Pub Date : 2011-08-30DOI: 10.15866/IREBIC.V2I4.1528
Emanuela Micheli, Matteo Martufi, A. Galati, M. Franceschin, P. Santis, M. Savino, S. Cacchione
G-quadruplex-forming are widespread in eukaryotic genomes. In particular, G-quadruplex motifs have been found in the promoter region of 40% human genes. One of these genes is hTERT, encoding the catalytic subunit of human telomerase, whose up-regulated expression is responsible for the unlimited proliferative potential of most cancer cells. hTERT core promoter exhibits a high potential for G-quadruplex formation, containing nine partially overlapping PQS (putative quadruplex sequence) in a G-rich region of 68 nucleotides. Here we show the formation of a superstructure in the hTERT promoter deriving from the simultaneous folding of three adjacent G-quadruplex structures. Interestingly, G-quadruplex ligands are able to stabilize hTERT G-quadruplex structures and to alter transcription from the hTERT promoter, suggesting that the formation of a G-quadruplex superstructure could play a role in regulating gene transcription
g -四聚体形成在真核生物基因组中广泛存在。特别是，在40%的人类基因的启动子区域发现了g -四重基序。其中一个基因是hTERT，编码人类端粒酶的催化亚基，其上调表达是大多数癌细胞无限增殖潜力的原因。hTERT核心启动子显示出g -四重体形成的高潜力，在68个核苷酸的g -富区包含9个部分重叠的PQS(假定的四重体序列)。在这里，我们展示了hTERT启动子中由三个相邻的g -四重结构同时折叠而形成的上层结构。有趣的是，g -四重体配体能够稳定hTERT g -四重体结构并改变hTERT启动子的转录，这表明g -四重体上层结构的形成可能在调节基因转录中发挥作用
{"title":"G-Quadruplex Superstructure in the hTERT Core Promoter: Stabilization by Monomer Self-Stacking","authors":"Emanuela Micheli, Matteo Martufi, A. Galati, M. Franceschin, P. Santis, M. Savino, S. Cacchione","doi":"10.15866/IREBIC.V2I4.1528","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I4.1528","url":null,"abstract":"G-quadruplex-forming are widespread in eukaryotic genomes. In particular, G-quadruplex motifs have been found in the promoter region of 40% human genes. One of these genes is hTERT, encoding the catalytic subunit of human telomerase, whose up-regulated expression is responsible for the unlimited proliferative potential of most cancer cells. hTERT core promoter exhibits a high potential for G-quadruplex formation, containing nine partially overlapping PQS (putative quadruplex sequence) in a G-rich region of 68 nucleotides. Here we show the formation of a superstructure in the hTERT promoter deriving from the simultaneous folding of three adjacent G-quadruplex structures. Interestingly, G-quadruplex ligands are able to stabilize hTERT G-quadruplex structures and to alter transcription from the hTERT promoter, suggesting that the formation of a G-quadruplex superstructure could play a role in regulating gene transcription","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"81 1","pages":"153-155"},"PeriodicalIF":0.0,"publicationDate":"2011-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76782701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2011-08-30DOI: 10.15866/IREBIC.V2I4.1522
V. Zozulya, O. Ryazanova, I. Voloshin, L. Dubey, I. Dubey
The interaction of the novel cationic porphyrin – imidazophenazine conjugate (TMP3-Pzn), as well as its zinc (II) and manganese (III) metallocomplexes with intramolecular G-quadruplex formed by 22-mer oligodeoxynucleotide d[AGGG(TTAGGG)3] of human telomeric repeat (22G4) was studied. Techniques of absorption and polarized fluorescent spectroscopy as well as absorption melting at 295 nm were used. The binding affinity of the conjugates to the quadruplex was studied using titration experiments registering the dependence of the fluorescence intensity and polarization degree for porphyrin moieties on quadruplex/ligand molar ratio (P/D). All investigations were carried out in 2 mM phosphate buffer (pH6.9) containing 0.5 mM EDTA and 0.1 M NaCl. Spectroscopic characteristics of the TMP3-Pzn and ZnTMP3-Pzn conjugates evidence the formation of internal heterodimers with stacking between porphyrin and phenazine chromophores, although in the case of MnTMP3-Pzn it has not occurred. It was established that all the conjugates reveal high binding affinities to the intra-molecular G-quadruplex, probably, via external groove binding of porphyrin moiety. The complex formation is accompanied by the increase in the fluorescence intensity and polarization degree of porphyrin fragments. It should be noted that negligibly small fluorescence of manganese porphyrin moiety flames up by near 20 times under the binding, being the novel observation for manganese complex. It was found that ZnTMP3-Pzn and MnTMP3-Pzn stabilize the G-quadruplex structure increasing the transition midpoint temperature by 3 °C, whereas non-metallated TMP3-Pzn conjugate decreases it by approximately 2 °C. Despite of the opposite changes in G-quadruplex melting temperature, a simultaneous increase in the transition enthalpy and entropy was determined for all conjugates, which gives a some stabilizing increment in the Gibbs standard free energy. In the case of metal complexes, 10-fold increase in the 22G4 folding equilibrium constant at 37 °C was determined
