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.     

Structure of Poly (dT)·Poly (dA)·Poly (dT)

Abstract

The molecular structure of poly (dT)·poly (dA)·poly (dT) has been determined and refined using the continuous x-ray intensity data on layer lines in the diffraction pattern obtained from an oriented fiber of the DNA. The final R-value for the preferred structure is 0.29 significantly lower than that for plausible alternatives. The molecule forms a 12-fold right- handed triple-helix of pitch 38.4 Å and each base triplet is stabilized by a set of four Crick-Watson-Hoogsteen hydrogen bonds. The deoxyribose rings in all the three strands have C2′-endo conformations. The grooveless cylindrical shape of the triple-helix is consistent with the lack of lateral organization in the fiber.     

Melting Behavior and Stability of (dA)8·(dT)8 Double Helix

Abstract

Melting behavior and stability of double helix of octadeoxyribonucleotides, (dA)₈·(dT)₈, have been studied by a UV measurement and a calculation of nearest-neighbor model. The helix of (dA)₈·(dT)₈ exhibited the thermodynamic parameters similar to those of B-form DNA.     

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.     

The Structure of Poly(dA)· poly(dT) as Revealed by an X-ray Fibre Diffraction

Abstract

X-ray diffraction in fibres revealed that the calcium salt of poly(dA) · poly(dT) is a 10-fold double helix with a pitch of 3.23 nm. The opposite sugar-phosphate chains in the refined model are characterized by a complete conformational equivalence and contain sugars in a conformation close to C2′-endo.

As a result a new model of the sodium salt of poly(dA) · poly(dT)has been constructed, which is different from the Heteronomous DNA proposed earlier (S. Arnott et al., Nucl. Acids Res. 11, 4141 (1983)). The new model of Na-poly(dA) · poly(dT) has conformationally similar opposite chains; it is a structure of the B-type, rather like that of Ca-poty(dA) · poly(dT).     

Molecular mechanics calculations of dA12·dT12 and of the curved molecule d(GCTCGAAAAA)4·d(TTTTTCGAGC)4

Using the AMBER software package (Weiner and Kollman 1981) substantially modified for electrostatic contributions, the structural energies of the double-stranded oligonucleotides dA₁₂·dT₁₂ and d(GCTCGAAAAA)₄·d(TTTTTCGAGC)₄ were minimized. Using various starting structures for the molecule dA₁₂·dT₁₂, one final structure is obtained which possesses the experimentally determined properties of poly(dA)·poly(dT). This structure is an A-form-B-form-hybrid structure similar to that of Arnott et al. (1983). The dA-strand is similar to an A-form while the dT-strand is similar to normal B-form. This structure and separately optimized B-form sequence stretches were used to construct the double-stranded fragment d(GCTCGAAAAA)₄ which again was optimized. This sequence, when imbedded in a DNA fragment as contiguous repeats, shows a gel migration anomaly which has been interpreted as stable curvature of the DNA (Diekmann 1986). The calculated structure of this sequence indeed has a curved helix axis and is discussed as a model for curved DNA. A theoretical formalism is presented which allows one to calculate the structural parameters of any nucleic acid double helix in two different geometrical representations. This formalism is used to determine the parameters of the base-pair orientations of the curved structure in terms of wedge as well as cylindrical parameters. In the structural model presented here, the curvature of the helix axis results from an alternation of two different DNA structures in which the base-pairs possess different angles with the helix axis (cylinder tilt). Resulting from geometric restraints, a negative cylinder tilt angle correlates strongly with the closing of the minor groove (wedge roll). The blocks with different structure are not exactly coincident with the dA₅-blocks and the B-DNA stretches. Within the dA₅ block, base-pair tilt and wedge roll adopt large values which proceed into the 3 flanking B-DNA sequence by about one base-pair. These properties of the structure calculated here are discussed in terms of different models explaining DNA curvature.     

