Complex-Formation of Ethidium Bromide with Poly[d(A-T)]·Poly[d(A-T)]

Abstract

The interaction of Ethidium Bromide (EtBr) with double-stranded (ds-) and single-stranded (ss-) poly[d(A-T)] was studied in different ionic strengths solutions. Optical spectroscopy and Scatchard analysis results indicate that the ligand interacts to both helix and coiled structures of the polynucleotide by “strong” and “weak” binding modes. The association parameters (binding constant—K—and the number of nucleotides corresponding to a binding site—n) of the strong type of interaction were found to be independent of Na+ concentration. Weak interaction occurs at low ionic strength and/or high EtBr concentration. Estimated binding parameters of EtBr with ss- and ds-polynucleotide are in good agreement with those for EtBr-B-DNA complexes. Data obtained provided an evidence for a stacking interaction of EtBr with single stranded poly[d(A-T)].     

Bh-DNA: Variations of the Poly[d(A)] · Poly[d(T)] Structure within the Framework of the Fibre Diffraction Studies

Abstract

A refinement of the recent results for poly[d(A)] · poly[d(T)] (Alexeev et al., J. Biomol. Struct. Dyn. 4, 989 (1987)) involving additional parameters of the base-pair structure and of the sugar- phosphate backbone expands the conformational potential of this polynucleotide of the B type to include the possibility of bifurcated hydrogen bonds of the kind recently discovered in crystalline deoxyoligonucleotide with lone d(A)_n · d(T)_n stretch (Nelson et al., Nature 330, 221 (1987)).

Still, analysis of the available data and energy calculations do not seem to indicate that the bifurcated H-bonds are a crucial factor responsible for the anomalous structure of the d(A)_n · d(T)_n sequence. The unique structural properties of poly [d(A)] · poly[d(T)] can hardly be explained without taking into account its interactions with the double-layer hydration spine in the minor groove. In view of the hydration mechanism stabilizing poly [d(A)] · poly [d(T)] and of the polynucleotide's heteronomous prehistory (Arnott et al., Nucleic Acids Res. 11, 4141 (1983)) we suggest that this B-type structure be called B_h.     

Thermodynamics of B-Z Transition of Poly[d(G-C)] in a Water-Ethanol Solution. The “Tie Calorimetry”

Abstract

Poly[d(G-C)] in a 55% ethanol solution undergoes a transition from the Z form to the B form when the temperature is increased from 20° to 50°C. The enthalpy of the transition, ΔH_BA =—1.4 kcal/mol, has been determined with a “tie” polyamine which stabilizes the Z conformation. This value has been shown to be practically independent of ionic strength within the range of 5 x 10⁴ M—2 x 10³ M NaCl.     

Parallel-Stranded Oligonucleotides with Alternating d(A-isoG)/d(T·C) and d(A·G)/d(T·m5isoC) Sequences

Abstract

Parallel-stranded (ps) DNA hairpins with alternating d(A-isoG)/d(T·C) (designated as ps-t1) and d(A·G)/d(T·m⁵isoC) (ps-t2) sequences were studied by means of UV, CD and fluorescence spectroscopy. The thermostability of d(A·G)/d(T·m⁵isoC) sequence was close to that of aps d(G·A)/d(T·C). The stability of the ps d(A·isoG)/d(T·C) sequence was even higher than that of a related anti-parallel-stranded (aps) d(G·A)/d(T·C) sequence, being unique for ps DNAs studied so far.     

Interaction of a dimeric distamycin analog with poly(dA)poly(dT), poly[d(A–T)]poly[d(A–T)], and duplex O<Subscript>23</Subscript> at the origin of replication of the herpes simplex virus