研究了新型阳离子卟啉-咪唑吩啉偶联物(TMP3-Pzn)及其锌(II)、锰(III)金属配合物与22聚寡脱氧核苷酸d[AGGG(TTAGGG)3]构成的分子内g -四联体(22G4)的相互作用。采用了吸收和偏振荧光光谱技术以及295 nm吸收熔融技术。通过滴定实验研究了卟啉偶联物与四联体的结合亲和力，并记录了卟啉部分的荧光强度和极化程度与四联体/配体摩尔比(P/D)的关系。所有研究均在含有0.5 mM EDTA和0.1 M NaCl的2 mM磷酸盐缓冲液(pH6.9)中进行。TMP3-Pzn和ZnTMP3-Pzn偶联物的光谱特征证明卟啉和非那嗪发色团之间形成了内部异源二聚体，尽管MnTMP3-Pzn没有发生这种情况。结果表明，所有缀合物与分子内的g -四重体具有较高的结合亲和力，可能是通过卟啉片段的外部凹槽结合。配合物的形成伴随着卟啉片段荧光强度和极化程度的增加。值得注意的是，锰卟啉部分可以忽略不计的小荧光在结合下上升了近20倍，这是锰配合物的新观察。结果表明，ZnTMP3-Pzn和MnTMP3-Pzn稳定了g -四相结构，使转变中点温度升高了3℃，而非金属化的TMP3-Pzn共轭物使转变中点温度降低了约2℃。尽管g -四相熔点的温度变化相反，但所有共轭物的转变焓和熵同时增加，这使得吉布斯标准自由能有一定的稳定增量。在金属配合物的情况下，在37℃时，22G4的折叠平衡常数增加了10倍
{"title":"Spectroscopic Studies on Binding of Porphyrin-Phenazine Conjugate to Intramolecular G-Quadruplex Formed by 22-mer Oligonucleotide","authors":"V. Zozulya, O. Ryazanova, I. Voloshin, L. Dubey, I. Dubey","doi":"10.15866/IREBIC.V2I4.1522","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I4.1522","url":null,"abstract":"The interaction of the novel cationic porphyrin – imidazophenazine conjugate (TMP3-Pzn), as well as its zinc (II) and manganese (III) metallocomplexes with intramolecular G-quadruplex formed by 22-mer oligodeoxynucleotide d[AGGG(TTAGGG)3] of human telomeric repeat (22G4) was studied. Techniques of absorption and polarized fluorescent spectroscopy as well as absorption melting at 295 nm were used. The binding affinity of the conjugates to the quadruplex was studied using titration experiments registering the dependence of the fluorescence intensity and polarization degree for porphyrin moieties on quadruplex/ligand molar ratio (P/D). All investigations were carried out in 2 mM phosphate buffer (pH6.9) containing 0.5 mM EDTA and 0.1 M NaCl. Spectroscopic characteristics of the TMP3-Pzn and ZnTMP3-Pzn conjugates evidence the formation of internal heterodimers with stacking between porphyrin and phenazine chromophores, although in the case of MnTMP3-Pzn it has not occurred. It was established that all the conjugates reveal high binding affinities to the intra-molecular G-quadruplex, probably, via external groove binding of porphyrin moiety. The complex formation is accompanied by the increase in the fluorescence intensity and polarization degree of porphyrin fragments. It should be noted that negligibly small fluorescence of manganese porphyrin moiety flames up by near 20 times under the binding, being the novel observation for manganese complex. It was found that ZnTMP3-Pzn and MnTMP3-Pzn stabilize the G-quadruplex structure increasing the transition midpoint temperature by 3 °C, whereas non-metallated TMP3-Pzn conjugate decreases it by approximately 2 °C. Despite of the opposite changes in G-quadruplex melting temperature, a simultaneous increase in the transition enthalpy and entropy was determined for all conjugates, which gives a some stabilizing increment in the Gibbs standard free energy. In the case of metal complexes, 10-fold increase in the 22G4 folding equilibrium constant at 37 °C was determined","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"40 1","pages":"112-119"},"PeriodicalIF":0.0,"publicationDate":"2011-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84849809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2011-08-30DOI: 10.15866/IREBIC.V2I4.1525
Luca Ginnari-Satriani, V. Casagrande, A. Alvino, Alessandro Altieri, Pierre Murat, E. Defrancq, C. Lombardo, S. Neidle, A. Bianco, G. Ortaggi, M. Franceschin
We report here a study of the binding affinity of a triazatruxene based G-quadruplex ligand and three derivatives to G-quadruplex structures and their selectivity with respect to duplex DNA. The parent compound AZATRUX is the best compound of the series, both in terms of affinity and selectivity
