Folding pathways of human telomeric type-1 and type-2 G-quadruplex structures

We have investigated new folding pathways of human telomeric type-1 and type-2 G-quadruplex conformations via intermediate hairpin and triplex structures. The stabilization energies calculated by ab initio methods evidenced the formation of a hairpin structure with Hoogsteen GG base pairs. Further calculations revealed that the G-triplet is more stable than the hairpin conformation and equally stable when compared to the G-tetrad. This indicated the possibility of a triplex intermediate. The overall folding is facilitated by K(+) association in each step, as it decreases the electrostatic repulsion. The K(+) binding site was identified by molecular dynamics simulations. We then focused on the syn/anti arrangement and found that the anti conformation of deoxyguanosine is more stable than the syn conformation, which indicated that folding would increase the number of anti conformations. The K(+) binding to a hairpin near the second lateral TTA loop was found to be preferable, considering entropic effects. Stacking of G-tetrads with the same conformation (anti/anti or syn/syn) is more stable than mixed stacking (anti/syn and vice versa). These results suggest the formation of type-1 and type-2 G-quadruplex structures with the possibility of hairpin and triplex intermediates.     

Separation of carrier-free210Bi and UX1 from210Pb and U,respectively, using silica gel as ion exchanger

Radiochemical separations of carrier-free²¹⁰Bi and UX₁ activities from²¹⁰Pb and U, respectively, have been carried out using a silica gel column.²¹⁰Pb was adsorbed in the column as molybdate and²¹⁰Bi passed unadsorbed. Lead activity was next removed with 25 ml of 0.1 M HNO₃. In the case of separation of UX₁, the coloured carbonate complex of U was removed from the silica surface by washing with saturated sodium carbonate solution, keeping UX₁ retained, and finally UX₁ was washed out with 25 ml of conc. HNO₃. Studies of the beta decay of²¹⁰Bi and the γ-spectrum analysis of UX₁ has shown that the separated products in both cases are of high radiochemical purity. The processes in each case took less than one hour and the yield was satisfactory.     

Induction of a remarkable conformational change in a human telomeric sequence by the binding of naphthyridine dimer: inhibition of the elongation of a telomeric repeat by telomerase

The binding of a dimeric form of the 2-amino-1,8-naphthyridine derivative (naphthyridine dimer) to a human telomeric sequence, TTAGGG, was investigated by UV melting, CD spectra, and CSI-MS measurements. Both the 9-mer d(TTAGGGTTA) and the 15-mer d(TTAGGGTTAGGGTTA) showed apparent melting temperatures (T(m)) of 45.6 and 63.6 degrees C, respectively, in the presence of naphthyridine dimer (30 microM) in sodium cacodylate buffer (50 mM, pH 7.0) containing 100 mM NaCl. The CD spectra at 235 and 255 nm of the 9-mer increased in intensity accompanied with strong induced CDs at 285 and 340 nm upon complex formation with naphthyridine dimer. UV titration of the binding of naphthyridine dimer to the 9-mer at 320 nm showed a hypochromism of the spectra. A Scatchard plot of the data showed the presence of multiple binding sites with different association constants. Cold spray ionization mass spectrometry of the complex between naphthyridine dimer and the 9-mer clearly showed that one to three molecules of the ligand bound to the dimer duplex of the 9-mer. Telomeric repeat elongation assay showed that the binding of naphthyridine dimer to the telomeric sequence inhibits the elongation of the sequence by telomerase.     

Detection of the G-quadruplex-TMPyP4 complex by 2-aminopurine modified human telomeric DNA

2-Aminopurine (Ap) modified human telomere sequences were used to monitor the specific complex formation of the G-quadruplex and 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4).     

