Packing features of the all-AT oligonucleotide d(AAATTT)

We describe the packing features of the oligonucleotide duplex d(AAATTT)2, as determined by X-ray diffraction. There is little information on sequences that only contain A and T bases. The present structure confirms that these sequences tend to pack as a helical arrangement of stacked oligonucleotides in a B conformation with Watson-Crick hydrogen bonding. Our results demonstrate that the virtual TA base step between stacked duplexes has a negative twist that improves base stacking. This observation is consistent with the low stability of TA base steps in B-form DNA.     

The four repeat Giardia lamblia telomere forms tetramolecular G-quadruplex with antiparallel topology

Abstract

Guanine rich DNA sequences of regulatory genomic regions form secondary structures known as G-quadruplexes usually stabilized by tetrads of Hoogsteen hydrogen bonded guanines. The in vivo existence of G-quadruplexes ascertains their biological roles. Human telomeric repeats are the most studied G-rich sequences. The four repeat Giardia telomeric sequence (TAGGG)₄ differs from its human counterpart (TTAGGG)_4, by deletion of one T at the G-tract intervening site of each repeat. We show here that whilst the two repeat Giardia telomeric sequence (TAGGG)₂ forms parallel and antiparallel quadruplexes with tetramolecular topology exclusively, the four repeat version (TAGGG)₄ forms a tetramolecular (antiparallel) and unimolecular (parallel) quadruplexes in Na⁺. The tetramolecular (antiparallel) G-quadruplex formed by four repeats of Giardia telomeric sequence is stabilized by the additional Watson-Crick bonding between its intervening TA bases aligned in antiparallel fashion. Four stranded antiparallel quadruplex for four repeats of any telomeric sequence have not been characterized till date. We hypothesize that telomeric association in antiparallel fashion, (via G-overhangs to form tetramolecular quadruplex) could be a biologically relevant molecular event. Further, coexistence of Hoogsteen as well as Watson-Crick base pairing might give insight for recognition of conformationally diverse DNA structures by ligands.

Communicated by Ramaswamy H. Sarma     

A Theoretical Investigation on the Sequence Selective Binding of Daunomycin to Double-Stranded Polynucleotides

Abstract

Theoretical computations are performed on the structural and energetical factors involved in the sequence selective binding of daunomycin (DNM) to six representative self- complementary double-stranded hexanucleotides: d(CGTACG)₂, d(CGATCG)₂, d(CITACI)₂, d(TATATA)₂, d(CGCGCG)₂ and d(TACGTA)₂. The conformational angles of the hexanucleotides are fixed in values found in the representative crystal structure of the d(CGTACG)₂- DNM complex. The intermolecular DNM-hexanucleotide interaction energies and the conformational energy changes of DNM upon binding are computed and optimized in the framework of the SIBFA procedure, which uses empirical formulas based on ab initio SCF computations. Among the two regularly alternating hexanucleotides, d(TATATA)₂ and d(CGCGCG)₂, a stronger binding is predicted for the former, in agreement with experimental results obtained with poly(dA-dT)-poly(dA-dT) and poly(dG-dC)<<poly(dG-dC). Altogether, however, among the six investigated sequences, the strongest complexes are computed for the mixed hexanucleotides d(CGATCG)₂ and d(CGTACG)₂, containing the intercalation site between two CG base pairs and an adjacent TA base pair. This situation may be related to the increased affinity of DNM for GC rich DNA's and to the situation in the crystal structure of the DNM-d(CGTACG)₂ complex. Analysis of the intrinsic base sequence preferences expressed by the individual constituents of DNM, namely the daunosamine side chain, the chromophore ring and its two 9-hydroxyl and 9-acetoxy substituents, reveals that the overall sequence preference found is the result of a rather intricate interplay of intrinsic sequence preferences, in particular at the level of daunosamine and the 9-hydroxyl substituent. Altogether, it is seen that the selective base pair recognition by daunomycin cannot, in general, be defined in terms of the two base pairs implicated in the intercalation site alone (with the exception of homogeneous AT or GC base sequences) but must be expressed in terms of a triplet of base pairs.     

