Discrimination of hairpin polyamides with an alpha-substituted-gamma-aminobutyric acid as a 5'-TG-3' reader in DNA minor groove

Pyrrole-imidazole (Py-Im) polyamides containing stereospecifically alpha-amino- or alpha-hydroxyl-substituted gamma-aminobutyric acid as a 5'-TG-3' recognition element were synthesized by machine-assisted Fmoc solid-phase synthesis. Their binding properties to predetermined DNA sequences containing a core binding site of 5'-TGCNCA-3'/3'-ACGN'GT-5' (N.N' = A.T, T.A, G.C, and C.G) were then systematically studied by surface plasmon resonance (SPR). SPR results revealed that the pairing of stereospecifically alpha-amino-/alpha-hydroxyl-substituted gamma-aminobutyric acids, (R or S)-alpha,gamma-diaminobutyric acid (gammaRN or gammaSN) and (R or S)-alpha-hydroxyl-gamma-aminobutyric acid (gammaRO or gammaSO), side-by-side with beta-alanine (beta) in such polyamides significantly influenced the DNA binding affinity and recognition specificity of hairpin polyamides in the DNA minor groove compared with beta/beta, beta/gamma, and gamma/beta pairings. More importantly, the polyamide Ac-Im-gammaSO-ImPy-gamma-ImPybetaPy-beta-Dp (beta/gammaSO) favorably binds to a hairpin DNA containing a core binding site of 5'-TGCNCA-3'/3'-ACGN'GT-5' (N.N' = A.T) with dissociation equilibrium constant (K(D)) of 1.9 x 10(-)(7) M over N.N' = T.A with K(D) = 3.7 x 10(-)(6) M, with a 19-fold specificity. By contrast, Ac-Im-gammaSN-ImPy-gamma-ImPybetaPy-beta-Dp (beta/gammaSN) binds to the above sequence with N.N' = A.T with K(D) = 8.7 x 10(-)(7) M over N.N' = T.A with K(D) = 8.4 x 10(-)(6) M, with a 9.6-fold specificity. The results also show that the stereochemistry of the alpha-substituent, as well as the alpha-substituent itself may greatly alter binding affinity and recognition selectivity of hairpin polyamides to different DNA sequences. Further, we carried out molecular modeling studies on the binding by an energy minimization method, suggesting that alpha-hydroxyl is very close to N3 of the 3'-terminal G to induce the formation of hydrogen bonding between hydroxyl and N3 in the recognition event of the polyamide Ac-Im-gammaSO-ImPy-gamma-ImPybetaPy-beta-Dp (beta/gammaSO) to 5'-TGCNCA-3'/3'-ACGN'GT-5' (N.N' = A.T). Therefore, SPR assays and molecular modeling studies collectively suggest that the (S)-alpha-hydroxyl-gamma-aminobutyric acid (gammaSO) may act as a 5'-TG-3' recognition unit.     

Interaction of the substrate radical and the 5'-deoxyadenosine-5'-methyl group in vitamin B(12) coenzyme-dependent ethanolamine deaminase

The distance and relative orientation of the C5' methyl group of 5'-deoxyadenosine and the substrate radical in vitamin B(12) coenzyme-dependent ethanolamine deaminase from Salmonella typhimurium have been characterized by using X-band two-pulse electron spin-echo envelope modulation (ESEEM) spectroscopy in the disordered solid state. The (S)-2-aminopropanol-generated substrate radical catalytic intermediate was prepared by cryotrapping steady-state mixtures of enzyme in which catalytically exchangeable hydrogen sites in the active site had been labeled by previous turnover on (2)H(4)-ethanolamine. Simulation of the time- and frequency-domain ESEEM requires two types of coupled (2)H. The strongly coupled (2)H has an effective dipole distance (r(eff)) of 2.2 A, and isotropic coupling constant (A(iso)) of -0.35 MHz. The weakly coupled (2)H has r(eff) = 3.8 A and A(iso) = 0 MHz. The best (2)H ESEEM time- and frequency-domain simulations are achieved with a model in which the hyperfine couplings arise from one strongly coupled hydrogen site and two equivalent weakly coupled hydrogen sites located on the C5' methyl group of 5'-deoxyadenosine. This model indicates that the unpaired electron on C1 of the substrate radical and C5' are separated by 3.2 A and are thus at closest contact. The close proximity of C1 and C5' indicates that C5' of the 5'-deoxyadenosyl moiety directly mediates radical migration between cobalt in cobalamin and the substrate/product site over a distance of 5-7 A in the active site of ethanolamine deaminase.     