人类端粒DNA的分子识别及其作用机制探讨

核酸中富含短的G-碱基重复的序列可以形成一种复杂的高级结构,称为G-四链体（G-quadruplex）.在基因组中,借助生物信息学发现这类富G序列广泛分布在基因的启动子区,特别是那些参与到复制中去的基因,例如癌基因.同时发现这类序列在mRNA的5′非翻译区（5′UTR）也广泛存在.这类序列在染色体末段端粒部位的存在及功能已得到充分阐明.已知端粒富含G-碱基序列,其3′末端以单链状态存在,这使得在一些小分子的选择性作用下端粒序列很容易形成G-四链体结构,进而破坏端粒结构,影响端粒酶活性.已知端粒酶在超过85%的肿瘤中过量表达,因此,端粒酶已经成为抗癌药物设计的特殊靶点,是目前本领域的研究热点之一.已发现系列配体通过有效抑制端粒酶而表现高的抗肿瘤活性.本文主要综述了近年来端粒G-四链体分子识别及其药物靶向的最新进展,并对其作用机理做了进一步的分析和探讨.     

Factors determining the performance of triple quadrupole, quadrupole ion trap and sector field mass spectrometers in electrospray ionization tandem mass spectrometry of oligonucleotides. 1. Comparison of performance characteristics

The performance of triple-stage quadrupole (TSQ), quadrupole ion trap (QIT), and double focusing sector field (DFSF) mass spectrometers for the generation of fragment ions to obtain sequence information about oligonucleotides was compared. Upon electrospray ionization (ESI), the charge-state distribution of candidate precursor ions not only varied significantly with the type of mass spectrometer, but also with the size and sequence of the investigated oligonucleotides. While concentration limits of detection for an octanucleotide were in the 100 pmol/L range on the QIT and in the 5-10 nmol/L range on the TSQ and DFSF instruments, those of a 24-mer were in the 2-13 nmol/L range on all three instruments. Reproducibility of mass determination, an important prerequisite for reliable identification of fragment ions, was highest on the TSQ with 0.0037% relative standard deviation over three days. Finally, the tandem mass spectra of a dimethoxytritylated pentanucleotide recorded on the three instruments were compared. Relatively simple spectra dominated by complete series of fragment ions of the (a-B) and w type were obtained on the QIT. Complete series of (a-B) and w ions were also observed on the TSQ. However, additional fragments belonging to the b, c, d, x and z series were found in the spectrum. In the spectrum recorded after in-source fragmentation in the DFSF, only fragments corresponding to the loss of a nucleobase and a complete series of w ions were observed. All three mass spectrometers were suitable for the generation of fragment ions, from which the complete nucleotide sequence of the pentanucleotide could be deduced.     

Structure and ion selectivity of the open potential-dependent potassium channel

The structure and ion selectivity of the potential-dependent potassium channel is investigated. It is shown that the channel constructed by joining the α-subunit with the β-subunit concave, when the axial symmetry axes coincide, is the potential-dependent potassium channel in the open state.     

Mechanisms and nucleation characteristics of the pressure-induced B1-B2 transition in potassium halides: a question of ion hardness and softness

The transformation of potassium bromide from the B1 to the high-pressure B2 structure type is investigated by means of molecular dynamics simulations and compared to previous studies of KF and KCl. The underlying simulation scheme is based on the transition path sampling approach, which allows an unbiased investigation of the phase transition and offers a unique perspective for studying the involved mechanisms at the atomistic level of detail. Our analysis reveals identical mechanisms for the overall transition in KF, KCl, and KBr, but rather dissimilar characteristics of the nucleation and growth of phases. The transformation of KCl may be initiated by both K+ and Cl- ion displacement, exhibiting no preference for either species. However, for KF and KBr, we identified a clear favoring of column-wise F- and K+ displacement, respectively. Such tendencies have important implications on the morphogenesis of the phase nuclei and account for the observation of short-ranged coexisting nucleation centers, resulting in the formation of nanosized twin domains separated by mirror planes on completion of the transition. On the basis of a systematic study of potassium halides, we present a conclusive explanation for the observed nucleation characteristics, which is expected to be of general relevance to pressure-induced phase transitions in ionic compounds.     

