Solvatochromism of a Novel Betaine Dye Derived from Purine

A novel solvatochromic betaine dye has been synthesized from xanthosine and characterized spectroscopically by UV-vis in a broad range of solvents. The dye 9-(2',3',5'-tri-O-acetyl-beta-d-ribofuranosyl)-2-(pyridinium-1-yl)-9H-purin-6-olate, 1a, exhibits solvent-induced spectral band shifts that are (2)/(3) as large as that of the betaine known as Reichardt's dye, which forms the basis of the E(T)(30) solvent polarity scale. Moreover, the dye 1a is a ribonucleoside and hence has the potential application as a polarity probe for application in RNA oligonucleotides. The isomeric dye 6-(pyridinium-1)-yl-9H-purin-2-olate, 2a, has also been synthesized and exhibits slightly smaller solvatochromic band shifts. The new betaine dyes have also been studied by comparing the experimental and calculated solvatochromic shifts based on the calculation of the UV/vis absorption spectra, using a combination of methods with density functional theory (DFT). The COSMO continuum dielectric method, an applied electric field term in the Hamiltonian, and time-dependent density functional theory (TD-DFT) methods were used to obtain absorption energies, ground-state dipole moments, and the difference dipole moment between the ground and excited states. The calculations predict a lower energy absorption band of charge-transfer character that is highly solvatochromic, and a higher energy absorption band that has pi-pi character which is not solvatochromic, in agreement with the experimental data. For Reichardt's dye the difference dipole moment between the ground and excited state (Deltamu = mu(e) - mu(g)) was also calculated and compared to experiment: Deltamu(calcd) = -6 D and Deltamu(exptl) = -9 +/- 1 D.(1) The ground-state dipole moment was found to be mu(g)(calcd) = 18 D and mu(g)(exptl) = 14.8 +/- 1.2 D.(1).

Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions

Structures of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 have been determined by NMR spectroscopy under low salt conditions. All protons and phosphorus nuclei resonances have been assigned. Signals of H5'/5" have been assigned stereospecifically. All 3JH,H and 3JP,H coupling constants have been measured. The structures were determined and refined using an iterative relaxation matrix procedure (IRMA) and the restrained MD simulation. Both duplexes form half-turn, right-handed helices with several conformational features which deviate significantly from a canonical A-RNA structure. Duplexes are characterised as having C3'-endo sugar pucker, very low base-pair rise and high helical twist and inclination angles. Helices are overwound with <10 bp per turn. There is limited inter-strand guanine stacking for CG steps. Within CG steps of both duplexes, the planes of the inter-strand cytosines are not parallel while guanines are almost parallel. For the GC steps this pattern is reversed. The 2'-O-methyl groups are spatially close to the 5'-hydrogens of neighbouring residues from the 3'-side and are directed towards the minor groove of 2'-O-Me(CGCGCG)2 forming a hydrophobic layer. Solution structures of both duplexes are similar; the effect of 2'-O-methylation on the parent RNA structure is small. This suggests that intrinsic properties imposed by alternating CG base pairs govern the overall conformation of both duplexes.

Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA

The molecular and crystal structure of 2'-O-Me (CGCGCG)2 has been determined using synchrotron radiation at near-atomic resolution (1.30 A), the highest resolution to date in the RNA field. The crystal structure is a half-turn A-type helix with some helical parameters deviating from canonical A-RNA, such as low base pair rise, elevated helical twist and inclination angles. In CG steps, inter-strand guanines are parallel while cytosines are not parallel. In steps GC this motif is reversed. This type of regularity is not seen in other RNA crystal structures. The structure includes 44 water molecules and two hydrated Mg2+ions one of which lies exactly on the crystallographic 2-fold axis. There are distinct patterns of hydration in the major and the minor grooves. The major groove is stabilised by water clusters consisting of fused five- and six-membered rings. Minor groove contains only a single row of water molecules; each water bridges either two self-parallel cytosines or two self-parallel guanines by a pair of hydrogen bonds. The structure provides the first view of the hydration scheme of 2'-O-methylated RNA duplex.

High salt solution structure of a left-handed RNA double helix

Right-handed RNA duplexes of (CG)n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix (CGCGCG)2 determined in 6 M NaClO4. This is the first nucleic acid motif determined at such high salt. Sequential assignments of non-exchangeable proton resonances of the Z-form were based on the hitherto unreported NOE connectivity path [H6(n)-H5'/H5''(n)-H8(n+1)-H1'(n+1)-H6(n+2)] found for left-handed helices. Z-RNA structure shows several conformational features significantly different from Z-DNA. Intra-strand but no inter-strand base stacking was observed for both CpG and GpC steps. Helical twist angles for CpG steps have small positive values (4-7 degrees), whereas GpC steps have large negative values (-61 degrees). In the full-turn model of Z-RNA (12.4 bp per turn), base pairs are much closer to the helix axis than in Z-DNA, thus both the very deep, narrow minor groove with buried cytidine 2'-OH groups, and the major groove are well defined. The 2'-OH group of cytidines plays a crucial role in the Z-RNA structure and its formation; 2'-O-methylation of cytidine, but not of guanosine residues prohibits A to Z helicity reversal.