A pyrazine-based fluorescence-enhancing ligand with a high selectivity for thymine in AP site-containing DNA duplexes

A fluorescent pyrazine derivative, 3,5-diamino-6-chloro-2-pyrazine carbonitrile (DCPC), is presented as a promising light-up ligand for single-nucleotide polymorphisms (SNPs) typing. In solutions buffered to pH 7.0 (I = 0.11 M, at 5 degrees C), DCPC can bind to thymine selectively over other nucleobases opposite an abasic site in DNA duplexes (5'-GTGTG CGTTG ANA TGGAC GCAGA-3'/3'-CACAC GCAAC TXT ACCTG CGTCT-5', X = abasic site, N = target nucleotide) with a dissociation constant of 2.6 microM. The binding of DCPC is accompanied by a significant enhancement of its fluorescence (lambda(max), 412 nm), and the response is highly selective to thymine base. These binding and sensing properties allow a clear detection of thymine-related mutations present in polymerase chain reaction (PCR) amplification products.     

Hydrogen abstraction from deoxyribose by a neighbouring uracil-5-yl radical

Hydrogen abstraction from the C1' and C2' positions of deoxyadenosine by a neighbouring uracil-5-yl radical in the 5'-AU*-3' DNA sequence is explored using DFT. This hydrogen abstraction is the first step in a sequence leading to single or double strand break in DNA. The uracil-5-yl radical can be the result of photolysis or low-energy electron (LEE) attachment. If the radical is produced by photolysis the neighbouring adenine will become a cation radical and if it is produced by LEE the adenine will remain neutral. The hydrogen abstraction reactions for both cases were investigated. It is concluded that it is possible for the uracil-5-yl to abstract hydrogen from C1' and C2'. When adenine is neutral there is a preference for the C1' site and when the adenine is a radical cation the C2' site is the preferred. If adenine is positively charged, the rate-limiting step when abstracting hydrogen from C1' is the formation of an intermediate crosslink between uracil and adenine. This crosslink might be avoided in dsDNA, making C1' the preferred site for abstraction.     

Reversible molecular switching of ruthenium bis(bipyridyl) groups bonded to oligothiophenes: effect on electrochemical and spectroscopic properties

We report the preparation of complexes in which ruthenium(II) bis(bipyridyl) groups are coordinated to oligothiophenes via a diphenylphosphine linker and a thienyl sulfur (P,S bonding) to give [Ru(bpy)(2)PT(3)-P,S](PF(6))(2) (bpy = 2,2'-bipyridyl, PT(3) = 3'-(diphenylphosphino)-2,2':5',2' '-terthiophene), [Ru(bpy)(2)PMeT(3)-P,S](PF(6))(2) (PMeT(3) = 3'-(diphenylphosphino)-5-methyl-2,2':5',2' '-terthiophene), [Ru(bpy)(2)PMe(2)T(3)-P,S](PF(6))(2) (PMe(2)T(3) = 5,5' '-dimethyl-3'-(diphenylphosphino)-2,2':5',2' '-terthiophene), and [Ru(bpy)(2)PDo(2)T(5)-P,S](PF(6))(2) (PDo(2)T(5) = 3,3' ' '-didodecyl-3' '-diphenylphosphino-2,2':5',2' ':5' ',2' ':5' ',2' ' '-pentathiophene). These complexes react with base, resulting in the complexes [Ru(bpy)(2)PT(3)-P,C]PF(6), [Ru(bpy)(2)PMeT(3)-P,C]PF(6), [Ru(bpy)(2)PMe(2)T(3)-P,C]PF(6), and [Ru(bpy)(2)PDo(2)T(5)-P,C]PF(6), where the thienyl carbon is bonded to ruthenium (P,C bonding). The P,C complexes revert back to the P,S bonding mode by reaction with acid; therefore, metal-thienyl bonding is reversibly switchable. The effect of interaction of the metal groups in the different bonding modes with the thienyl backbone is reflected by changes in alignment of the thienyl rings in the solid-state structures of the complexes, the redox potentials, and the pi --> pi transitions in solution. Methyl substituents attached to the terthiophene groups allow observation of the effect of these substituents on the conformational and electronic properties and aid in assignments of the electrochemical data. The PT(n)() ligands bound in P,S and P,C bonding modes also alter the electrochemical and spectroscopic properties of the ruthenium bis(bipyridyl) group. Both bonding modes result in quenching of the oligothiophene luminescence. Weak, short-lived Ru --> bipyridyl MLCT-based luminescence is observed for [Ru(bpy)(2)PDo(2)T(5)-P,S](PF(6))(2), [Ru(bpy)(2)PT(3)-P,C]PF(6), [Ru(bpy)(2)PMeT(3)-P,C]PF(6), and [Ru(bpy)(2)PMe(2)T(3)-P,C]PF(6), and no emission is observed for the alternate bonding mode of each complex.     