2-aza-2'-deoxyadenosine: synthesis, base-pairing selectivity, and stacking properties of oligonucleotides

2-Aza-2'-deoxyadenosine (2, z2Ad) is synthesized via its 1,N6-etheno derivative 7 and enzymatically deaminated to 2-aza-2'-deoxyinosine (3). Compound 2 is converted into the phosphoramidite building block 10b. This is employed in solid-phase oligonucleotide synthesis. The 2-azapurine base forms a strong base pair with guanine, but a much weaker one with adenine, thymine, and cytosine. Oligonucleotide duplexes with dangling nucleotide residues, such as 2-aza-2'-deoxyadenosine and 7-deaza-2'-deoxyadenosine (4, c7Ad), either on one or both termini, are synthesized, and the thermal stability of the duplexes is correlated with the hydrophobic properties of the dangling nucleotide residues.     

Determination of sodium,potassium, calcium and magnesium cations in biodiesel by ion chromatography

This work reports an ion chromatographic (IC) method for the quantitative determination of inorganic cations (Na⁺, K⁺, Mg²⁺ and Ca²⁺) in biodiesel samples that were synthesized from different vegetable oils and fat. The proposed method uses water extraction, heating and ultrasound. The limits of detection (LOD) for each ion, in milligrams of the analyte per kilogram of biodiesel (mg kg⁻¹), were respectively: 0.11 (Na⁺); 0.42 (K⁺); 0.23 (Ca²⁺); and 0.36 (Mg²⁺). The accuracy of the method was studied through recovery tests. For comparison, two samples were also analyzed using an Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES) procedure. The paired Student t test and the Snedecor F test showed that both methods offer equivalent results in terms of accuracy and precision. The operational simplicity, accuracy and precision of the proposed method suggest that it can be a good alternative for the determination of inorganic cations in biodiesel samples.     

Microwave spectrum,conformational preference,barrier to internal rotation,and centrifugal distortion of 1-amino-2-propanol

The microwave spectrum of CH₃CH(OH)CH₂NH₂ has been investigated in the 26.5–39.7 GHz region. One rotamer with an intramolecular hydrogen bond formed between hydroxyl and ammo groups was assigned. This conformation is also characterized by having the methyl group anti to the amino group. Other forms, if they exist, must be at least 1 kcal mole^?1 less stable. Four vibrationally excited states belonging to three different normal modes were assigned and the barrier to internal rotation of the methyl group was found to be 3173 ± 100 cal mole^?1.     

Two-repeat human telomeric d(TAGGGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution: distinct topologies, thermodynamic properties, and folding/unfolding kinetics

We demonstrate by NMR that the two-repeat human telomeric sequence d(TAGGGTTAGGGT) can form both parallel and antiparallel G-quadruplex structures in K(+)-containing solution. Both structures are dimeric G-quadruplexes involving three stacked G-tetrads. The sequence d(TAGGGUTAGGGT), containing a single thymine-to-uracil substitution at position 6, formed a predominantly parallel dimeric G-quadruplex with double-chain-reversal loops; the structure was symmetric, and all guanines were anti. Another modified sequence, d(UAGGGT(Br)UAGGGT), formed a predominantly antiparallel dimeric G-quadruplex with edgewise loops; the structure was asymmetric with six syn guanines and six anti guanines. The two structures can coexist and interconvert in solution. For the latter sequence, the antiparallel form is more favorable at low temperatures (<50 degrees C), while the parallel form is more favorable at higher temperatures; at temperatures lower than 40 degrees C, the antiparallel G-quadruplex folds faster but unfolds slower than the parallel G-quadruplex.     

