Retention of nucleic acids in ion‐pair reversed‐phase high‐performance liquid chromatography depends not only on base composition but also on base sequence

The study on nucleic acid retention in ion‐pair reversed‐phase high‐performance liquid chromatography mainly focuses on size‐dependence, however, other factors influencing retention behaviors have not been comprehensively clarified up to date. In this present work, the retention behaviors of oligonucleotides and double‐stranded DNAs were investigated on silica‐based C₁₈ stationary phase by ion‐pair reversed‐phase high‐performance liquid chromatography. It is found that the retention of oligonucleotides was influenced by base composition and base sequence as well as size, and oligonucleotides prone to self‐dimerization have weaker retention than those not prone to self‐dimerization but with the same base composition. However, homo‐oligonucleotides are suitable for the size‐dependent separation as a special case of oligonucleotides. For double‐stranded DNAs, the retention is also influenced by base composition and base sequence, as well as size. This may be attributed to the interaction of exposed bases in major or minor grooves with the hydrophobic alky chains of stationary phase. In addition, no specific influence of guanine and cytosine content was confirmed on retention of double‐stranded DNAs. Notably, the space effect resulted from the stereostructure of nucleic acids also influences the retention behavior in ion‐pair reversed‐phase high‐performance liquid chromatography.     

Thermal Stability of Modified i‐Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

In continuation of our investigation of characteristics and thermodynamic properties of the i‐motif 5′‐d[(CCCTAA)₃CCCT)] upon insertion of intercalating nucleotides into the cytosine‐rich oligonucleotide, this article evaluates the stabilities of i‐motif oligonucleotides upon insertion of naphthalimide (1H‐benzo[de]isoquinoline‐1,3(2H)‐dione) as the intercalating nucleic acid. The stabilities of i‐motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures (T_m) and circular dichroism spectra at different pH values and conditions (crowding and non‐crowding). This study indicated a positive effect of the naphthalimide intercalating nucleotides on the stabilities of the i‐motif structures compared to the wild‐type structure which is in contrast to a previous observation for a pyrene‐intercalating nucleotide showing a decrease in T_m values.     

The α‐L‐Threofuranosyl‐(3′→2′)‐oligonucleotide System (‘TNA'): Synthesis and Pairing Properties

Our studies of α‐L ‐Threofuranosyl‐(3′→2′)‐oligonucleotides (‘TNA') are part of a systematic experimental inquiry into the base‐pairing properties of potentially natural nucleic acid alternatives taken from RNA's close structural neighborhood. TNA is an efficient Watson‐Crick base‐pairing system and has the capability of informational cross‐pairing with both RNA and DNA. This property, together with the system's constitutional and (presumed) generational simplicity, warrants special scrutiny of TNA in the context of the search for chemical clues to RNA's origin.     

Targeting of Single‐Stranded Oligonucleotides through Metal‐Induced Cyclization of Short Complementary Strands

A new strategy to cyclize short synthetic oligonucleotides on DNA or RNA target strands is described. The approach is based on metal‐templated cyclization of short synthetic oligonucleotides conjugated with two chelating 2,2′ : 6′,2′′‐terpyridine (Tpy) moieties at their 3′‐ and 5′‐ends. Cyclization after metal addition (Zn²⁺, Fe²⁺) was demonstrated by means of thermal‐denaturation experiments, MALDI‐Q‐TOF‐MS, and gel electrophoresis (PAGE). 1D‐ and 2D‐NMR Experiments were performed to analyze the association of complementary strands after metal‐mediated cyclization. Our protocol allows the efficient circularization of synthetic oligonucleotides. Thereby, the hybridization on a complementary strand was more efficient with an RNA target strand and a 2′‐O‐methylated circularized oligomer.     

Molecular‐Dynamics Studies of Single‐Stranded Hexitol,Altritol, Mannitol,and Ribose Nucleic Acids (HNA,MNA, ANA,and RNA,Resp.) and of the Stability of HNA⋅RNA,ANA⋅RNA,and MNA⋅RNA Duplexes