Sequence-specific alkylation by Y-shaped and tandem hairpin pyrrole-imidazole polyamides

To extend the target DNA sequence length of the hairpin pyrrole-imidazole (Py-Im) polyamide 1, we designed and synthesized Y-shaped and tandem hairpin Py-Im polyamides 2 and 3, which possess 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI) as DNA-alkylating moieties. High-resolution denaturing polyacrylamide gel electrophoresis by using 5'-Texas-Red-labeled 465 base pair (bp) DNA fragments revealed that conjugates 2 and 3 alkylated the adenine of the target DNA sequences at nanomolar concentrations. Conjugate 2 alkylated adenine N3 at the 3' end of two 8 bp match sequences, 5'-AATAACCA-3' (site A) and 5'-AAATTCCA-3' (site C), while conjugate 3 recognized one 10 bp match sequence, 5'-AGAATAACCA-3' (site A) in the 465 bp DNA fragments. These results demonstrate that seco-CBI conjugates of Y-shaped and tandem hairpin polyamides have extended their target alkylation sequences.     

Neomycin-neomycin dimer: an all-carbohydrate scaffold with high affinity for AT-rich DNA duplexes

A dimeric neomycin-neomycin conjugate 3 with a flexible linker, 2,2'-(ethylenedioxy)bis(ethylamine), has been synthesized and characterized. Dimer 3 can selectively bind to AT-rich DNA duplexes with high affinity. Biophysical studies have been performed between 3 and different nucleic acids with varying base composition and conformation by using ITC (isothermal calorimetry), CD (circular dichroism), FID (fluorescent intercalator displacement), and UV (ultraviolet) thermal denaturation experiments. A few conclusions can be drawn from this study: (1) FID assay with 3 and polynucleotides demonstrates the preference of 3 toward AT-rich sequences over GC-rich sequences. (2) FID assay and UV thermal denaturation experiments show that 3 has a higher affinity for the poly(dA)·poly(dT) DNA duplex than for the poly(dA)·2poly(dT) DNA triplex. Contrary to neomycin, 3 destabilizes poly(dA)·2poly(dT) triplex but stabilizes poly(dA)·poly(dT) duplex, suggesting the major groove as the binding site. (3) UV thermal denaturation studies and ITC experiments show that 3 stabilizes continuous AT-tract DNA better than DNA duplexes with alternating AT bases. (4) CD and FID titration studies show a DNA binding site size of 10-12 base pairs/drug, depending upon the structure/sequence of the duplex for AT-rich DNA duplexes. (5) FID and ITC titration between 3 and an intramolecular DNA duplex [d(5'-A(12)-x-T(12)-3'), x = hexaethylene glycol linker] results in a binding stoichiometry of 1:1 with a binding constant ～10(8) M(-1) at 100 mM KCl. (6) FID assay using 3 and 512 hairpin DNA sequences that vary in their AT base content and placement also show a higher binding selectivity of 3 toward continuous AT-rich than toward DNA duplexes with alternate AT base pairs. (7) Salt-dependent studies indicate the formation of three ion pairs during binding of the DNA duplex d[5'-A(12)-x-T(12)-3'] and 3. (8) ITC-derived binding constants between 3 and DNA duplexes have the following order: AT continuous, d[5'-G(3)A(5)T(5)C(3)-3'] > AT alternate, d[5'-G(3)(AT)(5)C(3)-3'] > GC-rich d[5'-A(3)G(5)C(5)T(3)-3']. (9) 3 binds to the AT-tract-containing DNA duplex (B* DNA, d[5'-G(3)A(5)T(5)C(3)-3']) with 1 order of magnitude higher affinity than to a DNA duplex with alternating AT base pairs (B DNA, d[5'-G(3)(AT)(5)C(3)-3']) and with almost 3 orders of magnitude higher affinity than a GC-rich DNA (A-form, d[5'-A(3)G(5)C(5)T(3)-3']).     