{"title":"Effects of Protein Binding on DNA G-Quadruplex Structures","authors":"Luca Ginnari-Satriani, V. Casagrande, A. Alvino, Alessandro Altieri, Pierre Murat, E. Defrancq, C. Lombardo, S. Neidle, A. Bianco, G. Ortaggi, M. Franceschin","doi":"10.15866/IREBIC.V2I4.1525","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I4.1525","url":null,"abstract":"We report here a study of the binding affinity of a triazatruxene based G-quadruplex ligand and three derivatives to G-quadruplex structures and their selectivity with respect to duplex DNA. The parent compound AZATRUX is the best compound of the series, both in terms of affinity and selectivity","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"16 1","pages":"135-141"},"PeriodicalIF":0.0,"publicationDate":"2011-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74590609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2011-08-30DOI: 10.15866/IREBIC.V2I4.1523
V. P. Ma, Ka-Ho Leung, D. Chan, W. Lam, C. Leung, Dik‐Lung Ma
In this review, we summarize recent findings in the development of c-myc G-quadruplex ligands. Several features such as expanded aromatic rings, flexible molecules, dinuclear metal complexes, oligomers and G-quartet based ligands have been demonstrated to be advantageous for providing higher selectivity towards the c-myc G-quadruplex over duplex structures. High throughput screening methods including competition dialysis, G4 FID, FRET-based melting assay, direct ELISA and in silico virtual screening for analyzing the interaction between the ligands and the c-myc G-quadruplex are discussed. In particular, in silico virtual screening has been demonstrated to be a valuable means for the discovery of selective G-quadruplex ligands. Using this approach, ligands selective for the c-myc G-quadruplex have been successfully identified
本文综述了近年来c-myc - g四联体配体的研究进展。扩展芳环、柔性分子、双核金属配合物、低聚物和基于g -四重奏的配体等特征已被证明有利于对c-myc g -四重体提供比双相结构更高的选择性。讨论了用于分析配体与c-myc g -四联体相互作用的高通量筛选方法，包括竞争透析、G4 FID、基于fret的熔融法、直接ELISA和计算机虚拟筛选。特别是，在硅虚拟筛选已被证明是一个有价值的手段，发现选择性g -四重体配体。使用这种方法，已经成功地鉴定了c-myc g -四重体的选择性配体
{"title":"Recent Development of c-myc G-Quadruplex Ligands","authors":"V. P. Ma, Ka-Ho Leung, D. Chan, W. Lam, C. Leung, Dik‐Lung Ma","doi":"10.15866/IREBIC.V2I4.1523","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I4.1523","url":null,"abstract":"In this review, we summarize recent findings in the development of c-myc G-quadruplex ligands. Several features such as expanded aromatic rings, flexible molecules, dinuclear metal complexes, oligomers and G-quartet based ligands have been demonstrated to be advantageous for providing higher selectivity towards the c-myc G-quadruplex over duplex structures. High throughput screening methods including competition dialysis, G4 FID, FRET-based melting assay, direct ELISA and in silico virtual screening for analyzing the interaction between the ligands and the c-myc G-quadruplex are discussed. In particular, in silico virtual screening has been demonstrated to be a valuable means for the discovery of selective G-quadruplex ligands. Using this approach, ligands selective for the c-myc G-quadruplex have been successfully identified","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"55 1","pages":"120-128"},"PeriodicalIF":0.0,"publicationDate":"2011-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76007042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2011-08-30DOI: 10.15866/IREBIC.V2I4.1526
E. J. Baldassarri, M. G. Ortore, C. Ferrero, S. Finet, F. Spinozzi, P. Mariani
It is well known that the formation of G-quadruplex by guanosine derivatives strongly depends on counter-ions. To investigate quadruplex stability in the presence of different counter-ions and in the absence of a covalent axial backbone, high-pressure X-ray diffraction experiments have been performed on lyotropic phases of guanosine 5’-monophosphate (GMP) in the form of sodium and ammonium salts. As a result, concentration-pressure phase diagrams were obtained in a pressure range from 1 bar to about 2 kbar, and the structural properties of the different phases derived. Interestingly, cholesteric (Ch) and hexagonal (H) columnar phases were found in both GMP salts, but during compression a reverse behavior was detected: in GMP sodium salt, pressure induces a H-Ch phase transition, while in GMP ammonium salt the induced transition is Ch-H. Different counter-ion stabilization, which control quadruplex length and the consequence of lateral interactions, probably explain such observation