CD Spectral Comparisons of the Acid-Induced Structures of Poly[d(A)]Poly[r(A)], Poly[d(C)], and Poly[r(C)]

Abstract

CD spectra were used to compare the acid-induced structural transitions of poly[d(A)] and poly[d(C)] with those of poly[r(A)] and poly[r(C)], respectively. The types of base pairing were probably the same in the acid self-complexes of both A-containing polymers and in the acid self-complexes of both C-containing polymers. Similar base pairings were indicated by similarities in the difference CD spectra showing the changes during the first major acid- induced transitions of the polymers. Information from the CD spectra and pK_a values of the transitions suggested that the transitions for the RNA polymers involved similar structural changes. The two DNA polymers were markedly different. Single-stranded poly [d(A)] was in the most stacked structure and had the lowest pK^a for forming an acid self-complex. Single-stranded poly[d(C)] was in the least stacked structure and had the highest pK_a for forming a protonated duplex.     

Surfactant–copper(II) Schiff base complexes: synthesis,structural investigation,DNA interaction,docking studies,and cytotoxic activity

A series of surfactant–copper(II) Schiff base complexes (1–6) of the general formula, [Cu(sal-R₂)₂] and [Cu(5-OMe-sal-R₂)₂], {where, sal?=?salicylaldehyde, 5-OMe-sal?=?5-methoxy- salicylaldehyde, and R₂?=?dodecylamine (DA), tetradecylamine (TA), or cetylamine (CA)} have been synthesized and characterized by spectroscopic, ESI-MS, and elemental analysis methods. For a special reason, the structure of one of the complexes (2) was resolved by single crystal X-ray diffraction analysis and it indicates the presence of a distorted square-planar geometry in the complex. Analysis of the binding of these complexes with DNA has been carried out adapting UV-visible-, fluorescence-, as well as circular dichroism spectroscopic methods and viscosity experiments. The results indicate that the complexes bind via minor groove mode involving the hydrophobic surfactant chain. Increase in the length of the aliphatic chain of the ligands facilitates the binding. Further, molecular docking calculations have been performed to understand the nature as well as order of binding of these complexes with DNA. This docking analysis also suggested that the complexes interact with DNA through the alkyl chain present in the Schiff base ligands via the minor groove. In addition, the cytotoxic property of the surfactant–copper(II) Schiff base complexes have been studied against a breast cancer cell line. All six complexes reduced the visibility of the cells but complexes 2, 3, 5, and 6 brought about this effect at fairly low concentrations. Analyzed further, but a small percentage of cells succumbed to necrosis. Of these complexes (6) proved to be the most efficient aptotoxic agent.     

Relationship Between Curved DNA Conformations and Slow Gel Migration

Abstract

We propose some specific DNA conformations that explain, in terms of molecular conformations, the anomalous gel electrophoretic behavior of the sequences (VA₄T₄X)₁, and (V₂A₃X₂)₁ where V and X are either G or C. Previously (J. Biomole. Struct. Dyn. 4, 41, 1986) we considered hydrophobic interactions a mong aliphatic hydrocarbon groups in A/T sequences. In the sequences (T)_n · (A)_n, the T's are slightly bent to yield structures with tightly stacked methyl groups along one side of the major groove. By folding together the two pairs of stacked methyls on the opposite sides of the major groove, TTAA might yield a relatively sharp bend. On this basis, we show below that the sequences (VT₄A₄X)₁ might form a very tightly coiled super-helix whereas the sequences (VA₄T₄X)₁ form a broad super-helix of radius ~ 120 A for i = 25. The sequence (V₂A₃T₃X₂)₁ forms a slightly smaller radius super-helix. The time of passage through the gel has been taken to be inversely proportional to the smallesuiimension of the molecule. Specifically we are taking the ratio of the apparent molecular weight to the actual molecular weight to be related to the moment of inertia I₁ about the smallest principal axis of the molecular conformation. We find a good fit to the experimental gel mobility data of Hagerman (2) if we assume this ratio to be proportional to (I₁)^1/5.     