Preferred RNA binding sites for a threading intercalator revealed by in vitro evolution

In pursuit of small molecules capable of controlling the function of RNA targets, we have explored the RNA binding properties of peptide-acridine conjugates (PACs). In vitro evolution (SELEX) was used to isolate RNAs capable of binding the PAC Ser-Val-Acr-Arg, where Acr is an acridine amino acid. The PAC binds RNA aptamers selectively and with a high degree of discrimination over DNA. PAC binding sites contain the base-paired 5'-CpG-3' sequence, a known acridine intercalation site. However, RNA structure flanking this sequence causes binding affinities to vary over 30-fold. The preferred site (K(D) = 20 nM) contains a base-paired 5'-CpG-3' step flanked on the 5' side by a 4 nt internal loop and the 3' side by a bulged U. Several viral 5'- and 3'-UTR RNA sequences that likely form binding sites for this PAC are identified.     

Relationship between electrochemical potentials and substitution reaction rates of ferrocene-containing β-diketonato rhodium(I) complexes; cytotoxicity of [Rh(FcCOCHCOPh)(cod)

A series of ferrocene-containing rhodium complexes of the type [Rh(FcCOCHCOR)(cod)] (cod = 1,5-cyclooctadiene) with R = CF(3), 1, (E(pa)(Rh) = 269; E(o)'(Fc) = 329 mV vs. Fc/Fc(+)), CCl(3), 2, (E(pa) = 256; E(o)' = 312 mV), CH(3), 3, (E(pa) = 177; E(o)' = 232 mV), Ph = C(6)H(5), 4, (E(pa) = 184; E(o)' = 237 mV), and Fc = ferrocenyl = (C(5)H(5))Fe(C(5)H(4)), 5, (E(pa) = 135; E(o)'(Fc1) = 203; E(o)'(Fc2) = 312 mV), have been studied electrochemically in CH(3)CN. Results indicated that the rhodium(I) centre is irreversibly oxidised to Rh(III) in a two-electron transfer process before the ferrocenyl fragment is reversibly oxidized in a one-electron transfer process. The peak anodic (oxidation) potential, E(pa), (in V vs. Fc/Fc(+)) of the rhodium core in 1-5 relates to k(2), the second-order rate constant for the substitution of (FcCOCHCOR)(-) with 1,10-phenanthroline in [Rh(FcCOCHCOR)(cod)] to form [Rh(phen)(cod)](+) in methanol at 25 °C with the equation lnk(2) = 39.5 E(pa)(Rh) - 3.69, while the formal oxidation potential of the ferrocenyl groups in 1-5 relates to k(2) by lnk(2) = 40.8 E(o)'(Fc)-6.34. Complex 4 (IC(50) = 28.2 μmol dm(-3)) was twice as cytotoxic as the free FcCOCH(2)COPh ligand having IC(50) = 54.2 μmol dm(-3), but approximately one order of magnitude less toxic to human HeLa neoplastic cells than cisplatin (IC(50) = 2.3 μmol dm(-3)).     

Three-dimensional quantitative structure-activity relationship of nucleosides acting at the A3 adenosine receptor: analysis of binding and relative efficacy

The binding affinity and relative maximal efficacy of human A3 adenosine receptor (AR) agonists were each subjected to ligand-based three-dimensional quantitative structure-activity relationship analysis. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) used as training sets a series of 91 structurally diverse adenosine analogues with modifications at the N6 and C2 positions of the adenine ring and at the 3', 4', and 5' positions of the ribose moiety. The CoMFA and CoMSIA models yielded significant cross-validated q2 values of 0.53 (r2 = 0.92) and 0.59 (r2 = 0.92), respectively, and were further validated by an external test set (25 adenosine derivatives), resulting in the best predictive r2 values of 0.84 and 0.70 in each model. Both the CoMFA and the CoMSIA maps for steric or hydrophobic, electrostatic, and hydrogen-bonding interactions well reflected the nature of the putative binding site previously obtained by molecular docking. A conformationally restricted bulky group at the N6 or C2 position of the adenine ring and a hydrophilic and/or H-bonding group at the 5' position were predicted to increase A3AR binding affinity. A small hydrophobic group at N6 promotes receptor activation. A hydrophilic and hydrogen-bonding moiety at the 5' position appears to contribute to the receptor activation process, associated with the conformational change of transmembrane domains 5, 6, and 7. The 3D-CoMFA/CoMSIA model correlates well with previous receptor-docking results, current data of A3AR agonists, and the successful conversion of the A3AR agonist into antagonists by substitution (at N6) or conformational constraint (at 5'-N-methyluronamide).     