Determination of 6-keto-PGF1 alpha, 2,3-dinor-6-keto-PGF1 alpha, thromboxane B2, 2,3-dinor-thromboxane B2, PGE2, PGD2 and PGF2 alpha in human urine by gas chromatography-negative ion chemical ionization mass spectrometry

A method for quantification of 6-keto-PGF1 alpha, 2,3-dinor-6-keto-PGF1 alpha TXB2, 2,3-dinor TXB2, PGE2, PGD2 and PGF2 alpha in human urine samples, using gas chromatography-negative ion chemical ionization mass spectrometry, is described. Deuterated analogues were used as internal standards. Methoximation was carried out in urine samples which were subsequently applied to phenylboronic acid cartridges, reversed-phase cartridges and thin-layer chromatography. The eluents were further derivatized to pentafluorobenzyl ester trimethylsilyl ethers for final quantification by gas chromatography-mass spectrometry. The overall recovery was 77% for tritiated 6-keto-PGF1 alpha and 55% for tritiated TXB2. Urinary levels of prostanoids were determined in a group of six volunteers before and after intake of the thromboxane synthase inhibitor Ridogrel, and related to creatinine clearance.     

Comparison of equilibrium ion density distribution and trapping force in penning, Paul, and combined ion traps

Starting from the classical Boltzmann distribution, we obtain the ion density distribution in the limit of either high temperature/low density (Coulomb interaction energy much less than ion kinetic energy) or low temperature/high density (kinetic energy much less than Coulomb interaction energy), and the trapping force for an ion cloud in Penning ion cyclotron resonance, Paul (quadrupole), and combined (Paul trap in a uniform axial static magnetic field) traps. At equilibrium (total angular momentum conserved), the ion cloud rotates at a constant frequency in Penning and combined traps. In a Penning trap, the maximum ion density is proportional to B ²/m (B is magnetic field and m is the mass of ions), whereas the maximum ion density in a Paul trap is proportional to (V _rf ² /mΩ² r ₀ ⁴ ), with Mathieu equation axial q value <0.4 to satisfy the pseudopotential approximation. Ion maximum densities in both Penning and Paul ion traps depend on the trapping field (magnetic or electric) and ion mass, but not on ion charge. In a Penning trap at maximum ion density (zero pressure), the radial (but not the axial) trapping potential is mass dependent, whereas both radial and axial potentials in a Paul trap at maximum ion density are mass dependent.     

Substrate binding and sequence preference of the proteasome revealed by active-site-directed affinity probes

Background: The proteasome is a multicatalytic protease complex responsible for most cytosolic protein breakdown. The complex has several distinct proteolytic activities that are defined by the preference of each for the carboxyterminal (P1) amino acid residue. Although mutational studies in yeast have begun to define substrate specificities of individual catalytically active β subunits, little is known about the principles that govern substrate hydrolysis by the proteasome.Results: A series of tripeptide and tetrapeptide vinyl sulfones were used to study substrate binding and specificity of the proteasome. Removal of the aromatic amino-terminal cap of the potent tripeptide vinyl sulfone proteasome inhibitor 4-hydroxy-3-iodo-2-nitrophenyl-leucinyl-leucinyl-leucine vinyl sulfone resulted in the complete loss of binding and inhibition. Addition of a fourth amino acid (P4) to the tri-leucine core sequence fully restored inhibitory potency. 1251-labeled peptide vinyl sulfones were also used to examine inhibitor binding and to determine the correlation of subunit modification with inhibition of peptidase activity. Changing the amino acid in the P4 position resulted in dramatically different profiles of β-subunit modification.Conclusions: The P4 position, distal to the site of hydrolysis, is important in defining substrate processing by the proteasome. We observed direct correlations between subunit modification and inhibition of distinct proteolytic activities, allowing the assignment of activities to individual β subunits. The ability of tetrapeptides, but not tripeptide vinyl sulfones, to act as substrates for the proteasome suggests there could be a minimal length requirement for hydrolysis by the proteasome. These studies indicate that it is possible to generate inhibitors that are largely specific for individual β subunits of the proteasome by modulation of the P4 and carboxy-terminal vinyl sulfone moieties.     