The influence of the orientation of a 3′‐OH group on the conformation and stability of hexitol oligonucleotides in complexes with RNA and as single strands in aqueous solution was investigated by molecular‐dynamics (MD) simulations with AMBER 4.1. The particle mesh Ewald (PME) method was used for the treatment of long‐range electrostatic interactions. An equatorial orientation of the 3′‐OH group in the single‐stranded D ‐mannitol nucleic acid (MNA) m(GCGTAGCG) and in the complex with the RNA r(CGCAUCGC) has an unfavorable influence on the helical stability. Frequent H‐bonds between the 3′‐OH group and the O−C(6′) of the phosphate backbone of the following nucleotide explain the distorted conformation of the MNA⋅RNA complex as well as that of the single MNA strand. This is consistent with experimental results that show lowered hybridization potentials for MNA⋅RNA complexes. An axial orientation of the 3′‐OH group in the D ‐altritol nucleic acid (ANA) a(GCGTAGCG) leads to a stable complex with the complementary RNA r(CGCAUCGC), as well as to a more highly preorganized single‐stranded ANA chain. The averaged conformation of the ANA⋅RNA complex is similar to that of A‐RNA, with only minor changes in groove width, helical curvature, and H‐bonding pattern. The relative stabilities of ANA⋅RNA vs. HNA⋅RNA (HNA=D ‐hexitol nucleic acid without 3′‐OH group) can be explained by differences in restricted movements, H‐bonds, and solvation effects.     

Synthesis and bioactivity of O‐ethyl phosphorodiamidates derived from quinazolin‐4‐ones and either amino acid esters or fatty amines

Synthesis of several O‐ethyl phos‐phorodiamidates derived from unsubstituted, or 6‐bromo‐, or 6‐nitro‐3‐amino‐2‐methyl‐3H‐quinazolin‐4‐one and either amino acid esters or fatty amines is described. These compounds showed high insecticidal activity toward mosquito larvae, with lethal concentrations LC₅₀ and LC₉₀ as low as 0.028 and 1.724 ppm, respectively. The highest activity was observed with those compounds containing both a nitro substituent and a 10‐carbon‐atom fatty‐amine moiety. Multiple regression analysis was used to explain the larvicidal activity variation of these compounds. The larvicidal activity generally decreased according to the following order of amino acid moieties: glutamic acid > methionine > glycine > alanine > phenylalanine. © 1999 John Wiley & Sons, Inc. Heteroatom Chem 10: 455–460, 1999     

Efficient Synthesis of Dimeric Oxazoles,Piperidines and Tetrahydroisoquinolines from N‐Substituted 2‐Oxazolones

A mild and practical method for the construction of heterocycles from N‐substituted 2‐oxazolones through cascade, BF₃?Et₂O/H₂O‐catalyzed reactions involving iminium ion generation and trapping by external or internal olefinic and aryl moieties is described. Mechanistic and computational studies revealed the strong protic acid HBF₄ as the initiating catalyst for these cascade reactions. Providing access to novel molecular diversity, these processes may facilitate chemical biology studies, drug discovery efforts and natural products synthesis.     

Facile and Effective Synthesis of Siloxane‐Based Polyamines

Linear and cyclic polysiloxanes with pendant amine moieties have been synthesized via the [(C₆H₅)₃P]₃RhCl‐catalyzed dehydrogenative alcoholysis of poly(methylhydrosiloxane) (PMHS) or cyclotetra‐(methylhydrosiloxane) (D4H) with hydroxyalkylamines.     

Structure and Reactivity of Al−O(H)−Al Moieties in Siloxide Frameworks: Solution and Gas‐Phase Model Studies

Even though aluminas and aluminosilicates have found widespread application, a consistent molecular understanding of their surface heterogeneity and the behavior of defects resulting from hydroxylation/dehydroxylation remains unclear. Here, we study the well‐defined molecular model compound, [Al₃(μ₂‐OH)₃(THF)₃(PhSi(OSiPh₂O)₃)₂], 1 , to gain insight into the acid–base reactivity of cyclic trinuclear Al₃(μ₂‐OH)₃ moieties at the atomic level. We find that, like zeolites, they are sufficiently acidic to catalyze the isomerization of olefins. DFT and gas phase vibrational spectroscopy on solvent‐free and deprotonated 1 show that the six‐membered ring structure of its Al₃(μ₂‐OH)₃ core is unstable with respect to deprotonation of one of its hydroxy groups and rearranges into two edge‐sharing four‐membered rings. This renders Al_IV?O(H)?Al_IV units strong acid sites, and all results together suggest that their acidity is similar to that of zeolitic Si_IV?O(H)?Al_IV groups.     