Structure of Poly(dA)·Poly(dT) is not Identical to the AT Rich Regions of the Single Crystal Structure of CGCGAATTBrCGCG. The Consequence of this to Netropsin Binding to Poly(dA)·Poly(dT)

Abstract

The basic assumption of Dickerson and Kopka (J. Biomole. Str. Dyns. 2, 423, 1985) that the conformation of poly(dA)·poly(dT) in solution is identical to the AT rich region of the single crystal structure of the Dickerson dodecamer is not supported by any experimental data. In poly(dA)·poly(dT), NOE and Raman studies indicate that the dA and dT units are conformationally equivalent and display the (anti-S-type sugar)-conformation; incorporation of this nucleotide geometry into a double helix leads to a conventional regular B-helix in which the width of the minor groove is 8A. The derived structure is consistent with all available experimental data on poly(dA)·poly(dT) obtained under solution conditions. In the crystal structure of the dodecamer, the dA and dT units have distinctly different conformations—dA residues adopt (anti, S-type sugar pucker), while dT residues belong to (low anti, N-type sugar pucker). These different conformations of the dA and dT units along with the large propeller twist can be accommodated in a double helix in which the minor groove is shrunk from 8A to less than 4A. In the conventional right handed B-form of poly(dA)·poly(dT) with the 8A wide minor groove, netropsin has to bind asymmetrically along the dA strand to account for the NOE and chemical shift data and to generate a stereochemically sound structure (Sarma et al, J. Biomole. Str. Dyns. 2, 1085, 1985).     

Monte-Carlo Simulation of DNA Duplex Hydration. B and B′ Conformations of Poly(dA) · Poly(dT) Have Different Hydration Shells

Abstract

Monte-Carlo simulation of poly(dA) · poly(dT) hydration by 30 water molecules per nucleotide pair has been performed. Two B-family conformations, both with a 36° helical twist but with different minor groove widths, were considered. One conformation is Arnott's standard B form, the other one is specific for poly(dA) · poly(dT) B′ form with a narrowed minor groove. The mean energies and the mean numbers of water-water and water-DNA hydrogen bonds are close for the two conformations. Nevertheless, the hydration shell of the B' form differs drastically from that of the standard B form. The water arrangement in the minor groove of the B′ form resembles the spine of hydration in the central part of Dickerson's dodecamer d(CGCGAATTCGCG). No such spine is formed in the hydration shell of the usual B form with a wider minor groove. In this conformation water bridges between adenine N3 or thymine O2 and oxygen of the sugar ring of the neighbouring nucleotide along the chain can be formed (“strings” in Dickerson's decamer d(CCAAGATTGG)).     

Selective isolation of highly polymorphic (dC−dA)n · (dG−dT)n microsatellites by stringent hybridization

We defined a hybridization condition for isolation of clones carrying long (dC−dA)_n · (dG−dT)_n microsatellites from a genomic plasmid library. By using (dC−dA)₂₀ oligonucleotide as a probe and hybridizing under stringent conditions, more than two-thirds of the obtained plasmid carried the repeats that were longer than (dC−dA)₁₄ and higly polymorphic.     

Reaction–diffusion wave model for self-assembled network formation of poly(dA)·poly(dT) DNA on mica and HOPG surfaces

Deoxyribonucleic acid (DNA) is a vital molecule for life since it contains genetic information. However, DNA has recently been reported to have unique properties that make it suitable for bionanoelectronic applications, such as the possibility of electrical conductivity and self-organisation. Self-assembled DNA network structures have been observed on several substrates, but the detailed self-assembly mechanism has yet to be determined. The present study investigates self-assembled structures of DNA both theoretically and experimentally. We developed a reaction–diffusion model and used it to investigate pattern formations observed by atomic force microscopy. The computational results qualitatively replicate the network patterns of DNA molecules based on a quantitative agreement with the surface size and timescale. The model can account for the effect of the DNA concentration on pattern formation. Furthermore, peculiar geometric patterns are simulated for mica and highly oriented pyrolytic graphite surfaces.     

