Inhibition of telomerase by G-quartet DNA structures

The ends or telomeres of the linear chromosomes of eukaryotes are composed of tandem repeats of short DNA sequences, one strand being rich in guanine (G strand) and the complementary strand in cytosine. Telomere synthesis involves the addition of telomeric repeats to the G strand by telomere terminal transferase (telomerase). Telomeric G-strand DNAs from a variety of organisms adopt compact structures, the most stable of which is explained by the formation of G-quartets. Here we investigate the capacity of the different folded forms of telomeric DNA to serve as primers for the Oxytricha nova telomerase in vitro. Formation of the K(+)-stabilized G-quartet structure in a primer inhibits its use by telomerase. Furthermore, the octanucleotide T4G4, which does not fold, is a better primer than (T4G4)2, which can form a foldback structure. We conclude that telomerase does not require any folding of its DNA primer. Folding of telomeric DNA into G-quartet structures seems to influence the extent of telomere elongation in vitro and might therefore act as a negative regulator of elongation in vivo.     

Tetramerization of an RNA oligonucleotide containing a GGGG sequence.

Poly rG can form four-stranded helices. The Hoogsteen-paired quartets of G residues on which such structures depend are so stable that they will form in 5'-GMP solutions, provided that Na+ or K+ are present (see for example, refs 2-4). Telomeric DNA sequences, which are G-rich, adopt four-stranded antiparallel G-quartet conformations in vitro, and parallel tetramerization of G-rich sequences may be involved in meiosis. Here we show that RNAs containing short runs of Gs can also tetramerize. A 19-base oligonucleotide derived from the 5S RNA of Escherichia coli (strand III), 5'GCCGAUGGUAGUGUGGGGU3', forms a K(+)-stabilized tetrameric aggregate that depends on the G residues at its 3' end. This complex is so stable that it would be surprising if similar structures do not occur in nature.     

Formation of a stable triplex from a single DNA strand

Homopurine.homopyrimidine DNA sequences have been shown to form triple-stranded structures readily under appropriate conditions. Interest in DNA triplexes arises from potential applications of intermolecular triplexes as antisense inhibitors of gene expression and from the possibility that intramolecular triplexes may have a role in gene expression and recombination. We recently presented NMR evidence for triplex formation from the DNA oligonucleotides d(GA)4 and d(TC)4, which showed unambiguously that the second pyrimidine strand is Hoogsteen base paired and the cytosines are protonated at N3 as required. To obtain a more well defined triplex, and to provide a model for in vivo triplex structures, we have designed and synthesized a 28-base DNA oligomer with a sequence that could potentially fold to form a triplex containing both T.A.T and C+.G.C triplets. Our NMR results indicate that the conformation at pH 5.5 is an intramolecular triplex and that a significant amount of triplex remains even at pH 8.0.     

NMR study of parallel-stranded tetraplex formation by the hexadeoxynucleotide d(TG4T).

Multistranded DNA structures based upon guanine association have been proposed to be important in the structure of chromosome telomeres and in immunoglobulin class switching. Nucleic acids containing runs of guanine bases form a number of structures in vitro, including fold-back structures (Fig. 1a) and parallel-stranded quadruplex structures in DNA and RNA. The features of fold-back structures have now been determined at high-resolution. The different structures are probably based on a tetrad of hydrogen-bonded guanine bases (Fig. 1b), with buffer conditions and sequence effects mediating isomerization between the different forms. Here we use NMR spectroscopy to investigate the solution structure of the complex formed by the hexadeoxynucleotide d(TG4T) in the presence of sodium ions. We have observed the formation of a parallel-stranded quadruplex containing hydrogen-bonded tetrads of guanine. The parallel-stranded form differs significantly from the fold-back form, with individual nucleotide conformations being closer to those of B-form DNA.     

Crystal structure of parallel quadruplexes from human telomeric DNA

Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, are fundamental in protecting the cell from recombination and degradation. Disruption of telomere maintenance leads to eventual cell death, which can be exploited for therapeutic intervention in cancer. Telomeric DNA sequences can form four-stranded (quadruplex) structures, which may be involved in the structure of telomere ends. Here we describe the crystal structure of a quadruplex formed from four consecutive human telomeric DNA repeats and grown at a K(+) concentration that approximates its intracellular concentration. K(+) ions are observed in the structure. The folding and appearance of the DNA in this intramolecular quadruplex is fundamentally different from the published Na(+)-containing quadruplex structures. All four DNA strands are parallel, with the three linking trinucleotide loops positioned on the exterior of the quadruplex core, in a propeller-like arrangement. The adenine in each TTA linking trinucleotide loop is swung back so that it intercalates between the two thymines. This DNA structure suggests a straightforward path for telomere folding and unfolding, as well as ways in which it can recognize telomere-associated proteins.     