A Zeolite‐Like Zinc Phosphonocarboxylate Framework and Its Transformation into Two‐ and Three‐Dimensional Structures

Three zinc phosphonocarboxylates, Zn₂(pbc)₂?Hdma?H₃O?2H₂O ( 1 ), Zn(pbc)?Hdma ( 2 ), and Zn_4.5(pbc)₃(OH)(H₂O)_0.5?Hdma ( 3 ) (H₃pbc=4‐phosphonobenzoic acid, dma=dimethylamine) were synthesized by the mixed solvothermal reaction of Zn(Ac)₂?2H₂O and 4‐phosphonobenzoic acid in N,N‐dimethylformamide (DMF) and water. The zigzag and ladderlike chains completely constructed by triply fused 4‐membered rings (denoted SBU‐1) are linked by the organic moieties to form the 3D zeolite‐like structure 1 and the layered structure 2 , respectively. As for structure 3 , a new second building unit (SBU‐2) formed by the inset of the [Zn₃O₁₂] trimer into the 4‐membered ring as well as SBU‐1 is observed. The connections between the two types of SBUs lead to a “zinc phosphate” layer, which is linked by the organic groups to generate a 3D pillar‐layered structure. Both solution‐mediated and solid‐state transformations of 1 to 2 and 3 were observed. A possible mechanism for the transformation is proposed. Gas sorption studies show that 1 has accessible pores for methanol and water and exhibits size selectivity for alcohols.     

Stabilization of a Bimolecular Triplex by 3′‐S‐Phosphorothiolate Modifications: An NMR and UV Thermal Melting Investigation

Triplexes formed from oligonucleic acids are key to a number of biological processes. They have attracted attention as molecular biology tools and as a result of their relevance in novel therapeutic strategies. The recognition properties of single‐stranded nucleic acids are also relevant in third‐strand binding. Thus, there has been considerable activity in generating such moieties, referred to as triplex forming oligonucleotides (TFOs). Triplexes, composed of Watson–Crick (W–C) base‐paired DNA duplexes and a Hoogsteen base‐paired RNA strand, are reported to be more thermodynamically stable than those in which the third strand is DNA. Consequently, synthetic efforts have been focused on developing TFOs with RNA‐like structural properties. Here, the structural and stability studies of such a TFO, composed of deoxynucleic acids, but with 3′‐S‐phosphorothiolate (3′‐SP) linkages at two sites is described. The modification results in an increase in triplex melting temperature as determined by UV absorption measurements. ¹H NMR analysis and structure generation for the (hairpin) duplex component and the native and modified triplexes revealed that the double helix is not significantly altered by the major groove binding of either TFO. However, the triplex involving the 3′‐SP modifications is more compact. The 3′‐SP modification was previously shown to stabilise G‐quadruplex and i‐motif structures and therefore is now proposed as a generic solution to stabilising multi‐stranded DNA structures.     

Intermolecular π‐stacking and F...F interactions of fluorine‐substituted meso‐alkynylporphyrin

Two C2‐symmetric meso‐alkynylporphyrins, namely 5,15‐bis[(4‐butyl‐2,3,5,6‐tetrafluorophenyl)ethynyl]‐10,20‐dipropylporphyrin, C₅₀H₄₂F₈N₄, (I), and 5,15‐bis[(4‐butylphenyl)ethynyl]‐10,20‐dipropylporphyrin, C₅₀H₅₀N₄, (II), show remarkable π–π stacking that forms columns of porphyrin centers. The tetrafluorophenylene moieties in (I) show intermolecular interactions with each other through the F atoms, forming one‐dimensional ribbons. No significant π–π interactions are observed in the plane of the phenylene and tetrafluorophenylene moieties in either (I) or (II). The molecules of both compounds lie about inversion centers.     

Chemoselective Modification of Vinyl DNA by Triazolinediones

A new method for the post‐synthetic modification of nucleic acids was developed that involves mixing a phenyl triazolinedione (PTAD) derivative with DNA containing a vinyl nucleobase. The resulting reactions proceeded through step‐wise mechanisms, giving either a formal [4+2] cycloaddition product, or, depending on the context of nucleobase, PTAD addition along with solvent trapping to give a secondary alcohol in water. Catalyst‐free addition between PTAD and the terminal alkene of 5‐vinyl‐2′‐deoxyuridine (VdU) was exceptionally fast, with a second‐order rate constant of 2×10³ m ⁻¹ s⁻¹. PTAD derivatives selectively reacted with VdU‐containing oligonucleotides in a conformation‐selective manner, with higher yields observed for G‐quadruplex versus duplex DNA. These results demonstrate a new strategy for copper‐free bioconjugation of DNA that can potentially be used to probe nucleic acid conformations in cells.     