The binding of a dimeric distamycin analog (Pt–bis–Dst) to poly[d(A–T)]poly[d(A–T)], poly(dA)poly(dT), and duplex O₂₃ with the sequence 5’-GCCAATATATATATATTATTAGG-3’, which occurs at the origin of replication (OriS) of the herpes simplex virus, was studied via UV and CD spectroscopy. The synthetic polyamide differs from the natural antibiotic in having two distamycin moieties that are linked via a glycine cis-diamino platinum group. The Pt–bis–Dst binding to poly[d(A–T)]poly[d(A–T)] and poly(dA)poly(dT) reached saturation at approximately one ligand molecule per eight bp. As the ligand–base pair ratio further increased, the maximum wavelength band tended to shift toward longer wavelengths in the CD spectra of complexes with poly[d(A–T)]poly[d(A–T)] and a shoulder appeared in the 290–310 nm spectral region that was absent from the CD spectra of complexes with lower ligand coverages. At higher ligand–oligonucleotide molar ratios, Pt–bis–Dst could bind to poly[d(A–T)]poly[d(A–T)] in the form of hairpins or associations that result from interactions between the distamycin moieties of two neighbor Pt–bis–Dst molecules. The structures of the complexes were stabilized by interactions between the pirrolcarboxamide moieties of two Pt–bis–Dst molecules absorbed on adjacent overlapping binding sites. The interactions could also be responsible for the concentration-dependent spectral changes that were observed during the formation of a complex between Pt–bis–Dst and poly[d(A–T)]poly[d(A–T)]. Spectral changes were almost absent in the case of Pt–bis–Dst binding to poly(dA)poly(dT). The binding of Pt–bis–Dst to duplex O₂₃ reached saturation at two ligand molecules per duplex, which contained a cluster of 18 AT pairs. At higher molar-concentration ratios, duplex CD spectra underwent changes similar to those that were observed for Pt–bis–Dst binding to poly[d(A–T)]poly[d(A–T)]. Testing Pt–bis–Dst for antiviral activity identified 1.5 μg/mL as a concentration that halved the cytopathic effect of the herpes simplex virus on Vero E6 cells; the selectivity index of antiviral action was 65; cytotoxicity was relatively low. The Pt–bis–Dst concentration that caused the death of approximately half of the cells was estimated at 100 μg/mL.     

Structures for the polynucleotide complexes poly(dA) · poly(dT) and poly(dT) · poly(dA) · poly(dT)

X-ray diffraction analyses of fibers of polydeoxyadenylic acid · polydeoxythymidylic acid show that this molecule exists as a 10-fold double-helix with axial rise per nucleotide $\text{h = 3.24}\text{to}\text{3.29}\text{A}\text{?}$. The structure is very similar to B-DNA ($\text{h = 3.37}\text{A}\text{?}$) in having C3-exo furanose rings and base-pairs positioned centrally on the helix axis, but distinctive enough to have two packing modes, neither of which has been observed for B-DNA. Although the triple-stranded poly(dT) · poly(dA) · poly(dT) also has a large value of h(3.26 Å), each of the chains is a 12-fold helix of the A-genus with C3-endo furanose rings and bases displaced several Angstrom units from the helix axis.     

一种制备poly(Ⅰ)·poly(C)-滤纸的新方法

poly(1)·poly(C)-滤纸是一种亲和材料,可以用来吸附与双链核酸有亲和力的酶或蛋白。本文介绍用对-β硫酸酯乙砜基苯胺为活化剂制备poly(I)·poly(C)-滤纸的方法。poly(I)·poly(C)的结合容量为10—35μg/cm~2,用来吸附兔网织红细胞裂解液中2’-5’A合成酶效果良好。在一定范围内,酶活与被吸附裂解液量呈线性关系,说明可以用来定量检测未知样品中与poly(I)·poly(C)有亲和力的酶。poly(I)·poly(C)-滤纸在-20℃保存四个月亲和能力不变。本方法与文献报道的方法相比,操作简便试剂易得。     

Studies on synthetic chromatins containing poly(dA-dT)·poly(dA-dT) and poly(dG-dC)·poly(dG-dC)

