Ditopic Aza-Scorpiand Ligands Interact Selectively with ds-RNA and Modulate the Interaction upon Formation of Zn2+ Complexes

Nucleic acids are essential biomolecules in living systems and represent one of the main targets of chemists, biophysics, biologists, and nanotechnologists. New small molecules are continuously developed to target the duplex (ds) structure of DNA and, most recently, RNA to be used as therapeutics and/or biological tools. Stimuli-triggered systems can promote and hamper the interaction to biomolecules through external stimuli such as light and metal coordination. In this work, we report on the interaction with ds-DNA and ds-RNA of two aza-macrocycles able to coordinate Zn²⁺ metal ions and form binuclear complexes. The interaction of the aza-macrocycles and the Zn²⁺ metal complexes with duplex DNA and RNA was studied using UV thermal and fluorescence indicator displacement assays in combination with theoretical studies. Both ligands show a high affinity for ds-DNA/RNA and selectivity for ds-RNA. The ability to interact with these duplexes is blocked upon Zn²⁺ coordination, which was confirmed by the low variation in the melting temperature and poor displacement of the fluorescent dye from the ds-DNA/RNA. Cell viability assays show a decrease in the cytotoxicity of the metal complexes in comparison with the free ligands, which can be associated with the observed binding to the nucleic acids.     

Helically Assembled Pyrene Arrays on an RNA Duplex That Exhibit Circularly Polarized Luminescence with Excimer Formation

Circularly polarized luminescence (CPL) was observed in pyrene zipper arrays helically arranged on an RNA duplex. Hybridization of complementary RNA strands having multiple (two to five) 2′‐O‐pyrenylmethyl modified nucleosides affords an RNA duplex with normal thermal stability. The pyrene fluorophores are assembled like a zipper in a well‐defined helical manner along the axis of RNA duplex, which, upon 350 nm UV illumination, resulted in CPL emission with pyrene excimer formation. CPL (g_lum) levels observed for the pyrene arrays in dilute aqueous solution were +2×10^?2–+3.5×10^?2, which are comparable with |g_lum| for chiral organic molecules and related systems. The positive CPL signals are consistent with a right‐handed helical structure. Temperature dependence on CPL emission indicates that the stable rigid RNA structure is responsible for the strong CPL signals. The single pyrene‐modified RNA duplex did not show any CPL signal.     

Anomeric and Enantiomeric 2’-Deoxycytidines: Base Pair Stability in the Absence and Presence of Silver Ions

Dodecamer duplex DNA containing anomeric (α/β-d ) and enantiomeric (β-l /β-d ) 2’-deoxycytidine mismatches was studied with respect to base pair stability in the absence and presence of silver ions. Stable duplexes with silver-mediated cytosine–cytosine pairs were formed by all anomeric and enantiomeric combinations. Stability changes were observed depending on the composition of the mismatches. Most strikingly, the new silver-mediated base pair of anomeric α-d -dC with enantiomeric β-l -dC is superior to the well-noted β-d /β-d -dC pair in terms of stability. CD spectra were used to follow global helical changes of DNA structure.     

Spectroscopy Probing of the Formation,Recognition, and Conversion of a G‐Quadruplex in the Promoter Region of the bcl‐2 Oncogene

Which form to take? The interconversion between the G‐quadruplex and duplex DNA forms in the bcl‐2 promoter could be induced by fluctuations in the pH value or DNA and NH₄⁺ concentrations, by adding CH₃OH, and by introducing small molecules (cationic porphyrin and dehydrocorydaline; see scheme).

     

Synthesis of new chiral PNAs bearing a dipeptide-mimic monomer with two lysine-derived stereogenic centres

The synthesis of new chiral PNA analogues based on lysine is reported. In particular, l- and/or d-lysine-based PNA submonomers bearing two lysine side chains exactly spaced as in the dipeptide Lys-Lys were synthesized and incorporated in the middle of decameric PNA strands, obtaining four diastereomeric (LD, DL, LL and DD) lysine-based chiral PNAs. The hybridization with their complementary antiparallel DNA strand was studied by melting temperature determination and compared with the analogue achiral PNA and chiral PNAs bearing one residue with either of the two lysine enantiomers. The binding abilities were shown to be strongly dependent on the configuration of the stereogenic centres.     

Synthesis and properties of oligodeoxyribonucleotides containing 2’-<Emphasis Type="Italic">O</Emphasis>-(2,3-dihydroxypropyl)- and 2’-<Emphasis Type="Italic">O</Emphasis>-(2-oxoethyl)arabinouridine residues

2’-O-(2,3-Dihydroxypropyl)arabinouridine-containing oligodeoxyribonucleotides were synthesized starting from a new modified nucleoside, viz., 2’-O-(2,3-dihydroxypropyl)arabinouridine, and the corresponding 3’-phosphoramidite. Oxidation of these oligodeoxyribonucleotides with sodium periodate afforded oligonucleotides containing 2’-O-(2-oxoethyl)arabinouridine residues. Subsequent modification of the aldehyde-containing oligonucleotides involved the reactions with 9-hydrazinoacridine and N-aminooxyacetyl peptide and reductive amination by 4-(1-pyrenyl)butyrohydrazide and biotin hydrazide. Thermal stabilities of duplexes of modified oligodeoxyribonucleotides with complementary oligodeoxyribonucleotides are slightly lower than those of natural duplexes. Duplexes with complementary oligoribonucleotides are substantially destabilized.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 233–241, January, 2005.     

Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides

Continuous stacking hybridization of oligodeoxyribonucleotides with the stem of a preformed minihairpin structure of a DNA template was studied by thermal denaturation in solution. The thermodynamic parameters (H°, S°, and G°₃₇) were determined for the formation of all 16 possible types of coaxial stackings (or cooperative interactions) ^5" X*pY ^3"/^5" ZZ"3" (an asterisk stands for a nick) between the terminal complementary base pairs of two adjacent duplexes formed on a common DNA template. The maximum efficacy G°₃₇ of coaxial stacking (1 M NaCl, pH 7.4) was observed for the G*pC/GC interaction (–2.76 kcal mol^–1), whereas the minimum efficacy was observed for the T*pA/TA interaction (–0.85 kcal mol^–1). In the general case, the efficacy of the cooperative interaction at the X*pY/ZZ" junction does not correlate with the energy of formation of the corresponding unified XY/ZZ" dinucleotide pair in the structure of native DNA. The formation of a stack by the terminal oligonucleotide bases upon their continuous stacking hybridization makes the major and governing contribution to the energy of cooperative interaction.     

Chemical ligation as a method for the assembly of double-stranded nucleic acids: Modifications and local structure studies

A new procedure was developed as an alternative to the enzymatic assembly of natural and modified double-stranded DNAs using chemical reagent (chemical ligation). BrCN was suggested as an efficient coupling reagent, which induces superfast reactions in DNA duplexes. The physicochemical properties and the structure of new types of DNA duplexes, which are the substrates for chemical ligation, with breaks in phosphodiester chains, including concatemers, were studied. Chemical ligation was applied to prepare biologically active 17–200 base-pair double-stranded DNAs and DNA-RNA block-copolymers, to incorporate various modifications into DNA duplexes including pyrophosphate and phosphoramidate unnatural internucleotide bonds. The unique possibilities of this approach were demonstrated in the development of methods for circularization of oligodeoxy ribonucleotides and assembly of branched DNAs. The structural-kinetic concept of chemicalligation was created and the relationship between the reactivity of interacting groups and sequence-dependent local conformation of the ligation site in B-DNA was established. The lesser efficiency of chemical ligation of RNA fragments in comparison to that of DNA analogs was demonstrated and rationalized. This approach was used as a sensitive monitor of a stable double helix formation and third-strand binding to a DNA duplex.Translated from Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1889–1911, August, 1996.     

The spectroscopy, dynamics, and electronic structure of pyrenyl-dU nucleosides: P/dU charge transfer state photophysics

Various spectroscopies including UV-vis absorbance, emission, and emission quantum yield are combined with a variety of kinetics measurements including time resolved emission and nanosecond, picosecond, and femtosecond transient absorbance (TA) to systematize the P⁺/dU⁻ charge transfer (CT) state dynamics of a variety of pyrenyl-dU nucleoside conjugates in several solvents of varying polarity. These results are then analyzed further by means of electronic structure computations in vacuum and using two different solvent models. Finally, the excess electron dynamics of a number of DNA duplex structures substituted with two different pyrenyl-dU nucleosides and 5-XdU, where X=Br or F, electron traps are discussed in terms of achieving high yields of long-lived photoinduced CT products in DNA.     

β‐Cyclodextrin Duplexes That Are Connected through Two Disulfide Bonds: Potent Hosts for the Complexation of Organic Molecules

New tubular host molecules, which are composed of two β‐cyclodextrin macrocycles that are connected through two disulfide bonds, have been prepared by the air‐promoted oxidation of 6^I,6^IV‐dideoxy‐6^I,6^IV‐disulfanyl‐β‐cyclodextrin in aqueous solution. This reaction leads to three products: monomeric intramolecular disulfide and two dimeric species, which are termed as “non‐eclipsed” and “eclipsed” cyclodextrin duplexes. Oxidation at a concentration of the starting thiol of 0.1 mM gave the intramolecular disulfide as the major product whereas a concentration in the millimolar range afforded the dimeric species as the dominant products. The tubular structure of the “non‐eclipsed” isomer was unequivocally determined by X‐ray analysis. The binding affinities of the duplexes to a wide range of compounds, including fluorescent dyes and clinically used drugs Imatinib and Esomeprazol, were studied in water by ITC. For most guest compounds, the experimentally determined K_a values were in the range 10⁷–10⁸ M ^?1. These binding affinities are significantly higher than those found in the literature for analogous complexes with native cyclodextrins. In cases of binding of neutral or anionic guest molecules cyclodextrin duplexes outperformed cucurbiturils. A complex between a duplex and Nile blue was used to investigate its ability to penetrate the cytoplasmic membrane of HeLa cells. We found that the complex accumulated in the cell membrane but did not pass into cytosol. Importantly, the complex did not decompose to a significant extent under high dilution in the cellular environment.