Organolathanide-catalyzed regioselective intermolecular hydroamination of alkenes, alkynes, vinylarenes, di- and trivinylarenes, and methylenecyclopropanes. Scope and mechanistic comparison to intramolecular cyclohydroaminations

Organolanthanide complexes of the type Cp'(2)LnCH(SiMe(3))(2) (Cp' = eta(5)-Me(5)C(5); Ln = La, Nd, Sm, Lu) and Me(2)SiCp' '(2)LnCH(SiMe(3))(2) (Cp' ' = eta(5)-Me(4)C(5); Ln = Nd, Sm, Lu) serve as efficient precatalysts for the regioselective intermolecular hydroamination of alkynes R'Ctbd1;CMe (R' = SiMe(3), C(6)H(5), Me), alkenes RCH=CH(2) (R = SiMe(3), CH(3)CH(2)CH(2)), butadiene, vinylarenes ArCH=CH(2) (Ar = phenyl, 4-methylbenzene, naphthyl, 4-fluorobenzene, 4-(trifluoromethyl)benzene, 4-methoxybenzene, 4-(dimethylamino)benzene, 4-(methylthio)benzene), di- and trivinylarenes, and methylenecyclopropanes with primary amines R' 'NH(2) (R' ' = n-propyl, n-butyl, isobutyl, phenyl, 4-methylphenyl, 4-(dimethylamino)phenyl) to yield the corresponding amines and imines. For R = SiMe(3), R = CH(2)=CH lanthanide-mediated intermolecular hydroamination regioselectively generates the anti-Markovnikov addition products (Me(3)SiCH(2)CH(2)NHR' ', (E)-CH(3)CH=CHCH(2)NHR' '). However, for R = CH(3)CH(2)CH(2), the Markovnikov addition product is observed (CH(3)CH(2)CH(2)CHNHR' 'CH(3)). For internal alkynes, it appears that these regioselective transformations occur under significant stereoelectronic control, and for R' = SiMe(3), rearrangement of the product enamines occurs via tautomerization to imines, followed by a 1,3-trimethylsilyl group shift to stable N-SiMe(3)-bonded CH(2)=CMeN(SiMe(3))R' ' structures. For vinylarenes, intermolecular hydroamination with n-propylamine affords the anti-Markovnikov addition product beta-phenylethylamine. In addition, hydroamination of divinylarenes provides a concise synthesis of tetrahydroisoquinoline structures via coupled intermolecular hydroamination/subsequent intramolecular cyclohydroamination sequences. Intermolecular hydroamination of methylenecyclopropane proceeds via highly regioselective exo-methylene C=C insertion into Ln-N bonds, followed by regioselective cyclopropane ring opening to afford the corresponding imine. For the Me(2)SiCp' '(2)Nd-catalyzed reaction of Me(3)SiCtbd1;CMe and H(2)NCH(2)CH(2)CH(2)CH(3), DeltaH() = 17.2 (1.1) kcal mol(-)(1) and DeltaS() = -25.9 (9.7) eu, while the reaction kinetics are zero-order in [amine] and first-order in both [catalyst] and [alkyne]. For the same substrate pair, catalytic turnover frequencies under identical conditions decrease in the order Me(2)SiCp' '(2)NdCH(SiMe(3))(2) > Me(2)SiCp' '(2)SmCH(SiMe(3))(2) > Me(2)SiCp' '(2)LuCH(SiMe(3))(2) > Cp'(2)SmCH(SiMe(3))(2), in accord with documented steric requirements for the insertion of olefinic functionalities into lanthanide-alkyl and -heteroatom sigma-bonds. Kinetic and mechanistic evidence argues that the turnover-limiting step is intermolecular C=C/Ctbd1;C bond insertion into the Ln-N bond followed by rapid protonolysis of the resulting Ln-C bond.     

Activated Sterically Strained C = N Bond in N-Arylsulfonyl-p-quinonemono- and Diimines: IX. Synthesis and Reactions of N-Tosyl-2,3,5,6-tetramethyl-1,4-benzoquinonimine

N-Tosyl-2'3'5'6-tetramethyl-1'4-benzoquinonimine as the other N-arylsulfonyl-1'4-benzo-quinonimines with an activated C = N bond reacts along 1'2-addition path with alcohols, sodium azideand along 1,2-addition-elimination path with aromatic amines. The higher activity of the C = N bond in theN-arylsulfonyl-1,4-benzoquinonimines is not due to the electronic character of the substituent attached to the ring (Cl, CH₃) but to steric influence resulting in increase in the bond angle C = N-S.     