{"title":"Pressure Effects on G-Quadruplex Structures Stabilized by Two Different Counter-Ions","authors":"E. J. Baldassarri, M. G. Ortore, C. Ferrero, S. Finet, F. Spinozzi, P. Mariani","doi":"10.15866/IREBIC.V2I4.1526","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I4.1526","url":null,"abstract":"It is well known that the formation of G-quadruplex by guanosine derivatives strongly depends on counter-ions. To investigate quadruplex stability in the presence of different counter-ions and in the absence of a covalent axial backbone, high-pressure X-ray diffraction experiments have been performed on lyotropic phases of guanosine 5’-monophosphate (GMP) in the form of sodium and ammonium salts. As a result, concentration-pressure phase diagrams were obtained in a pressure range from 1 bar to about 2 kbar, and the structural properties of the different phases derived. Interestingly, cholesteric (Ch) and hexagonal (H) columnar phases were found in both GMP salts, but during compression a reverse behavior was detected: in GMP sodium salt, pressure induces a H-Ch phase transition, while in GMP ammonium salt the induced transition is Ch-H. Different counter-ion stabilization, which control quadruplex length and the consequence of lateral interactions, probably explain such observation","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"67 4","pages":"142-146"},"PeriodicalIF":0.0,"publicationDate":"2011-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91441459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2011-08-30DOI: 10.15866/IREBIC.V2I4.1527
L. Dubey, Mykola M. Ilchenko, V. Zozulya, O. Ryazanova, P. Pogrebnoy, I. Dubey
New conjugate of G-quadruplex ligand, cationic tris(methylpyridinium)porphyrin, and its Zn(II) and Mn(III) metal complexes with a neutral intercalating agent imidazophenazine were synthesized. The synthesis was based on the coupling of carboxyalkyl derivative of the porphyrin with N1-aminoalkylated dye. Spectral-fluorescent studies and density functional quantum-chemical calculations suggest the formation of intramolecular complexes between the two chromophores for non-metalated hybrid and zinc(II) derivative. The conjugates have been found to inhibit the growth of tumor cells of mouse Lewis lung carcinoma in vitro at micromolar concentrations. Metal complexes were several times more active than the non-metalated hybrid. The most efficient Zn(II) complex suppressed the tumor cells with IC50 5.9 M
{"title":"Synthesis, Structure and Antiproliferative Activity of Cationic Porphyrin - Imidazophenazine Conjugate","authors":"L. Dubey, Mykola M. Ilchenko, V. Zozulya, O. Ryazanova, P. Pogrebnoy, I. Dubey","doi":"10.15866/IREBIC.V2I4.1527","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I4.1527","url":null,"abstract":"New conjugate of G-quadruplex ligand, cationic tris(methylpyridinium)porphyrin, and its Zn(II) and Mn(III) metal complexes with a neutral intercalating agent imidazophenazine were synthesized. The synthesis was based on the coupling of carboxyalkyl derivative of the porphyrin with N1-aminoalkylated dye. Spectral-fluorescent studies and density functional quantum-chemical calculations suggest the formation of intramolecular complexes between the two chromophores for non-metalated hybrid and zinc(II) derivative. The conjugates have been found to inhibit the growth of tumor cells of mouse Lewis lung carcinoma in vitro at micromolar concentrations. Metal complexes were several times more active than the non-metalated hybrid. The most efficient Zn(II) complex suppressed the tumor cells with IC50 5.9 M","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"79 1","pages":"147-152"},"PeriodicalIF":0.0,"publicationDate":"2011-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86891183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2011-06-30DOI: 10.15866/IREBIC.V2I3.1516
Mykola M. Ilchenko, I. Dubey
The structures and energies of guanine quartets and octets in water were determined by DFT (Density Functional Theory) calculations using M06-2X functional and 6-31G(d, p) basic set. Guanine quartets in vacuum were found to have not only the Hoogsteen or bifurcated, but also mixed system of hydrogen bonds; in water the latter two forms are transformed into the classic Hoogsteen-type structure. Four stable configurations of G-octets with D4, C4 and S4 symmetry formed by the pairs of guanine quartets with Hoogsteen, bifurcated or mixed system of H-bonds were identified. The most advantageous structure of the G-octet molecular system in aqueous medium was shown to be S4-symmetric structure consisting of the pair of mixed Hoogsteen-bifurcated type G-quartets