Promoting the formation and stabilization of human telomeric G-quadruplex DNA, inhibition of telomerase and cytotoxicity by phenanthroline derivatives

Four new di-substituted phenanthroline-based compounds a-d have been designed and prepared, and they have been shown to induce the formation of anti-parallel structure of human telomeric G-quadruplex DNA by CD spectra. FRET assay indicates that the melting temperature increases (ΔT(m) values) of G-quadruplex in buffer (pH 7.4) containing 100 mM NaCl are 31.6, 34.6, 17.8 and 32.6 °C for the compounds (1.0 μM) a, b, c and d, respectively. Competitive FRET assay shows that the four compounds exhibit a high G-quadruplex DNA selectivity over duplex DNA. Three of the compounds are the potent telomerase inhibitors and HeLa cell proliferation inhibitors.     

Comparison of A+T-rich oligonucleotides with and without self-complementary sequence using ion-pair reversed-phase high-performance liquid chromatography/tandem electrospray ionization mass spectrometry

Both A+T-rich oligonucleotides with and without self-complementary sequences were analyzed using ion- pair reversed-phase liquid chromatography/electrospray ionization mass spectrometry (IP-RP-HPLC/ESI-MS) by tryethylammonium acetate (TEAA) and hexafluoroisopropanol (HFIP) buffer systems to study the characteristics of their retention behavior and electrospray ionization tandem mass spectrometry (ESI-MS/MS) response. The results indicated that the chain length had the same effect on the retention of A+T-rich oligonucleotides in both of TEAA and HFIP buffer systems but the sequence had a different impact on the retention in the two buffer systems. A+T- rich oligonucleotides with a self-complementary sequence were much shorter than those without in the TEAA buffer system whereas a slight difference was observed in the HFIP buffer system. Similar total ion current (TIC) intensity was observed both in oligonucleotides with or without self-complementary sequence. The opposite trend of a change in the TIC intensities with increasing chain length were observed in both the TEAA and HFIP buffer systems. A lower charge state was predominant in the TEAA buffer system whereas a higher charge state was mainly distributed in the HFIP buffer system. The oligonucleotides without self-complementary sequences had a higher charge state than those with self-complementary sequences. A- and T- are more esily formed at a higher charge state whereas the sequence fragments will be formed more easily at a lower charge state in both A+T-rich oligonucleotides with and without self-complementary sequences.     

Spectroscopic study of the interaction of actinomycin D with oligonucleotides carrying the central base sequences -XGCY- and -XGGCCY- using multivariate methods

The interactions of actinomycin D (ACTD) with the oligonucleotides 5′-CAAAGCTTTG-3′, 5′-CATGGCCATG-3′ and 5′-TATGGCCATA-3′ were investigated by means of acid–base titrations and mole-ratio and melting experiments monitored by molecular absorption and circular dichroism (CD) spectroscopies. For each experiment, CD and molecular absorption spectra were recorded at each point in the experiment, and later analyzed via appropriate multivariate data analysis methods. The study of the interactions between these oligonucleotides and ACTD at 25 °C showed the formation of an interaction complex with a stoichiometry of 1:1 (ACTD:duplex) and values for the log(formation constant) of 5.1 ± 0.3, 6.4 ± 0.2, and 5.6 ± 0.2, respectively. An additional interaction complex at higher temperatures was also detected, which might be related to the single-stranded forms of the oligonucleotides. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Generation and aromaticity of 2-silaimidazolium ion, a new pi-conjugated silylium ion

A novel cationic silaaromatic, 2-silaimidazolium cation (5), was synthesized by chloride abstraction from the corresponding chlorosilane (4) with [Et3Si(benzene)]+.TPFPB- (TPFPB- = tetrakis(pentafluorophenyl)borate); cation exists as a free silylium cation in solution due to bulky substituents on the five-membered ring.