Intramolecular cyclization of ruthenium vinylidene complexes with a tethering vinyl group: facile cleavage and reconstruction of the C-C double bond

Protonation of ruthenium acetylide complexes [M]-*C*CCPh2CH2CH=CH2 (2a, [M] = (eta5-C5H5)(P(OPh)3)(PPh3)Ru; 2a', [M] = (eta5-C5H5)(dppp)Ru; *C = 13C-labeled carbon atom) with HBF4 in ether produces [[M]=*C=CHCH2CPh2*CH=CH2][BF4] (4, 4') exclusively via a metathesis process of the terminal vinyl group with the *C=*C of the resulting vinylidene group. For 4 in methanol, bond reconstruction of the two labeled *C atoms readily takes place via a retro-metathesis process followed by a cyclization of the resulting vinylidene ligand giving the cyclic carbene complex 5, which is fully characterized by single-crystal X-ray diffraction analysis. The protonation of 2a in MeOH is followed by a cyclization, also giving 5. Deuterium-labeling study indicates that the C-C bond formation of this cyclization proceeds simultaneously with the formation of 4 consistent with facile cleavage and reconstruction of C=C bonds. For comparison, complex 4 in alcohol yields, besides 5, the corresponding alkoxycyclohexene 6. Formation of 6 from 4 also involves a skeletal rearrangement with reconstruction of the C=C bond. Interestingly, [[Ru']=*C=C(Me)CH2CPh2*CH=CH2][BF4] (8') originally from a complex with two connected labeled carbon atoms also undergoes reestablishment of the *C=*C bond yielding the cyclic allenyl complex 9'. 13C-labeling studies clearly reveal the reestablishment of two C=C double bonds in the transformation of both 4 to 5 and 8' to 9'. The proposed mechanism implicates a cyclobutylidene intermediate formed either via a regiospecific [2+2] cycloaddition of two double bonds in the ruthenium vinylidene 4 or via a cyclization of 4 giving a nonclassical ion intermediate followed by a 1,2-alkyl shift.     

Free radical chemistry of flavan-3-ols: determination of thermodynamic parameters and of kinetic reactivity from short (ns) to long (ms) time scale

The physical chemistry and the free radical chemistry of the most abundant polyphenolic flavan-3-ols in food, catechin, its methylated metabolites, and several methylated analogues, have been investigated by laser flash photolysis and cyclic voltammetry studies. Two independent phenoxyl radicals formed upon oxidation of flavan-3-ols have been characterized and identified unambiguously: a short-lived resorcinol-like radical characterized by an absorption band at lambda = 495 nm and a long-lived catechol-like transient absorbing at lambda = 380 nm. The determination of all the thermodynamic constants of each phenolic function of flavan-3-ols, namely, redox potential (E degrees (3') = 0.13(5) V/SCE, E degrees (4') = 0.11(0) V/SCE, E degrees (5) = 0.28(5) V/SCE) and microscopic dissociation constants (pK(a3') = 9.02, pK(a4') = 9.12, pK(a5) = 9.43, pK(a7) = 9.58) were performed. These values are discussed and compared to the prediction of the density functional theory calculations made on the different species catechin, catechin phenoxyl, and catechin phenolate for each phenolic site.     

Solution self-assembly, spontaneous deprotonation, and crystal structures of bipyrazolate-bridged metallomacrocycles with dimetal centers

A series of nanosized cavity-containing bipyrazolate-bridged metallomacrocycles with dimetal centers, namely, {[(bpy)M]8L4}(NO3)8 [L=3,3',5,5'-tetramethyl-4,4'-bipyrazolyl, Pd, Pt; 1,4-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene), Pd; and 1,4-bis-4'-(3',5'-dimethyl)-pyrazolylbiphenyl, Pd], {[(phen)M]8L4}(NO3)8 [L=3,3',5,5'-tetramethyl-4,4'-bipyrazolyl, Pd, Pt; 1,4-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene, Pd; and 1,4-bis-4'-(3',5'-dimethyl)-pyrazolylbiphenyl, Pd], {[(bpy)Pd]6L3}(NO3)6 [L=1,4-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene,], {[(phen)Pd]6L3}(NO3)6 [L=1,4-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene,], {[(bpy)Pd]4L2}(NO3)4 [L=1,3-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene, and 1,2-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene,], and {[(phen)Pd]4L2}(NO3)4 [L=1,3-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene, and 1,2-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene,] (where bpy=2,2'-bipyridine and phen=1,10-phenanthroline) have been synthesized through a directed self-assembly approach that involves spontaneous deprotonation of the 1H-bipyrazolyl ligands in aqueous solution. These complexes, with weak Pd(II)...Pd(II) or Pt(II)...Pt(II) interactions, have been characterized by elemental analysis, 1H and 13C NMR, cold-spray ionization or electrospray ionization mass spectrometry, UV-visible spectroscopy, and luminescence spectroscopy. Complexes and have also been characterized by single-crystal X-ray diffraction analysis.     