Crystallographic report: [N,N′‐Bis‐(6‐methylpyrid‐2‐ylium)‐(1R,2R)‐1,2‐diaminocyclohexane] bis‐[(p‐cymene)‐ trichlororuthenate(II)]

The chiral compound (H₂cydiampy)[RuCl₃(p‐cymene)]₂ has been obtained in high yield by treating [RuCl₂(p‐cymene)]₂ with an excess of hydrochloric acid in the presence of one equivalent of N,N′‐bis‐(6‐methylpyrid‐2‐yl)‐(1R,2R)‐1,2‐diaminocyclohexane (cydiampy). It crystallizes in the chiral tetragonal space group P4₃2₁2, with half of the atoms of the dication related to the other half by a crystallographic C₂ axis that also makes equivalent the two anionic metal moieties. Copyright © 2005 John Wiley & Sons, Ltd.     

Recognition and detection of oligonucleotides in the presence of chromosomal DNA based on entrapment within conducting-polymer networks

Overlapping voltammetric signals, accrued from redox processes of nucleobases, do not permit discrimination between short oligonucleotides and chromosomal DNA molecules when conventional electrochemical techniques are used. This article describes a new genoelectronic route for discriminating between short oligonucleotides and chromosomal DNA, based on the polypyrrole (PPy) doping process. Such a route relies on the profound effect of short nucleic acid dopants upon the redox activity of PPy, and hence on the square-wave voltammetric signal of the polymer-modified electrode in a blank electrolyte solution. The electropolymeric growth of PPy thus serves for preferential accumulation (by doping) of short oligonucleotides. High selectivity is demonstrated for voltammetric measurements of oligo(dG)₂₀ and oligo(dT)₂₀ in the presence of otherwise interfering ss- and ds-DNA. The signals for the oligonucleotides are also not affected by a large excess of chloride or phosphate ions. The response of the new preconcentration (doping)–medium-exchange–voltammetric protocol is proportional to the concentration of the oligonucleotide dopant. Such a new recognition process, based on the doping of conducting-polymer networks, enhances the scope of electroanalysis of nucleic acids.     

Mono‐ and Bis(pyrrolo)tetrathiafulvalene Derivatives Tethered to C60: Synthesis,Photophysical Studies,and Self‐Assembled Monolayers

A series of mono‐ (MPTTF) and bis(pyrrolo)tetrathiafulvalene (BPTTF) derivatives tethered to one or two C₆₀ moieties was synthesized and characterized. The synthetic strategy for these dumbbell‐shaped compounds was based on a 1,3‐dipolar cycloaddition reaction between aldehyde‐functionalized MPTTF/BPTTF derivatives, two different tailor‐made amino acids, and C₆₀. Electronic communication between the MPTTF/BPTTF units and the C₆₀ moieties was studied by a variety of techniques including cyclic voltammetry and absorption spectroscopy. These solution‐based studies indicated no observable electronic communication between the MPTTF/BPTTF units and the C₆₀ moieties. In addition, femtosecond and nanosecond transient absorption spectroscopy revealed, rather surprisingly, that no charge transfer from the MPTTF/BPTTF units to the C₆₀ moieties takes place on excitation of the fullerene moiety. Finally, it was shown that the MPTTF–C₆₀ and C₆₀–BPTTF‐C₆₀ dyad and triad molecules formed self‐assembled monolayers on a Au(111) surface by anchoring to C₆₀.     

4‐[N,N‐Bis(2‐hydroxy­imino‐2‐phenyl­ethyl)­amino]‐1,5‐di­methyl‐2‐phenyl‐2,3‐di­hydro‐1H‐pyrazol‐3‐one monohydrate

The title compound, C₂₇H₂₇N₅O₃·H₂O, is built up from pyrazolinone, phenyl and aceto­phenone oxime moieties. The 2‐­phenyl substituent is nearly perpendicular to the pyrazo­linone ring, with a dihedral angle of 87.66 (1)°. The aceto­phenone oxime moieties are twisted out of the pyrazolinone‐ring plane by 47.04 (1)°. The mol­ecules in the crystal pack in an antiparallel fashion and are held together by hydrogen‐bonded water mol­ecules and intermolecular O—H⋯O and O—H⋯N hydrogen bonds.     