Homooligomeric dA·dU and dA·dT Sequences in Parallel and Antiparallel Strand Orientation: Consequence of the 5-methyl Groups on Stability,Structure and Interaction with the Minor Groove Binding Drug HOECHST 33258

Abstract

Oligodeoxyribonucleotides containing dA·dU base combinations were shown to form parallel stranded DNA. CD spectra and hyperchromicity profiles provide evidence that the structure is very similar to that of a related parallel stranded dA·oligomer. Thermal denaturation studies show that these parallel dAdU sequences are significantly less stable than their dA·analogues in either antiparallel or parallel stranded orientations. The stabilizing effect of the 5- methyl group is similar for parallel and antiparallel sequences. The minor groove binding drug Hoechst 33258 binds with similar affinity to APS dA·and APS dA·dU sequences. However, binding to the PS dA·hairpin is significantly impaired as a consequence of the different groove dimensions and the presence of thymine methyl groups at the binding site. This results in an 8.6 kJmoF reduced free energy of binding for the PS dA·sequence. Replacement of the bulky methyl group with a hydrogen (ie. T -> U) results in significantly stronger Hoechst 33258 binding to the parallel dA·dU sequences with a penalty of only 4.1 kJmol^?1. Our data demonstrate that although Hoechst 33258 detects the altered groove, it is still able to bind a PS duplex containing dA·dU base pairs with high affinity, despite the large structural differences from its regular binding site in APS DNA.     

Alignment of (dA)·(dT) Homopolymer Tracts in Gene Flanking Sequences Suggests Nucleosomal Periodicity in D. discoideum DNA

Abstract

It has been shown that the frequency versus size distribution of A and T overlapping and non- overlapping homopolymer tracts of N>5 in D. discoideum gene flanking and intron regions are significantly greater than in coding regions(1). In the present report we demonstrate, that a spatial periodicity exists in long A and T tracts (N> 10) in long flanking sequences by scored alignments of those tracts (N> 10) with the nucleosomal repeat. A tract spacing was found at 185–190 bp that corresponds to a maximum alignment score. This is exactly the average spacing of D. discoideum nucleosomes determined experimentally. A majority of A and T tracts in flanking sequences are often spaced by short DNA stretches and the total length of adjacent A and T tracts plus the interrupting short DNA stretch corresponds closely to the average experimentally measured nucleosomal linker DNA size in D. discoideum-42 bp. These data suggest a model which has A and T runs of N> 10 bp in flanking DNA of D. discoideum organized in a regular phase with nonhomopolymer sequences along the DNA. This model has functional implications for A and T tracts, suggesting that they are found in nucleosomal linker DNA regions of chromatin during some necessary portion(s) of the life of the cell.     

Charge Transport in Poly(dG)–Poly(dC) and Poly(dA)–Poly(dT) DNA Polymers

We investigate the charge transport in synthetic DNA polymers built up from single type of base pairs. In the context of a polaronlike model, for which an electronic tight-binding system and bond vibrations of the double helix are coupled, we present estimates for the electron-vibration coupling strengths utilizing a quantum-chemical procedure. Subsequent studies concerning the mobility of polaron solutions, representing the state of a localized charge in unison with its associated helix deformation, show that the system for poly(dG)–poly(dC) and poly(dA)–poly(dT) DNA polymers, respectively possess quantitatively distinct transport properties. While the former supports unidirectionally moving electron breathers attributed to highly efficient long-range conductivity, the breather mobility in the latter case is comparatively restrained, inhibiting charge transport. Our results are in agreement with recent experimental results demonstrating that poly(dG)–poly(dC) DNA molecules acts as a semiconducting nanowire and exhibit better conductance than poly(dA)–poly(dT) ones.     

Analysis of calorimetric data for the binding of monomeric bis-benzimidazole,an analog of the Hoechst 33258 dye,to poly(dA) · poly(dT)

Monomeric bis-benzimidazole (MB) is an analog of the Hoechst 33258 dye. The enthalpy and entropy of MB binding were evaluated by analyzing the calorimetric data on MB reverse titration with poly(dA) · poly(dT). A mathematical model was developed to estimate the thermodynamic parameters of binding on the basis of calorimetric data. The results agree well with spectrophotometric data on the binding of analogous compounds. The model was used to estimate the parameters of binding with poly(dA) · poly(dT) for dimeric bis-benzimidazole (DB), which consists of two bis-benzimidazole monomers linked via a flexible chain. The ligand was assumed to produce different types of complexes with the polymer.     

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.     