Photochromic isomerization of a dinuclear molybdenum complex with ethylene-1,2-dithiolate and disulfur ligands: x-ray structures of the two isomers

A photochromic complex with disulfur and dimethyl-ethylene-1,2-dithiolate ligands, [Mo(2)(mu-S(2))(mu-S(2)C(2)Me(2))(2)(S(2)C(2)Me(2))(2)] (3), was synthesized and characterized. Photoirradiation of 3 with visible light resulted in the formation of the isomer (3'). The electronic spectrum of 3' has a new intense peak in the near infrared region, and in the dark, the spectrum returns to that of 3. X-ray structural analyses of 3.C(6)H(6) and 3' revealed a large conformational change of the bridging dithiolate ligands: the two ligands in 3' come very close to each other compared to those in 3.C(6)H(6). Crystal data: 3.C(6)H(6), monoclinic, space group C2/c, a = 15.193(4) A, b = 14.287(3) A, c = 14.685(4) A, beta = 105.30(1) degrees, V = 3074(1) A(3), Z = 4; 3', monoclinic, space group C2/c, a = 21.5400(8) A, b = 9.5232(5) A, c = 13.9828(2) A, beta = 118.924(1) degrees, V = 2510.5(2) A(3), Z = 4. (1)H NMR spectra of 3 (3.06, 3.05, 1.66, and 1.31 ppm) and 3' (2.90, 2.75, 2.14, and 1.97 ppm) are also reported: each spectrum has four signals due to methyl groups, which accords well with the fact that each of the molecules, 3.C(6)H(6) and 3', has a crystallographic 2-fold axis.     

Unsaturated didehydrodeoxycytidine drugs. 1. Impact of C=C positions in the sugar ring

The chemical names of a pair of recently synthesized antitumor drugs are given in the present study as 1',2'-didehydro-3',4'-deoxycytidine and 3',4'-didehydro-2',4'-deoxycytidine. The order of stabilities, geometries, and ionization potentials of the unsaturated sugar-modified cytidine derivatives is investigated quantum mechanically. Our density functional theory calculations based on the B3LYP/6-311++G** model reveal that 3',4'-didehydro-2',4'-deoxycytidine (SD-C2) is slightly more stable than its isomer, 1',2'-didehydro-3',4'-deoxycytidine, by an energy of 5.28 kJ x mol(-1) in isolation. The isomers structurally differ by only the C=C location in the sugar ring. However, the compounds exhibit an unusual orientation with a less puckered sugar ring; that is, 3',4'-didehydro-2',4'-deoxycytidine is determined to be a beta-nucleoside, which is a C1'-endo, north conformer with an anticlinal sugar ring, whereas 1',2'-didehydro-3',4'-deoxycytidine is neither an alpha-nucleoside nor a beta-nucleoside but is a C4'-endo, south conformer with an antiperiplanar sugar ring. The present study further indicates that the C=C double bond location imposes significant effects on their ionization potentials (IPs) and other important molecular properties such as molecular electrostatic potential (MEP). In addition, inner shell binding energy spectral variations with respect to the C=C bond exhibit more site dependence. The valence shell binding energy spectral changes are, on the other hand, significant and delocalized. The latter indicates that such changes in valence space are not isolated effects but are within the entire nucleoside. Finally, the present study suggests that the nearly 0.6 eV difference in the first ionization potentials (highest occupied molecular orbital) of the isomers is sufficiently large to identify them by further spectroscopic measures.     

Backbone dynamics in the DNA HhaI protein binding site

The dynamics of the phosphodiester backbone in the [5'-GCGC-3'] 2 moiety of the DNA oligomer [d(G 1A 2T 3A 4 G 5 C 6 G 7 C 8T 9A 10T 11C 12)] 2 are studied using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs nonstereospecifically deuterated on the 5' methylene group of nucleotides within the [5'-GCGC-3'] 2 moiety indicated that all of these positions are structurally flexible. Previous work has shown that methylation reduces the amplitude of motion in the phosphodiester backbone and furanose ring of the same DNA, and our observations indicate that methylation perturbs backbone dynamics through not only a loss of mobility but also a change of direction of motion. These NMR data indicate that the [5'-GCGC-3'] 2 moiety is dynamic, with the largest amplitude motions occurring nearest the methylation site. The change of orientation of this moiety in DNA upon methylation may make the molecule less amenable to binding to the HhaI endonuclease.     

