Rh(phen)2phi3+ as a shape-selective probe of triple helices

[Ru(bpy)2(7-CH3-dppz)](2+) and [Ru(phen)2(7-CH3-dppz)](2+) as metallointercalators that affect third-strand stabilization of the poly(U)˙poly(A)*poly(U) triplex

Stable RNA triplexes play key roles in many biological processes. However, due to Hoogsteen base pairing, triplexes are thermodynamically less stable than the corresponding duplexes. To understand the factors effecting the stabilization of RNA triplexes by octahedral ruthenium(ii) complexes, two Ru(ii) complexes, [Ru(bpy)2(7-CH3-dppz)](2+) (Ru) and [Ru(phen)2(7-CH3-dppz)](2+) (Ru), have been synthesized and characterized in this work. The interactions of the two Ru(ii) complexes with the poly(U)˙poly(A)*poly(U) triplex are investigated by spectrophotometry, spectrofluorometry, circular dichroism as well as viscometry. The results demonstrate that the two complexes are able to enhance the stability of the RNA triplex and serve as molecular "light switches" for the triplex. However, Ru and Ru affecting the stabilization of the third strand are significantly weaker than that of the Watson-Crick base-paired duplex, suggesting that the binding of the two complexes with the triplex is favored by the Watson-Crick base-paired duplex to a large extent. In addition, considering the nature of Ru and Ru, we presume that their binding differences may be due to different ancillary ligand effects. This study further advances our knowledge on the interaction of RNA triple-stranded structures with metal complexes, particularly with Ru(ii) complexes.

Interaction of octahedral ruthenium(II) polypyridyl complex [Ru(bpy)2(PIP)]2+ with poly(U)·poly(A)*poly(U) triplex: Increasing third-strand stabilization of the triplex without affecting the stability of the duplex

Triple-helical RNA are of interest because of possible biological roles as well as the potential therapeutic uses of these structures, while the stability of triplexes is usually weaker than that of the Watson-Crick base pairing duplex strand due to the electrostatic repulsion between three polyanionic strands. Therefore, how to increase the stability of the specific sequences of triplexes are of importance. In this paper the binding of a Ru(II) complex, [Ru(bpy)₂(PIP)]²⁺ (bpy=2.2'-bipyridine, PIP=2-phenyl-1H-imidazo[4,5-f]- [1,10]-phenanthroline), with poly(U)·poly(A)*poly(U) triplex has been investigated by spectrophotometry, spectrofluorometry, viscosimetry and circular dichroism. The results suggest that [Ru(bpy)₂(PIP)]²⁺ as a metallointercalator can stabilize poly(U)·poly(A)*poly(U) triplex (where · denotes the Watson-Crick base pairing and * denotes the Hoogsteen base pairing),while it stabilizes third-strand with no obvious effect on the duplex of poly(U)·poly(A), reflecting the binding of this complex with the triplex is favored by the Hoogsteen paired poly(U) third strand to a great extent.

Binding properties of ruthenium(II) complexes [Ru(bpy)2(ppn)](2+) and [Ru(phen)2(ppn)](2+) with triplex RNA: As molecular "light switches" and stabilizers for poly(U)·poly(A)*poly(U) triplex

Stable RNA triplexes play key roles in many biological processes, while triplexes are thermodynamically less stable than the corresponding duplexes due to the Hoogsteen base pairing. To understand the factors affecting the stabilization of RNA triplexes by octahedral ruthenium(II) complexes, the binding of [Ru(bpy)2(ppn)](2+) (1, bpy=2,2'-bipyridine, ppn=2,4-diaminopyrimido[5,6-b]dipyrido[2,3-f:2',3'-h]quinoxaline) and [Ru(phen)2(ppn)](2+) (2, phen=1,10-phenanthroline) to poly(U)·poly(A)*poly(U) (· denotes the Watson-Crick base pairing and * denotes the Hoogsteen base pairing) has been investigated. The main results obtained here suggest that complexes 1 and 2 can serve as molecular "light switches" and stabilizers for poly(U)·poly(A)*poly(U), while the effectiveness of complex 2 are more marked, suggesting that the hydrophobicity of ancillary ligands has a significant effect on the two Ru(II) complexes binding to poly(U)·poly(A)*poly(U). This study further advances our knowledge on the binding of RNA triplexes with metal complexes, particularly with octahedral ruthenium polypyridyl complexes.

Biophysical insights into the intercalative interaction of surfactant cobalt(III) complexes of certain diimine ligands bound to yeast tRNA: Effects of hydrophobicity

The interaction of two surfactant cobalt(III) complexes, cis-[Co(ip)₂(DA)₂](ClO₄)₃ 1 and cis-[Co(dpq)₂(DA)₂](ClO₄)₃ 2 where ip=imidazo[4,5-f][1,10]phenanthroline and dpq=dipyrido[3,2-d:2'-3'-f]quinoxaline with yeast tRNA have been explored by using electronic absorption, competitive binding, electrochemical studies and viscosity measurements. The results suggest that these complexes can bind to tRNA by intercalation. The presence of hydrophobic diimine ligand and the long aliphatic double chains of these complexes facilitate its intercalative interaction with the hydrophobic interior of the tRNA. The extent of tRNA binding of complex 2 has greater affinity than that of complex containing imidazo[4,5-f][1,10]phenanthroline ligands.