{"title":"Density Functional Study of the Structure of Guanine Octets in Aqueous Medium","authors":"Mykola M. Ilchenko, I. Dubey","doi":"10.15866/IREBIC.V2I3.1516","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I3.1516","url":null,"abstract":"The structures and energies of guanine quartets and octets in water were determined by DFT (Density Functional Theory) calculations using M06-2X functional and 6-31G(d, p) basic set. Guanine quartets in vacuum were found to have not only the Hoogsteen or bifurcated, but also mixed system of hydrogen bonds; in water the latter two forms are transformed into the classic Hoogsteen-type structure. Four stable configurations of G-octets with D4, C4 and S4 symmetry formed by the pairs of guanine quartets with Hoogsteen, bifurcated or mixed system of H-bonds were identified. The most advantageous structure of the G-octet molecular system in aqueous medium was shown to be S4-symmetric structure consisting of the pair of mixed Hoogsteen-bifurcated type G-quartets","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"78 1","pages":"82-86"},"PeriodicalIF":0.0,"publicationDate":"2011-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73852451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2011-06-30DOI: 10.15866/IREBIC.V2I3.1518
S. Masiero, Lucia Gramigna, P. Neviani, R. Perone, S. Pieraccini, G. Spada
Depending on the experimental conditions, lipophilic guanosines (LipoGs) can undergo different self-assembly pathways based on different H-bonded motifs, e.g. the cyclic discrete G-quartet and the “infinite” tape-like G-ribbon. The switching between different supramolecular motifs have been obtained by a variety of external stimuli. After a general presentation of the LipoG self-assembly, in this mini-review we will discuss, the case of three different stimuli. A first example is represented by chemical stimuli: addition of an alkali metal ion stabilizes the G-quartet while its removal shifts the equilibrium toward the G-ribbon. In the second case, a lipoG armed with a terthiophene unit undergoes a pronounced variation of its supramolecular organisation by changing the polarity of the solvent: in chloroform the derivative assembles via H-bonding in a guanosine driven structure, while in the more polar (and H-bond competing) acetonitrile different aggregates are observed, where the terthiophene chains are - stacked in a helicoidal arrangement. Finally, a third type of stimulus is represented by light: the photocontrolled self-assembly of a modified guanosine nucleobase with a photoactive unit at C8 is obtained selecting the appropriate wavelength
{"title":"Switching between Supramolecular Assemblies of Lipophilic Guanosine Derivatives Triggered by External Stimuli","authors":"S. Masiero, Lucia Gramigna, P. Neviani, R. Perone, S. Pieraccini, G. Spada","doi":"10.15866/IREBIC.V2I3.1518","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I3.1518","url":null,"abstract":"Depending on the experimental conditions, lipophilic guanosines (LipoGs) can undergo different self-assembly pathways based on different H-bonded motifs, e.g. the cyclic discrete G-quartet and the “infinite” tape-like G-ribbon. The switching between different supramolecular motifs have been obtained by a variety of external stimuli. After a general presentation of the LipoG self-assembly, in this mini-review we will discuss, the case of three different stimuli. A first example is represented by chemical stimuli: addition of an alkali metal ion stabilizes the G-quartet while its removal shifts the equilibrium toward the G-ribbon. In the second case, a lipoG armed with a terthiophene unit undergoes a pronounced variation of its supramolecular organisation by changing the polarity of the solvent: in chloroform the derivative assembles via H-bonding in a guanosine driven structure, while in the more polar (and H-bond competing) acetonitrile different aggregates are observed, where the terthiophene chains are - stacked in a helicoidal arrangement. Finally, a third type of stimulus is represented by light: the photocontrolled self-assembly of a modified guanosine nucleobase with a photoactive unit at C8 is obtained selecting the appropriate wavelength","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"22 1","pages":"87-95"},"PeriodicalIF":0.0,"publicationDate":"2011-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83741414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2011-06-30DOI: 10.15866/IREBIC.V2I3.1513
P. Šket, Rok Pirh, J. Plavec