Core histones, (H2A,H2B,H3,H4)₂, were reconstituted with the synthethic polynucleotides poly(dA-dT)·poly(dA-dT) and poly(dG-dC)·poly(dG-dC) to yield synthetic chromatins containing 200 basepairs per octamer. These synthetic chromatins displayed a 36% decrease in the circular dichroism (CD) peak ellipticity from the value of the polynucleotide free in solution; the poly(dA-dT)·poly(dA-dT)/chromatin showed an increase in the complexity of the thermal denaturation profile compared to that of the polynucleotide. Both the temperature of maximum $\text{d}\text{h}\text{d}\text{T}$ for each transition (T_m) and the relative amount of poly(dA-dT)·poly(dA-dT) in the synthetic chromatin melting in each of the four thermal transitions is a function of the ionic strength over the 0–5 mM sodium phosphate range (0.25 mM EDTA, pH 7.0); a shift of material toward higher melting transitions was observed with increasing ionic strength. The CD peak ellipticity value for both synthetic chromatins was ionic strength-independent over the 0–5 mM sodium phosphate range. These results are in contrast to those observed with $\text{H}\text{1}\text{H}\text{5}$ stripped chicken erythrocyte chromatin (Fulmer, A. and Fasman, G.D. (1979) Biopolymers 18, 2875–2891), where an ionic strength dependence was found. Differences in the CD spectra between poly(dA-dT)·poly(dA-dT)/chromatin, poly(dG-dC)·poly(dG-dC)/chromatin and $\text{H}\text{1}\text{H}\text{5}$ stripped chicken erythrocyte chromatin suggest subtle differences in assembly. Finally, the temperature dependence of the CD spectra of poly(dA-dT)·poly(dA-dT)-containing synthetic chromatin, which is similar to that for the polynucleotide, suggests the core histone bound polynucleotide has a large degree of conformational flexibility allowing it to undergo the premelt transition.     

Interpretation of DNA vibration modes: I-The guanosine and cytidine residues involved in poly(dG-dC)·poly(dG-dC) and d(CG)3·d(CG)3

Abstract

A normal coordinate analysis has been carried out on guanosine and cytidine residues appearing in oligo and polynucleotides by using a simplified valence force field that allows the vibrational spectra of 5′-dGMP and 2′-deoxycytidine molecules to be reproduced. The role of both C2′-endo and C3′-endo conformations on sugar pucker, as well as that of glycosidic torsion angle (χ), on several characteristic vibration modes of these residues have been studied. The present calculations based on a non-redundant set of internal coordinates preserving the harmonic approximation of the potential field, allows us to explain quite satisfactorily the modifications of the vibrational spectra in the 1550-1250 cm^?1 and 785-500 cm^?1 regions, when the right → left-handed conformational transition occurs.     

Interactions of bis-[μ-chloro-chlorotricarbonylruthenium(II)] and poly-[μ-dichloro-dicarbonylruthenium(II)] with nucleosides

The interactions of dimeric complex bis-[μ-chloro-chlorotricarbonylruthenium(II)], [Ru(CO)₃Cl₂]₂, and the polymeric complex poly-[μ-dichlorodicarbonylruthenium(II)], [Ru(CO)₂Cl₂]_x, with nucleosides (Nucl) in a 1:1 Ru:Nucl molar ratio for the dimer and 1:2 Ru:Nucl for the polymer, resulted in formation of the monomeric mononucleoside [Ru(CO)₃(Nucl)Cl₂] and bis-nucleoside [Ru(CO)₂(Nucl)₂Cl₂] complexes, respectively. The dimer [Ru(CO)₃Cl₂]₂ also gave the ionic bis-nucleoside complexes [Ru(CO)₃(Nucl)₂Cl]Cl in the molar ratio 1:2 Ru:Nucl. The mononucleoside complexes are stable in solution while the bis-nucleoside complexes tend to lose one nucleoside in strong complexing solvents, probably by solvent substitution. The complexes [Ru(CO)₃(Nucl)Cl₂] and [Ru(CO)₂(Nucl)₂Cl₂] with one N(1)H ionizable imino proton undergo ionization in alkaline solution and the complexes [Ru(CO)₃(NuclH⁺)Cl] and [Ru(CO)₂(NuclH⁺)₂], respectively, were isolated. In these deprotonated complexes the nucleosides behave as bidentate ligands, while in the protonated ones they act as monodentate. All Complexes were characterized by elemental analyses and various spectroscopic methods.     