Nuclear Overhauser Data and Stereochemical Considerations Suggest that Netropsin Binds Symmetrically Within the Minor Groove of Poly(dA)·Poly(dT), Forming Hydrogen Bonds with Both Strands of the Double Helix

Abstract

Sarma et al. (J. Biomol. Str. and Dynam. 2, 1085 (1985) have proposed, on the basis of nuclear magnetic resonance experiments on the complex of netropsin with poly(dA)·poly(dT), that the drug molecule lies asymmetrically along the dA side of the minor groove and makes hydrogen bonds only with the dA strand. If the crystal structure analyses of B-DNA (Fratini et al., J. Biol. Chem. 257, 14686 (1982)) and of its complex with netropsin (Kopka et al., J. Mol. Biol. 183, 553 (1985)) are any guide, this off-center, wide-groove model is stereochemically unlikely. More to the point, the off-center model is unnecessary to explain the observed nmr data. All of the nuclear Overhauser and other observations are fully explained by the structure seen in the x-ray crystal analysis, in which netropsin sits squarely centered within the minor groove, making bifurcated hydrogen bonds with both strands.     

Approximate bandwidths for π and σ energy states in poly (dA.dT)

Using energy levels of the π and σ orbitals for adenine and thymine obtained by the CNDO method, the widths of those levels for poly (dA · dT) are calculated approximately. The results indicate that the bands are very narrow and that the exciton theory provides the best approximation for these biopolymers. This investigation was supported in part by NIH Fellowship (1F03 CA 5296-01) from the National Cancer Institute. Operated by the Union Carbide Corporation for the U.S. Atomic Energy Commission.     

On the properties of Se ⋯N interaction: the analysis of substituent effects by energy decomposition and orbital interaction

The nature and strength of intermolecular Se ?N interaction between selenium-containing compounds HSeX (X = CH₃, NH₂, CF₃, OCH₃, CN, OH, NO₂, Cl, F), and NH₃ have been investigated at the MP2/aug-cc-pVDZ level. The Se ?N interaction is found to be dependent on the substituent groups, which greatly affect the positive electrostatic potential of Se atoms and the accepting electron ability of X-Se σ ^? antibonding orbital. Energy decomposition of the Se ?N interaction reveals that electrostatic and induction forces are comparable in the weak-bonded complexes and induction becomes more significant in the complexes with strong electron-withdrawing substituents. Natural bond orbital (NBO) analysis indicates that the primary source of the induction is the electron transfer from the N lone pair to the X-Se σ ^? antibonding orbital. The geometry of the complex and the interaction directionality of NH₃ to X-Se bond can be regarded as a consequence of the exchange-repulsion. The topological analysis on the electron density reveals the nature of closed-shell interaction in these X-Se ?N contacts. The Se ?N interaction in the complexes with the strong electron-withdrawing substituent has a partly covalent character.     

同聚DNA分子poly(dA)·poly(dT)主链的振动位移

基于同聚DNA分子poly(dA).poly(dT)的螺旋对称性,利用晶格动力学方法,计算了DNA分子poly(dA).poly(dT)主链振动的本征矢,探讨了振动位移矢量和线二色光谱的关系。结果表明,对应着磷酸双氧的反对称振动谱线可以用于直接确定磷酸根的取向,精度小于1°。其它谱线必须通过对分子的简正分析来帮助确定分子的结构。     

Differential inactivation of DNA polymerases α and β by aldehyde compounds

The effects of cyclohexanecarboxaldehyde, benzaldehyde and protocatechualdehyde on the activities of DNA polymerases α, β and E. coli DNA polymerase I were investigated. On direct addition of the aldehydes to the DNA polymerase assay mixture containing activated DNA or poly(dA) (dT)_12–18 as a template, DNA polymerase α was most strongly inhibited by the aldehyde compounds, while DNA polymerases β and I were resistant to such aldehyde inhibition. On preincubation of the enzymes with aldehyde, both DNA polymerases α and β were inactivated; however, DNA polymerase β was protected from the inactivation when activated DNA was added to the preincubation mixture. The inhibition of DNA polymerase α by aldehyde was noncompetitive with regard to the substrate dNTP and competitive with regard to the template DNA. The extent of inhibition of DNA polymerase α by aldehyde was partly reduced by the addition of cysteine to the reaction mixture.