Sequence selective recognition in the minor groove of dsDNA by pyrrole,imidazole-substituted bis-benzimidazole conjugates

A series of pyrrole, imidazole-substituted bis-benzimidazole conjugates, Py-Py-Im-gamma-biBenz, Py-Py-gamma-biBenz, Py-Im-gamma-biBenz, and Im-Py-gamma-biBenz (1-4), were prepared in an attempt to target dsDNA sequences possessing both A/T and G/C bps. The dsDNA interactions and sequence specificity of the conjugates have been characterized via spectrofluorometric titrations and thermal melting studies. All conjugates form 1:1 complexes with dsDNA at subnanomolar concentrations. The Im moiety selectively recognizes a G/C bp embedded in the A/T-rich binding site. This represents the first clear example of sequence selective recognition in a 1:1 motif.(1) The equilibrium association constant (K(1)) for complexation of a specific nine-bp dsDNA site, 5'-gcggTATGAAATTcgacg-3', by conjugate 1 is approximately 2.6 x 10(9) M(-1). Displacement of the G/C position or G/C-->A/T substitution within the nine-bp site decreases the K(1) by approximately 8-fold, whereas two continuous G/C bps decrease the K(1) by approximately 50-fold magnitude. The K(1) values for seven-bp dsDNA, 5'-gcggtaTGAAATTcgacg-3' and 5'-gcggtaCAAAATTcgacg-3', binding sites by conjugates Py-Im-gamma-biBenz (3) and Im-Py-gamma-biBenz (4) are approximately 2.3 x 10(9) and approximately 1.2 x 10(9) M(-1), respectively. However, the conjugates with no Im moiety, Py-Py-gamma-biBenz (2) and Py-Py-Py-gamma-biBenz (5 and 6), are specific for seven- to nine-bp A/T-rich sites and single A/T-->G/C bp substitution within the binding site decreases the K(1) values by 1-2 orders of magnitude.     

Remarkable stability of hairpins containing 2',5'-linked RNA loops.

We report here the results of a comparative study of hairpin loops that differ in the connectivity of phosphodiester linkages (3',5'- versus 2',5'-linkages). In addition, we have studied the effect of changing the stem composition on the thermodynamic stability of hairpin loops. Specifically, we constructed hairpins containing one of six stem duplex combinations, i.e., DNA:DNA ("DD"), RNA:RNA ("RR"), DNA:RNA ("DR"), 2',5'-RNA:RNA ("RR"), 2',5'-RNA:DNA ("RD"), and 2',5'-RNA:2',5'-RNA ("RR"), and one of three tetraloop compositions, i.e., 2',5'-RNA ("R"), RNA ("R"), and DNA ("D"). All hairpins contained the conserved and well-studied loop sequence 5'-...C(UUCG)G...-3' [Cheong et al. Nature 1990, 346, 680-682]. We show that the 2',5'-linked loop C(UUCG)G, i.e.,...C(3'p5')U(2'p5')U(2'p5')C(2'p5')G(2'p5')G(3'p5')..., like its "normal" RNA counterpart, forms an unusually stable tetraloop structure. We also show that the stability imparted by 2',5'-RNA loops is dependent on base sequence, a property that is shared with the regioisomeric 3',5'-RNA loops. Remarkably, we find that the stability of the UUCG tetraloop is virtually independent of the hairpin stem composition (DD, RR, RR, etc.), whereas the native RNA tetraloop exerts extra stability only when the stem is duplex RNA (R:R). As a result, the relative stabilities of hairpins with a 2',5'-linked tetraloop, e.g. ggac(UUCG)gtcc (T(m) = 61.4 degrees C), are often superior to those with RNA tetraloops, e.g. ggac(UUCG)gtcc (T(m) = 54.6 degrees C). In fact, it has been possible to observe the formation of a 2',5'-RNA:DNA hybrid duplex by linking the hybrid's strands to a (UUCG) loop. These duplexes (RD), which are not stable enough to form in an intermolecular complex [Wasner et al. Biochemistry 1998, 37, 7478-7486], were stable at room temperature (T(m) approximately 50 degrees C). Thus, 2',5'-loops have potentially important implications in the study of nucleic acid complexes where structural data are not yet available. Furthermore, they may be particularly useful as structural motifs for synthetic ribozymes and nucleic acid "aptamers".