配合物与G-四链体DNA相互作用的研究

端粒在维持基因组稳定、癌症和衰老相关的生理过程中发挥着重要作用,鸟嘌呤通过形成G-四分体平面堆积成G-四链体结构,DNA二级结构参与一些重要的生物调控过程。人们已经在生物体内发现G-四分体结构的存在,它们大量存在于基因的启动区域表明G-四链体可能参与调节基因表达。以G-四链体为新靶标设计能与G-四链体DNA相互作用的小分子,为开发抗癌药物提供了新途径。最近的许多研究证明金属配合物与G-四链体DNA具有有效的相互作用,有望开发成新的抗癌药物。     

An unusual DNA structure detected in a telomeric sequence under superhelical stress and at low pH

Telomeric sequences of DNA, which are found at the ends of linear chromosomes, have been attracting attention as potential sites for the formation of unusual DNA structures. They consist of (GnTm) or (GnATm) motifs (n greater than or equal to m) and, in the single-stranded state, form hairpins stabilized by non-canonical G.G pairs. In the duplex state and under superhelical stress they exhibit hypersensitivity to SI nuclease which by analogy with homopurine-homopyrimidine sequences may reflect the formation of an unusual structure. To determine whether this is the case we have inserted into a plasmid the Tetrahymena telomeric motif (G4T2).(A2C4) and probed it by two-dimensional gel electrophoresis, chemical modification and oligonucleotide binding. Our data demonstrate that, under superhelical stress and at low pH, the insert does indeed adopt a novel DNA conformation. We have concluded that in this structure the C-rich strand forms a hairpin stabilized by non-Watson-Crick base pairs C.C+ and A.A+, whereas the G-rich strand remains unstructured. We term this new DNA structure the (C,A)-hairpin.     

Circular dichroism spectra of different structures formed by the oligonucleotides

Under different conditions, oligonucleotides can form several different DNA structures such as duplex, triplex and quadruplex. All these structures exhibit an obvious difference in their CD spectra. The common characteristic is that they show a negative band at 240 nm, while in the range of 260–300 nm, the spectra are different from each other. Many factors such as chain direction, sugar puckering mode, orientation of the glycosyl bond, base stacking and sequence can affect their conformation and then show diversity and complexity in their spectra. By studying and comparing these spectra, more information about their conformations can be obtained to help predict some new structures. Furthermore, the spectra can also provide a base to study their potential biological functions.     

A sodium-potassium switch in the formation of four-stranded G4-DNA

Single-stranded complex guanine-rich DNA sequences from chromosomal telomeres and elsewhere can associate to form stable parallel four-stranded structures termed G4-DNA by a process that is anomalously dependent on the particular alkali metal cation that is present. The anomaly, which is not found in the formation of G4-DNA by oligonucleotides containing short, single runs of three or more guanines, is caused by potassium cations excessively stabilizing fold-back intermediate structures, or pathway by-products.     

Sequence-specific artificial photo-induced endonucleases based on triple helix-forming oligonucleotides

Homopyrimidine oligonucleotides bind to homopurine-homopyrimidine sequences of duplex DNA forming a local triple helix. This binding can be demonstrated either directly by a footprinting technique, gel assays, or indirectly by inducing irreversible reactions in the target sequence, such as photocrosslinking or cleavage. Binding occurs in the major groove with the homopyrimidine oligonucleotide orientated parallel to the homopurine strand. Thymine and protonated cytosine in the oligonucleotide form Hoogsteen-type hydrogen bonds with A.T and G.C Watson-Crick base pairs, respectively. Here we report that an 11-residue homopyrimidine oligonucleotide covalently attached to an ellipticine derivative by its 3' phosphate photo-induces cleavage of the two strands of a target homopurine--homopyrimidine sequence. To our knowledge, this is the first reported case of a sequence-specific artificial photoendonuclease. In addition we show that a strong binding site for a free ellipticine derivative is induced at the junction between the triplex and duplex structures on the 5' side of the bound oligonucleotide. On irradiation, cleavage is observed on both strands of DNA. This opens new possibilities for inducing irreversible reactions on DNA at specific sites by the synergistic action of a triple helix-forming oligonucleotide and an intercalating agent.     

配体二吡啶胺单氧化物的配位多样性

本文报道了以二吡啶胺单氧化物为配体的三个铜配合物的合成和X-射线衍射数据分析.在不同配位条件下,二吡啶胺单氧化物显示了配位多样性,配体酰胺上的氢原子发生转移或者消除,分子骨架在顺式和反式之间变换.此外,还发现了一个不同寻常的分子构型转换现象.     