Interaction between double stranded poly(dA-dT)·poly (dA-dT) and lucanthone

270 MHz ¹H NMR and theoretical studies indicate that the drug lucanthone forms intercalated complexes with the synthetic DNA poly(dA-dT)·poly(dA-dT). In the intercalated complex the long axis of the drug is perpendicular to the helix axis and parallel to the base pair axis, i.e., the long axis is perpendicular to the dyad axis.     

Interaction of 9-O-(ω-amino) alkyl ether berberine analogs with poly(dT)·poly(dA)*poly(dT) triplex and poly(dA)·poly(dT) duplex: a comparative study

Isoquinoline alkaloids and their analogs represent an important class of molecules for their broad range of clinical and pharmacological utility. These compounds are of current interest owing to their low toxicity and excellent chemo preventive properties. These alkaloids can play important role in stabilising the nucleic acid triple helices. The present study has focused on the interaction of five 9-O-(ω-amino) alkyl ether berberine analogs with the DNA triplex poly(dT)·poly(dA)*poly(dT) and the parent duplex poly(dA)·poly(dT) studied using various biophysical techniques. Scatchard analysis of the spectral data indicated that the analogs bind both to the duplex and triplex in a non-cooperative manner in contrast to the cooperative binding of berberine to the DNA triplex. Strong intercalative binding to the DNA triplex structure was revealed from ferrocyanide quenching, fluorescence polarization and viscosity results. Thermal melting studies demonstrated higher stabilization of the Hoogsteen base paired third strand of the DNA triplex compared to the Watson–Crick strand. Circular dichroism studies suggested a stronger perturbation of the DNA triplex conformation by the alkaloid analogs compared to the duplex. The binding was entropy-driven in each case and the entropy contribution to free energy increased as the length of the alkyl side chain increased. The analogs exhibited stronger binding affinity to the triple helical structure compared to the parent double helical structure.     

寡聚脱氧核苷酸d(G-C)_3的激光喇曼谱及其分析

用改进的固相磷酰三酯法合成了oligo-d(G-C)_3。以氩离子激光为激发光源,波长488nm.,在室温条件下,分别测定了纯化后的oligo-d(G-C)_3和其组分单体5’-dGMP和5’-dCMP的激光喇曼谱。观察到被测定的物质在300-2500cm~(-1)频率区间,各自都有其特征的谱形和喇曼峰。5’-dGMP和5’-dCMP谱中大多数特征峰在寡聚体的谱中消失,而在oligo-d(G-C)_3谱中出现了几处新的喇曼峰。经查证,峰832,851和899cm~(-1)系糖-磷酸主链的特征喇曼峰,另外几处峰与DNA的构象有关。实验结果表明oligo-d(G-C)_3在水溶液中(室温)主要以B-构象存在。     