It is well known that the presence of cations is necessary for G-quartet formation due to their role in reducing repulsions amongst guanine carbonyl oxygen atoms and additionally enhancing base-base stacking interactions. However, not much is known about the influence of anions on G-quadruplex formation by G-rich oligonucleotides in aqueous solution. In the presence of sodium halides, acetate, nitrate and BPh4- folding was almost complete, while only partial folding has been observed with NaBF4 and NaPF6. Detailed evaluation of 1H NMR spectra of d(G4T4G4)2 in the presence of nine different sodium salts indicates minor differences in loop regions as well as in structure of G-quadruplex core. Comparison of inter-proton distances obtained from NOESY spectra showed slightly different orientations of thymine residues in loop regions and changes in stacking interactions between G-quartets, which are most pronounced in the case of G-quadruplex folded in the presence of NaPF6
{"title":"Do Anions Exert any Structural Changes on Dimeric d(G4T4G4)2 Quadruplex in Aqueous Solution","authors":"P. Šket, Rok Pirh, J. Plavec","doi":"10.15866/IREBIC.V2I3.1513","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I3.1513","url":null,"abstract":"It is well known that the presence of cations is necessary for G-quartet formation due to their role in reducing repulsions amongst guanine carbonyl oxygen atoms and additionally enhancing base-base stacking interactions. However, not much is known about the influence of anions on G-quadruplex formation by G-rich oligonucleotides in aqueous solution. In the presence of sodium halides, acetate, nitrate and BPh4- folding was almost complete, while only partial folding has been observed with NaBF4 and NaPF6. Detailed evaluation of 1H NMR spectra of d(G4T4G4)2 in the presence of nine different sodium salts indicates minor differences in loop regions as well as in structure of G-quadruplex core. Comparison of inter-proton distances obtained from NOESY spectra showed slightly different orientations of thymine residues in loop regions and changes in stacking interactions between G-quartets, which are most pronounced in the case of G-quadruplex folded in the presence of NaPF6","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"66 1","pages":"68-73"},"PeriodicalIF":0.0,"publicationDate":"2011-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80187254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2011-06-30DOI: 10.15866/IREBIC.V2I3.1515
Romaric Bonnet, Pierre Murat, N. Spinelli, A. V. D. Heyden, P. Labbé, P. Dumy, E. Defrancq
We report on the design of a new biomolecular device based on the concept of Template Assembled Synthetic G-Quadruplex (TASQ), where quadruplex DNA structures are assembled on a scaffold for constraining G-quadruplex conformation. As a proof of concept, parallel-stranded conformation of G-quadruplex was prepared by using a cyclodecapeptide as the template. As anticipated the use of the scaffold allows the precise control of the conformation of the quadruplex and increases dramatically the stability of the motif. This device was used for investigating by Surface Plasmon Resonance the affinity of ligands for G-quadruplex DNA
{"title":"Template Assembled Synthetic G-Quadruplex: a Novel Biomolecular System for Investigating the Interactions of Ligands with Constrained Quadruplex Conformation","authors":"Romaric Bonnet, Pierre Murat, N. Spinelli, A. V. D. Heyden, P. Labbé, P. Dumy, E. Defrancq","doi":"10.15866/IREBIC.V2I3.1515","DOIUrl":"https://doi.org/10.15866/IREBIC.V2I3.1515","url":null,"abstract":"We report on the design of a new biomolecular device based on the concept of Template Assembled Synthetic G-Quadruplex (TASQ), where quadruplex DNA structures are assembled on a scaffold for constraining G-quadruplex conformation. As a proof of concept, parallel-stranded conformation of G-quadruplex was prepared by using a cyclodecapeptide as the template. As anticipated the use of the scaffold allows the precise control of the conformation of the quadruplex and increases dramatically the stability of the motif. This device was used for investigating by Surface Plasmon Resonance the affinity of ligands for G-quadruplex DNA","PeriodicalId":14377,"journal":{"name":"International Review of Biophysical Chemistry","volume":"77 1","pages":"78-81"},"PeriodicalIF":0.0,"publicationDate":"2011-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89916788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：