利用过氧化物模拟酶催化化学发光法检测钾离子

K+存在时,富含鸟嘌呤(Guanine)的特定序列单链DNA会发生构象变化形成G-四联体结构,从而能够与氯化血红素(hemin)结合生成具有过氧化物酶活性的模拟酶,对鲁米诺-H2O2化学发光体系具有强的催化作用.据此,提出了利用G-四联体-hemin-鲁米诺-H2O2化学发光体系测定K+的新方法.探讨了DNA浓度,he...     

Circular dichroism spectroscopic studies on structures formed by telomeric DNA sequences in vitro

Telomere plays an important role in cellular processes, such as cell aging, death and carcinogenisis. Having special sequences, it can form quadruplex structure in vitro. Circular dichroism (CD) spectroscopic studies show that TTAGGG, (TTAGGG)2 and (TTAGGG)4 can all form quadruplex in vitro and exist mainly as parallel quadruplex without metal ions. Both K+ and Na+ can stabilize the tetrameric structure and facilitate the forming of anti-parallel conformation. Furthermore, the conformations of quadruplex can also be affected by sequence length, the nature and concentration of metal ions.     

平面的BC_nN(n=1～5)团簇的结构和稳定性

在CCSD(T)/6-311+G(d)∥B3LYP/6-311+G(d)理论水平上系统研究了平面BCnN(n=1～5)团簇的几何结构和稳定性。BCnN(n=1～5)团簇的最低能量结构是线形结构。在BCnN(n=1～5)团簇的较低能量结构中,线形结构比环状结构以及含有支链的环状结构在能量上更有利。BCnN(n=1～5)团簇的最低能量结构的平均成键能、成键能增量、垂直电离能和垂直亲和能的研究结果显示,异构体BCN、BC3B和BC5N比它们相邻的团簇更稳定。     

配体二吡啶胺单氧化物的配位多样性(英文)

本文报道了以二吡啶胺单氧化物为配体的三个铜配合物的合成和X-射线衍射数据分析。在不同配位条件下,二吡啶胺单氧化物显示了配位多样性,配体酰胺上的氢原子发生转移或者消除,分子骨架在顺式和反式之间变换。此外,还发现了一个不同寻常的分子构型转换现象。     

草酰碘分子构型的量子化学研究

采用量子化学从头算的HF,MP2,QCISD方法和密度泛函中的B3LYP方法,在不同基组6-311G(d),6—311G(2df),6—311G(3df),6-311 G(3df)水平上对草酰碘中性分子(ICO)2作了构像分析．结果表明,在不同基组水平上,由MP2,QCISD,B3LYP方法均能得到草酰碘分子的交叉式构型和平面反式构型,与实验所得草酰卤化物的构型完全相符．     

Label-free selective sensing of Pb2+ lead(II) sensors based on the aggregation of a pyrene fluorescent probe

In the present work, we report a label-free fluorescence turn-on approach for the sensitive and selective sensing of Pb²⁺. Pyrene with one positive charge was used as the fluorescent probe, and thrombin aptamer (TBA), which was a G-rich oligonucleotide, was employed to form G-quadruplex with lead(II). When TBA and Pb²⁺ were mixed with lead(II) in an aqueous solution, it was folded into a stable G-quadruplex. Subsequently, a single-stranded nucleic acid-specific nuclease S1 was added. The G-quadruplex stabilized by Pb²⁺ lead(II) had markedly a significant resistant ability to nuclease S1 digestion. However, in the absence of Pb²⁺ lead(II), no quadruplex or less stable quadruplex was formed and TBA was digested by nuclease S1 in 3 min under the optimized experimental conditions. Finally, pyrene probe was mixed with oligonucleotide in Pb²⁺ lead(II). Electrostatic interactions between oligonucleotide (a polyanion) and the probe induced the aggregation of the probe, which in turn produced strong emission of the strong pyrene excimer emission. The intensity of the induced excimer emission was directly proportional to the amount of Pb²⁺ added. Our approach shows good selectivity and sensitivity for the detection of Pb²⁺ with a limit of detection limit as low as 800 nmol/L.     

Ab initio与密度泛函理论研究BeC3异构体的结构与稳定性

采用密度泛函理论和CCSD（T）方法对各种BeCs异构体进行了研究,获得了各异构体的平衡构型,并计算了各自的振动频率和相对能量．结果表明,Be原子通过与环型C3分子中的2个碳原子发生侧配作用而形成的5s是基态异构体,而1s,6s和1t都具有与5s相近的能量,都是BeC3的稳定异构体．