The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)(2) duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove

The crystal and molecular structure of 2'-O-Me(CGCGCG)(2) has been determined at 1.19 A resolution, at 100 K, using synchrotron radiation. The structure in space group P3(2)12 is a half-turn right-handed helix that includes two 2-methyl-2,4-pentanediol (MPD) molecules bound in the minor groove. The structure deviates from A-form RNA. The duplex is overwound with an average value of 9.7 bp per turn, characterised as having a C3'-endo sugar pucker, very low base pair rise and high helical twist and inclination angles. The structure includes 65 ordered water molecules. Only a single row of water molecules is observed in the minor groove due to the presence of hydrophobic 2'-O-methyl groups. As many as five magnesium ions are located in the structure. Two are in the major groove and interact with O(6) and N(7) of guanosine and N(4) of cytidine residues through their hydration spheres. This work provides the first example of molecular interactions of nucleic acids with MPD, which was used as a precipitant, cryo-solvent and resolution enhancing agent. The two MPD molecules intrude into the hydration network in the minor groove, each forming hydrogen bonds between their secondary hydroxyl group and exo-amino functions of guanosine residues. Comparison of the 2'-O-Me(CGCGCG)(2) structure in the P3(2)12 and P6(1)22 crystals delineates stability of the water network within the minor groove to dehydration by MPD and is of interest for evaluating factors governing small molecule binding to RNA. Intrusion of MPD into the minor groove of 2'-O-Me(CGCGCG)(2) is discussed with respect to RNA dehydration, a prerequisite of Z-RNA formation.

Carbostyril derivatives having potent beta-adrenergic agonist properties

Derivatives carrying a substituent in the para position of the phenyl group of 8-hydroxy-5-[2-[(1-phenyl-2-methylprop-2-yl)amino]-1-hydroxyethyl] carbostyril (10) were prepared and their effects on beta-adrenoceptors evaluated in vitro. Unsubstituted compound 10, iodo 11, amino 12, and bromoacetamido 13 derivatives (all racemic) bound to the receptor with 15-100-fold lower dissociation constants than that of (-)-isoproterenol. All the above compounds stimulated adenylate cyclase more potently than (-)-isoproterenol. The intrinsic activities of compounds 10 and 12 were equal to that of (-)-isoproterenol. The intrinsic activities of compounds 11 and 13 were 1.3 and 1.2 times that of (-)-isoproterenol, respectively. Treatment of membrane preparations with bromoacetamido derivative 13 resulted in an irreversible loss of binding sites, and thus, 13 seems to be an alkylating affinity label for beta-adrenoceptors.

Affinity labels for beta-adrenoceptors: preparation and properties of alkylating beta-blockers derived from indole

New alkylating ligands derived from indole with high affinity for beta-adrenoceptors were synthesized and their properties examined. N8-(Bromoacetyl)-N1-[3-(4-indolyloxy)-2-hydroxypropyl]-(Z)-1,8-dia mino-p- menthane (8) and its N1,N8 isomer (9) were prepared by the reaction of bromoacetyl bromide with a product of the condensation of 4-indolyl glycidyl ether with (Z)-1,8-diamino-p-menthane. A similar reaction employing 2-cyano-4-indolyl glycidyl ether yielded the respective cyano derivatives 10 and 11. Apparent affinities (Ki, M) for beta-adrenoceptors on membrane preparations from rat heart and lung were 4.6 X 10(-10) and 1.34 X 10(-9) for 8, 2.3 X 10(-8) and 4.5 X 10(-9) for 9, 6.1 X 10(-10) and 1.49 X 10(-9) for 10, and 1.83 X 10(-9) and 2.78 X 10(-9) for 11, respectively. When membranes were preincubated with the above ligands (1 X 10(-8) M, 30 min, 30 degrees C) and then washed extensively, reduction in the concentration of specific binding sites of [3H]dihydroalprenolol ranged from 7% to 76% and there was no change in KD of the remaining binding sites. (+/-)-Alprenolol and (-)-isoproterenol, but not (+)-isoproterenol, when included with the alkylating ligands in the preincubation mixtures, prevented the reduction in concentration of [3H]dihydroalprenolol binding sites. Compounds 8-11 alone did not stimulate adenylate cyclase activity in rat heart homogenates. However, these compounds inhibited (-)-isoproterenol-stimulated adenylate cyclase activity with Ki values ranging between 5 X 10(-9) and 60 X 10(-9) M. These results suggest that high-affinity irreversible beta-adrenergic antagonists were obtained that may be useful for in vivo studies of beta-adrenoceptors.