Effects of Six‐Membered Carbohydrate Rings on Structure,Stability, and Kinetics of G‐Quadruplexes

We have evaluated the conformational, thermal, and kinetic properties of d(TGGGGT) analogues with one or five of the ribose nucleotides replaced with the carbohydrate residues hexitol nucleic acid (HNA), cyclohexenyl nucleic acid (CeNA), or altritol nucleic acid (ANA). All of the modified oligonucleotides formed G‐quadruplexes, but substitution with the six‐membered rings resulted in a mixture of G‐quadruplex structures. UV and CD melting analyses showed that the structure formed by d(TGGGGT) modified with HNA was stabilized whereas that modified with CeNA was destabilized, relative to the structure formed by the unmodified oligonucleotide. Substitution at the fourth base of the G‐tract with ANA resulted in a greater stabilization effect than substitution at the first G residue; substitution with five ANA residues resulted in significant stabilization of the G‐quadruplex. A single substitution with CeNA at the first base of the G‐tract or five substitutions with HNA resulted in striking deceleration or acceleration of G‐quadruplex formation, respectively. Our results shed light on the effect of the sugar moiety on the properties of G‐quadruplex structures.     

Syntheses and crystal structures of triorganotin (IV) derivatives with 2,2′‐bipyridine‐4,4′‐dicarboxylic acid

Four organotin complexes with 2,2′‐bipyridine‐4,4′‐dicarboxylic acid, H₂dcbp: (Ph₃n)₂(dcbp) 1 , [(PhCH₂)₃n]₂(dcbp) ⋅ 2CH₃OH 2 , [(Me₃Sn)₂(dcbp)]_n 3 , [(Bu₃Sn)₂(dcbp)]_n 4 have been synthesized. The complexes 1–4 were characterized by elemental, IR, ¹H, ¹³C, ¹¹⁹n NMR, and X‐ray crystallographic analyses. Crystal structures show that complex 1 is a monomer with one ligand coordinated to two triorganotin moieties, and a 1D infinite polymeric chain generates via intermolecular C H⋅⋅⋅N hydrogen bond; complex 2 is also a monomer and forms a 2D network by intermolecular O–H⋅⋅⋅O weak interaction; both of complexes 3 and 4 form 2D network structures where 2,2′‐bipyridine‐4,4′‐dicarboxylate acts as a tetradentate ligand coordinated to trimethyltin and tri‐n‐butyltin ions, respectively. © 2009 Wiley Periodicals, Inc. Heteroatom Chem 20:19–28, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20506     

Dual Amplified Electrochemical Immunosensor for Hepatitis B Virus Surface Antigen Detection Using Hemin/G‐Quadruplex Immobilized onto Fe3O4‐AuNPs or (Hemin‐Amino‐rGO‐Au) Nanohybrid

A sensitive electrochemical immunosensor for Hepatitis B virus surface antigen (HBsAg) detection was fabricated based on hemin/G‐quadruplex interlaced onto Fe₃O₄‐AuNPs or hemin ‐amino‐reduced graphene oxide nanocomposite (H‐amino‐rGO‐Au). G‐quadruplex DNAzyme, which is composed of hemin and guanine‐rich nucleic acid, is an effective signal amplified tool for its outstanding peroxidase activity and Fe₃O₄‐AuNPs or (H‐amino‐rGO‐Au) nanocomposites with quasi‐enzyme activity provide appropriate support for the immobilization of hemin/G‐quadruplex. The target protein was sandwiched between the primary antibody immobilized on the GO and secondary antibody immobilized on the Fe₃O₄‐AuNPs or (H‐amino‐rGO‐Au) nanocomposites and glutaraldehyde was used as linking agent for the immobilization of primary antibody on the surface of GO. Both Fe₃O₄‐AuNPs and H‐amino‐rGO‐Au nanocomposite and also hemin/G‐quadruplex can cooperate the electrocatalytic reduction of H₂O₂ in the presence of methylene blue as mediator. The proposed immunosensor has a wide linear dynamic range of 0.1 pg/ml to 300 pg/ml with a detection limit of 60 fg/ml when Fe₃O₄‐AuNPs was used for immobilization of hemin/G‐quadruplex, while the dynamic range and DL were 0. 1–1000 pg/mL and 10 fg/mL, respectively in the presence of H‐amino‐rGO‐ Au nanocomposite as platform for immobilizing of hemin/G‐quadruplex. The proposed immunosensor was also used for analysis of HBsAg in spiked human serum samples with satisfactory results.