双股寡聚d(G-C)6 DNA Z-构象的形成及其构象转换的动态研究

研究揭示,生物信息的形成,传递与DNA构象的多样性,特别是其中的左手螺旋Z-构象DNA（Z-DNA）相关.在机体DNA链中,普遍存在的特异序列结构d（C-G）n和d（G-C）n片段易形成Z-构象.但对d（G-C）n序列结构的寡聚体Oligo-d（G-C）n,（n小于8）能转换形成Z-DNA片段少见报道.为促进对Z-DNA尤其是其中的短片段Z-DNA与生物功能的相关性研究,我们对合成并纯化后的寡聚体Oligo-d（G-C）n,n分别为4,6,8,10, 及Oligo-d（C-G）6和多聚体poly-d（G-C）500-900进行Z-构象的形成和其构象转换的比较研究.研究结果发现：①d（GpCpGpCpGpCpGpCpGpCpGpC）是d（G-C）n序列结构中能转换形成Z-构象的最短片段（n＝6）.其转换成Z-构象能力有链长依赖性（poly d（G-C）500-900易于Oligo-d（G-C）6）;②Oligo-d（G-C）6的Z-构象形成能力因溶液中的介质性质不同而异.Co（NH3）3＋〉Mg2＋〉Na＋;C1O-4〉Cl-,因此要求盐溶液的浓度差异很大.③PH7.2,室温条件下,在MgCl2, NaClO4, NaCl溶液浓度分别由0 mol/L增至6.0 mol/L,Oligo-d（G-C）6的B、Z构象转换都出现：B-构象相对稳定期,B-、Z-构象转换跃迁期和Z-构象相对稳定期.每个阶段要求跨越的盐浓度变迁范围也因所用介质而异.当溶液中Oligo-d（G-C）6 B-构象、Z-构象各占50%（θ1/2）时,其盐浓度分别为1.72 mol/L（MgCl2）,2.88 mol/L（NaClO4）,3.85 mol/L（NaCl）.④Oligo-d（G-C）6的B-,Z-构象转换程度受盐浓度影响：当Oligo-d（G-C）6处于最适条件和不同盐溶液其浓度为θ（12）浓度时,温度由8 ℃→22 ℃,在MgCl2,NaClO4溶液中的Oligo-d（G-C）6形成Z-构象能力增加,当由22 ℃→60 ℃,MgCl2溶液中的Z-构象Oligo-d（G-C）6加速增加,而在NaClO4溶液中则是急速向B-型Oligo-d（G-C）6方向转换;温度变化对处于NaCl溶液中的Oligo-d（G-C）6B-、Z-构象相对平衡影响较小.⑤甲基化胞嘧啶即Oligo-d（G-mC）6或d（mC-G）6均增大Z-构象形成能力.⑥在4 mol/L MgCl2溶液中的Oligo-d（G-C）6或Oligo-d（C-G）6或poly d（G-C）500-900的UVab谱、UVcd谱均显示出非B-型或Z-型DNA的新谱型.并且有链长依赖性和因溶液浓度改变出现构象可逆性转变.提示在Oligo-d（G-C）6的构象转换过程中可能存在新构象＂X＂型,即BZX构象转换模式.     

多种功能的poly(C)-结合蛋白

细胞内的RNA一般不会单独存在,而是与各种各样的RNA结合蛋白（RBPs）绑定在一起,形成核糖核蛋白复合体（RNP complexes）影响着RNA的加工与转归. Poly(C) 结合蛋白是一类重要的RNA结合蛋白,可分为两组：hnRNP K 和PCBP1 4. 它们以序列特异的方式与核酸嘧啶富含区相结合. 这类蛋白具有共同的结构模体（motif）,即hnRNP K 同源（KH）域. KH域是与mRNA结合的结构基础,也是机体内调控系统的组成部分,可使得Poly(C) 结合蛋白参与蛋白/核酸、蛋白/蛋白之间的相互作用,范围涉及复制、转录、mRNA稳定和翻译控制过程等. 对Poly(C) 结合蛋白功能的深刻认识可使我们洞察多种疾病的病理生理过程.     

Synthesis and structures of porphyrin complexes of scandium: ClSc(TTP)·2(C 10H 7Cl) and O[Sc(TTP)] 2·6THF

A facile, high yield metallation procedure is reported for the insertion of Sc into H ₂(TTP) (TTP= dianion of meso-tetratolylporphyrin) using anhydrous ScCl ₃. Single crystal X-ray structures are reported for ClSc(TPP)·2(C ₁₀H ₇Cl) ( 1) and O[Sc(TTP)] ₂·6THF ( 2). Compound 1: space group P2 ₁/c with a = 19.850(17), b = 28.822(24), c = 9.954(9)Å, β = 95.71(7)°, Z = 4; 2: space group P2/n, a = 16.952(9), b = 16.737(5), c = 19.93(1)Å, β = 112.56(5)°, Z = 4. Compounds 1 and 2 both had large amounts of poorly ordered solvents in the lattice which resulted in rather high R factors in the range of 12–14%. In 1, the Sc is five-coordinate (4N and 1Cl) and is centered 0.68Åabove the plane defined by the four porphyrin nitrogens. For 2, the Sc is 0.82Åfrom the plane and contains a non-linear μ-oxide bridge with a ScO Sc angle of 109(3)°, but with essentially coplanar porphyrin rings.