Interactions of octahedral ruthenium(II) polypyridyl complexes with the RNA triplex poly(U)•poly(A)*poly(U) effect on the third-strand stabilization

Stable triplexes play key roles in many biological processes. Due to the Hoogsteen base pairing, triplexes are, however, thermodynamically less stable than the corresponding duplexes. The poor stabilization of these structures limits their practical applications under physiological conditions. To understand the factors effect on the stabilization of RNA triplexes by octahedral ruthenium(II) complexes, the interactions of [RuL2(uip)](2+) {where L = 2,2'-bipyridine (bpy) or 1,10-phenanthroline phen, uip = 2-(5-uracil)-1H-imidazo[4,5-f][1,10]phenanthroline} with the RNA triplex poly(U)•poly(A)*poly(U) are examined by spectrophotometry, spectrofluorometry, circular dichroism, and viscosimetry in this work. The main results obtained here suggest that the third-strand stabilization depends on the hydrophobicity effects of ancillary ligands bpy and phen.

DENSITY FUNCTIONAL THEORY/TIME-DEPENDENT DENSITY FUNCTIONAL THEORY STUDY ON THE STRUCTURES AND SOLVENT EFFECTS ON THE ELECTRONIC SPECTRA OF Ru(II) POLYPYRIDYL COMPLEXES: [Ru(bpy)2(L)]2+ (L = CNOIP, HPIP, DPPZ, TAPIP)

The structures and solvent dependence of electronic spectra of four Ru ( II ) polypyridyl complexes: [ Ru ( bpy )2 CNOIP ]2+, bpy = 2,2-bipyridine and CNOIP = 2-(2-chloro-5-nitrophenyl)imidazo[4,5-f][1,10]phenanthroline (Ru-1); [ Ru ( bpy )2 HPIP ]2+, HPIP = 2-(2-hydroxyphenyl) imidazo[4,5-f][1,10]phenanthroline ( Ru -2); [ Ru ( bpy )2 DPPZ ]2+, DPPZ = dipyrido[3,2:a-2′,3′:c]-phenazine ( Ru -3); [ Ru ( bpy )2 TAPIP ]2+, TAPTP = 4,5,9,18-tetraazaphenanthreno-[9,10-b]triphenylene ( Ru -4) have been carried out by density functional theory/time-dependent density functional theory in vacuum and nine solvents are described by the conductor-like polarized continuum model. The calculated results show that the solvent has a strong effect on the electron distribution of molecular orbitals and character of charge transfer. In water, the simulated absorption spectra (λmax) are in accordance with experimental data. The computational results also indicate the electronic spectra of Ru ( II ) polypyridyl complexes: [ Ru ( bpy )2( L )]2+ is very sensitive to the intercalative ligands L = CNOIP, HPIP, DPPZ, TAPIP in the presence of solvent. It was noted that the trend of transition intensity of complexes strongly depends on the polarity of solvents. In the present polar solvents, the transition intensity trend of Ru -4 > Ru -1 > Ru -2 > Ru -3 was obtained, but in the case of nonpolar solvents, the transition intensity trend is Ru -4 > Ru -3 > Ru -1 > Ru -2. Among the four polypyridyl complexes, [ Ru ( bpy )2 TAPIP ]2+( Ru -4) exhibits the strongest oscillator strength in all nine solvents.

Biophysical studies of a ruthenium(II) polypyridyl complex binding to DNA and RNA prove that nucleic acid structure has significant effects on binding behaviors

The interactions of a metal complex [Ru(phen)(2)PMIP](2+) {Ru=ruthenium, phen=1,10-phenanthroline, PMIP=2-(4-methylphenyl)imidazo[4,5-f]1,10-phenanthroline} with yeast tRNA and calf thymus DNA (CT DNA) have been investigated comparatively by UV-vis spectroscopy, fluorescence spectroscopy, viscosity measurements, isothermal titration calorimetry (ITC), as well as equilibrium dialysis and circular dichroism (CD). Spectroscopic studies together with ITC and viscosity measurements indicate that both binding modes of the Ru(II) polypyridyl complex to yeast tRNA and CT DNA are intercalation and yeast tRNA binding of the complex is stronger than CT DNA binding. ITC experiments show that the interaction of the complex with yeast tRNA is driven by a moderately favorable enthalpy decrease in combination with a moderately favorable entropy increase, while the binding of the complex to CT DNA is driven by a large favorable enthalpy decrease with a less favorable entropy increase. The results from equilibrium dialysis and CD suggest that both interactions are enantioselective and the Delta enantiomer of the complex may bind more favorably to both yeast tRNA and CT DNA than the Lambda enantiomer does, and that the complex is a better candidate for an enantioselective binder to yeast tRNA than to CT DNA. Taken together, these results indicate that the structures of nucleic acids have significant effects on the binding behaviors of metal complexes.

