectable in solution when the Ad/Pt molar ratio is 2:1. The trinuclear compound cis -[L2Pt{9-MeAd(,H)}]3(NO3)3 (5) (L = PMe2Ph), containing an NH2 -deprotonated nucleobase bridging the metal centers through the N1 and N6 atoms, is quantitatively formed when the dinuclear hydroxo complex cis -[Pt(,-OH)L2]2(NO3)2 (6) reacts with 9-MeAd in CH3CN solution. The isolated complex was fully characterized by multinuclear NMR spectroscopy and mass spectrometry. It appears to be stable in solution in CH3CN and chlorinated solvents, whereas in DMSO it partially converts into a new species, probably the dinuclear analog cis -[PtL2{9-MeAd(,H)}]2(NO3)2, in which the adenine maintains its coordination mode. At equilibrium the trinuclear/dinuclear species molar ratio is 20:1. Through the addition of a stoichiometric amount of nitrate 1 to a DMSO solution of 5 we were able to generate the diplatinated compound 4 in high yield. Complex 4 displays a new coordination mode for the adeninate ion, with N1 bonded to one platinum atom whereas N6 and N7 are chelated to a second one. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Synthesis of 3,-BODIPY-Labeled Active Esters of Nucleotides and a Chemical Primer Extension Assay on BeadsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 19 2010Kerstin Gießler Abstract A solution-phase synthesis of active esters of 3,-fluorophore-labeled deoxynucleoside 5,-monophosphates was developed for thymine and cytosine as nucleobases by using two different BODIPY dyes. Starting from the respective 2,-amino-2,,3,-dideoxynucleoside-5,-monophosphate, the fluorescent oxyazabenzotriazolides can be prepared in one-pot procedures involving labeling and activation. Screening of a range of supports led to a chemical primer extension assay on beads with in situ detection of nucleobases in target DNA through optical read-out. [source] A Practical and Efficient Approach to PNA Monomers Compatible with Fmoc-Mediated Solid-Phase Synthesis Protocols,EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 34 2008Andrea Porcheddu Abstract A straightforward synthesis of orthogonally protected PNA monomers is described. Protected aminoethylglycine (Aeg) monomers were efficiently prepared by reductive amination of N -Fmoc-glycinaldehyde with glycine methyl ester and the subsequent acylation of the free amine with N -bis-Boc-protected nucleobase acetic acids. The exocyclic amine group of the nucleobases, including the notoriously difficult-to-protect guanine nucleobase, was protected with a bis-Boc carbamate group; this increased the solubility of the nucleobases in the most common organic solvents. The current protocol allows all Aeg monomers to be prepared on both the micro- and macroscale, which avoids or minimizes the use of toxic reagents or solvents, and moreover, cheap starting materials are used. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Uniformly Nucleobase-Functionalized ,-Peptide Helices: Watson,Crick Pairing or Nonspecific AggregationEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 33 2007Angelina Weiß Abstract The organization and architecture of helices is fundamental in folding of protein tertiary structures. Therefore, stable ,-peptide helices are used as models for the selective organization of secondary structures. Nucleobases are already established as recognition elements to organize two ,-peptide helices in antiparallel orientation. The investigation of ,-peptide helices uniformly functionalized with one type of nucleobases provided further insight in the recognition mode and requirements for specific interaction within the linear and very rigid helical backbone topology. Specific helix interaction based on base pair recognition is predominant as soon as Watson,Crick pairing is allowed. If the hydrogen bonding donor/acceptor pattern prohibits the Watson,Crick geometry, a quite stable nonspecific interaction was found based on aromatic interactions or on a nonspecific hydrogen bonding network. The latter aggregation was also confirmed with tyrosine side chains.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Divergent and Linear Solid-Phase Synthesis of PNA Containing Thiazole Orange as Artificial BaseEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 15 2005Dilip V. Jarikote Abstract Fluorescent nucleobase surrogates provide nucleic acids with interesting properties. We have recently introduced thiazole orange as base surrogate into PNA and found that the so-called FIT (Forced Intercalation of Thiazole orange) PNA probes signal hybridization by enhancements of fluorescence. Common approaches of modifying nucleobases or introducing nucleobase surrogates draw upon the usage of monomer building blocks that have been synthesized in solution phase. The need to prefabricate a base-modified building block can hold up progress if several base modifications or base surrogates are to be evaluated. Herein, a method for divergent solid-phase synthesis is presented that serves the purpose to facilitate the screening for base surrogates that fluoresce upon hybridization. An Fmoc/Aloc-protected submonomer allowed the application of commonly used Fmoc-based solid-phase synthesis protocols while removal of the fully orthogonal Aloc group enabled the on-resin introduction of base surrogates after the linear chain assembly had been completed. The divergent solid-phase synthesis strategy is automatable, gives overall yields matching those of linear solid-phase synthesis and, most importantly, provides rapid access to any kind of base-modified PNA. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Chemical Approach for the Study of the ,Kissing Complex' of Moloney murine leukaemia VirusHELVETICA CHIMICA ACTA, Issue 7 2008Sébastien Porcher Abstract The replication of Moloney murine leukaemia virus relies on the formation of a stable homodimeric ,kissing complex' of a GACG tetraloop interacting through only two C,G base pairs flanked of 5,-adjacent unpaired adenosines A9. Previous NMR investigations of a model stem loop 1 has not permitted to reveal the origin of this interaction. Therefore, with the aim of deeper comprehension of the phenomena, the model sequence 10 was prepared where position 9 has been substituted for a nucleoside offering a wider , -stacking. In this context, the wyosine phosphoramidite building block 2 was prepared and incorporated by adapting the conditions of the automated synthesis and developing original templated enzymatic ligation. However, no ,kissing interaction' has been observed for this model sequence 10 due to steric hindrance as confirmed by computational simulation. Consequently, several other model sequences, 18, 23,26, containing modified nucleosides were prepared. Finally, the importance of the cross-loop H-bond between G8 and G11 nucleobases was revealed by preparing a 18mer RNA hairpin 27, where the guanosine G8 has been substituted for inosine. The latter, which does not possess a C3 amino function compared to guanosine, is unable to form any ,kissing complex' demonstrating the importance of this secondary interaction in the formation of the complex. [source] | |||||||||||||||||||||||||||||||||||||