beta-Adrenergic antagonists with multiple pharmacophores: persistent blockade of receptors

beta-Adrenergic antagonists containing from one to four identical pharmacophores were prepared and studied. These compounds had the general structure R2NCH(CH3)CH2[-OCH2CH(CH3)-]2-8NR2, where R is either H or an aryl-OCH2CHOHCH2 group. Synthesis was achieved by reaction of aryl glycidyl ethers with Jeffamines, which are primary diamines used in the manufacture of plastics. The following aryl groups were used: 2-allyphenyl, 4-(2-methoxyethyl)phenyl, 1-naphthyl, and 4-methoxyphenyl. The first three correspond to moieties of the established drugs alprenolol, metoprolol, and propranolol, respectively. The affinities of these compounds for beta-adrenergic receptors of rat heart and lung were estimated by measuring their ability to compete with the specific binding of (-)-[3H]-dihydroalprenolol. Compounds containing one pharmacophore bound to the receptors with affinities comparable to those of the parent drugs and the blockade of receptors could be dissociated by successive washes as easily as were those of the parent drugs. Compounds containing two or three pharmacophores had somewhat lower affinities for receptors, but the resulting blockade was persistent even after successive washing.

Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex

The structures of two crystal forms of the RNA 16-mer with the sequence GUGGUCUGAUGAGGCC, grown in the presence of a high concentration of sulphate ions, have been determined using synchrotron radiation at 1.4- and 2.0-A resolution. RNA with this sequence is known as one of the two strands of the noncleavable form of the hammerhead ribozyme. In both crystal structures, two G(syn)-G(anti) noncanonical base pairs are observed in the middle of a 14 base-pair (bp) duplex having 5'-dangling GU residues. Both structures contain sulphate anions interacting with the G-G bp stabilizing G in its syn conformation and bridging the two RNA strands. In both cases the interactions take place in the major groove, although the anions are accommodated within different helix geometries, most pronounced in the changing width of the major groove. In one structure, where a single sulphate spans both G-G pairs, the major groove is closed around the anion, while in the other structure, where each of the two G-G pairs is associated with a separate sulphate, the groove is open. This work provides the first examples of a G-G pair in syn-anti conformation, which minimizes the purine-purine clash in the center of the duplex, while utilizing its residual hydrogen bonding potential in specific interactions with sulphate anions.

Highly efficient fluorescent interstrand photo-crosslinking of DNA duplexes labeled with 5-fluoro-4-thio-2'-o-methyluridine

The formation of a fluorescent photoadduct between 5-fluoro-4-thiouridine ((FS) U), in the sequence context 5'-A(FS) UA-3' and incorporated into a synthetic oligonucleotide either at its 3'- or 5'-end, and one of the thymines of the TAT motif in a complementary target DNA strand led to photo-crosslinking of the two strands for several oligonucleotide constructs. Enzymatic digestion, MS, UV, and fluorescence spectral analyses of the interstrand crosslinked oligonucleotides revealed the identity of the thymidine that participates in the photo-crosslinking reaction as well as the diastereomeric structures of the crosslinks. The proposed pathways of interstrand photo-crosslinking are supported by experiments with isotopically labeled oligonucleotide constructs and visualized by means of molecular dynamics simulations.

The NMR conformation study of the complexes of deoxycytidine kinase (dCK) and 2'-deoxycytidine/2'-deoxyadenosine

The structures of the bound 13C/2H double-labelled 2'(R/S), 5'(R/S)-2H2-1',2',3',4',5'-13C5-2'-deoxyadenosine and the corresponding 2'-deoxycytidine moieties in the complexes with human deoxycytidine kinase (dCK) have been characterized for the first time by the solution NMR spectroscopy, using Transferred Dipole-Dipole Cross-correlated Relaxation and Transferred nOe experiments. It has been shown that the ligand adopts a South-type sugar conformation when bound to dCK.

Z-RNA. The synthesis of 2'-O-[13C]methyl- and 5-methyl-analogs of ribo-CGCGCG

Chemical synthesis of 2'-O-[13C]methyl-rCGCGCG and 5-methyl-rCGCGCG using support-aided phosphoramidite method is presented. 2'-O-Methyl guanosine derivative was separated from its 3'-O-methyl counterpart using transient 5',3'-O-silylation with 1,3-dichloro-1,1,3,3-tetraisopropyldisiloxane (Markiewicz reagent). The hexamers were obtained in a purity suitable for NMR studies.

Photoaddition of 5-bromouracil to uracil in oligonucleotides leading to 5,5'-bipyrimidine-type adducts: mechanism of the photoreaction

5-Bromouracil ((Br)U) modified di- and hexanucleotides having (Br)U flanked on the 5' or the 3' side by uracil (U) have been synthesized, and their photochemical reactivity was examined under the conditions of irradiation with near UV light. The results indicate that the primary photochemical process in all of these compounds involves the formation of an intermediate cyclobutane phodoadduct composed of (Br)U and U, which undergoes further photochemically and thermally induced transformations to 5,5'-bipyrimidine type adducts.