Efficiency of a programmed -1 ribosomal frameshift in the different subtypes of the human immunodeficiency virus type 1 group M

The synthesis of the Gag-Pol polyprotein, the precursor of the enzymes of the human immunodeficiency virus type 1 (HIV-1), requires a programmed -1 ribosomal frameshift. This frameshift has been investigated so far only for subtype B of HIV-1 group M. In this subtype, the frameshift stimulatory signal was found to be a two-stem helix, in which a three-purine bulge interrupts the two stems. In this study, using a luciferase reporter system, we compare, for the first time, the frameshift efficiency of all the subtypes of group M. Mutants of subtype B, including a natural variant were also investigated. Our results with mutants of subtype B confirm that the bulge and the lower stem of the frameshift stimulatory signal contribute to the frameshift in addition to the upper stem-loop considered previously as the sole participant. Our results also show that the frameshift stimulatory signal of all of the other subtypes of group M can be folded into the same structure as in subtype B, despite sequence variations. Moreover, the frameshift efficiency of these subtypes, when assessed in cultured cells, falls within a narrow window (the maximal deviation from the mean value calculated from the experimental values of all the subtypes being approximately 35%), although the predicted thermodynamic stability of the frameshift stimulatory signal differs between the subtypes (from -17.2 kcal/mole to -26.2 kcal/mole). The fact that the frameshift efficiencies fall within a narrow range for all of the subtypes of HIV-1 group M stresses the potential of the frameshift event as an antiviral target.

Characterization of the frameshift stimulatory signal controlling a programmed -1 ribosomal frameshift in the human immunodeficiency virus type 1

Synthesis of the Gag-Pol protein of the human immunodeficiency virus type 1 (HIV-1) requires a programmed -1 ribosomal frameshifting when ribosomes translate the unspliced viral messenger RNA. This frameshift occurs at a slippery sequence followed by an RNA structure motif that stimulates frameshifting. This motif is commonly assumed to be a simple stem-loop for HIV-1. In this study, we show that the frameshift stimulatory signal is more complex than believed and consists of a two-stem helix. The upper stem-loop corresponds to the classic stem-loop, and the lower stem is formed by pairing the spacer region following the slippery sequence and preceding this classic stem-loop with a segment downstream of this stem-loop. A three-purine bulge interrupts the two stems. This structure was suggested by enzymatic probing with nuclease V1 of an RNA fragment corresponding to the gag/pol frameshift region of HIV-1. The involvement of the novel lower stem in frameshifting was supported by site-directed mutagenesis. A fragment encompassing the gag/pol frameshift region of HIV-1 was inserted in the beginning of the coding sequence of a reporter gene coding for the firefly luciferase, such that expression of luciferase requires a -1 frameshift. When the reporter was expressed in COS cells, mutations that disrupt the capacity to form the lower stem reduced frameshifting, whereas compensatory changes that allow re-formation of this stem restored the frameshift efficiency near wild-type level. The two-stem structure that we propose for the frameshift stimulatory signal of HIV-1 differs from the RNA triple helix structure recently proposed.

Binding of the Delta- and Lambda-Enantiomers of [Ru(dmphen)(2)dpq](2+) to the Hexanucleotide d(GTCGAC)(2)

1H NMR spectroscopy and viscosity measurements have been used to study the oligonucleotide binding of the Delta- and Lambda-enantiomers of the metal complex [Ru(dmphen)(2)dpq](2+) (dmphen = 2,9-dimethyl-1,10-phenanthroline and dpq = dipyrido[3,2-f:2',3'-h]quinoxaline). The addition of either enantiomer to d(GTCGAC)(2) induced large upfield shifts and significant broadening for the hexanucleotide imino and metal complex dpq resonances. These data coupled with the observed increase in the melting transition midpoint of the hexanucleotide duplex upon addition of either enantiomer suggests that both Delta- and Lambda-[Ru(dmphen)(2)dpq](2+) bind by intercalation. A significant number of metal complex to hexanucleotide NOE contacts were observed in NOESY spectra of d(GTCGAC)(2) with added Delta- or Lambda-[Ru(dmphen)(2)dpq](2+). The observed intermolecular NOEs were consistent with both enantiomers intercalating between the G(4)A(5) bases of one strand and the T(2)C(3) bases of the complementary strand. Intermolecular NOEs from the dmphen protons were only observed to protons located in the hexanucleotide minor groove. Alternatively, NOE contacts from the dpq protons were observed to both major and minor groove protons. The NOE data suggest that the dpq ligand of the Delta-enantiomer intercalates deeply into the hexanucleotide base stack while the Lambda-enantiomer can only partially intercalate. Viscosity measurements were consistent with the proposed intercalation binding models. The addition of the Delta-enantiomer increased the relative viscosity of the DNA solution, while a decrease in the relative viscosity of the DNA was observed upon addition of the Lambda-metal complex. These results confirm our proposal that octahedral metallointercalators can intercalate from the minor groove. In addition, the results demonstrate that the left-handed enantiomer of [Ru(dmphen)(2)dpq](2+) prefers to intercalate from the narrow minor groove despite only being able to partially insert a polycyclic aromatic ligand into the DNA base stack.