Disordered Single Crystal Evidence for a Quadruple Helix Formed by Guanosine 5′-Monophosphate

Abstract

The disodium salt of guanosine 5′-monophosphate (5′-GMP) has been crystallized earlier in an orthorhombic array. We have obtained a new crystal form of 5′-GMP at pH 8 which reveals a clear helical nature, with guanine bases stacked perpendicular to the helix axis. Although the X-ray pictures show partial disorder, they can be indexed on a hexagonal net with a = b = 28.6 Å,c = 9.8 Å, V= 6942ų(1Å = 0.1 nm). The probable space group is P6₄, and past experience with ca. 600 ų per base in oligonucleotide crystals suggests that the cell contains 12 GMP molecules. The crystal packing parameters and the intensity distribution agree with a model of three hydrogen-bonded guanine tetrads in the unit cell, stacked so as to build a quadruple helix similar to that proposed earlier from fiber studies (Zimmerman, S.B., J. Mol. Biol. 106, 663–672 (1976)).     

Comparative analysis of estrogen receptor gene polymorphisms in apes

Polymorphic microsatellite repeats in the promoter region of estrogen receptor α gene (ESRα and the intron 6 region of estrogen receptor β gene (ESRβ) have been reported in human populations. To examine the evolutional state of both repeats, we surveyed the corresponding regions in DNA sequences from the following great apes and gibbons: 56 chimpanzees, 3 bonobos, 16 gorillas, 20 orangutans and 60 gibbons (four species: 17 of Hylobates agilis, 11 of H. lar, 15 of H. muelleri, and 17 of H. syndactylus). In the corresponding region of the TA repeat of human ESRα, chimpanzees and bonobos had two motifs in the repeat tract, (TA)_7–9 and (CA)_4–6. Gorillas had the (TA)_9–10 repeat tracts and orangutans had monomorphic (TA)₇ repeats. Although all great apes maintained the TA expansion, all gibbon sequences contained (TA)₂, implying that the CA dinucleotide expansion arose in the ancestor of chimpanzees and bonobos. The nucleotide sequences of ESRβ showed a very complex repeat pattern in apes. The human sequences had a non-variable preceding sequence at (CA) _n , (GA)₂(TA)₈(CA)₄(TA). In apes that region included {(TA) _n (CA) _n } _n . Gibbon sequences included (TATG) _n and (TATC) _n and no regular construction was observed. A deletion event in the reverse primer site seems to have occurred in the orangutan lineage. In addition, a great diversity of allele length was detected in each gibbon species.     

Nature of the Stacking of Nucleic Acid Bases in Water: a Monte Carlo Simulation

Abstract

The results of a Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked dimers and hydrogen-bonded base pairs are presented. Simulations have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting of 200 water molecules). It has been shown that the stacking interactions of uracil and thymine molecules in water arise mainly due to the increase in the water-water interaction during the transition from monomers to dimer. It has been found out that stacked base associates are more preferable than base pairs in water. This preference is mainly due to the energetically more favourable structure of water around the stack.     

Analysis and location of a rice BAC clone containing telomeric DNA sequences

BAC2, a rice BAC clone containing (TTTAGGG)_n homologous sequences, was analyzed by Southern hybridization and DNA sequencing of its subclones. It was disclosed that there were many tandem repeated satellite DNA sequences, called TA352, as well as simple tandem repeats consisting of TTTAGGG or its variant within the BAC2 insert. A 0. 8 kb (TTTAGGG)_n-containing fragment in BAC2 was mapped in the telomere regions of at least 5 pairs of rice chromosomes by using fluorescencein situ hybridization (FISH). By RFLP analysis of low copy sequences the BAC2 clone was localized in one terminal region of chromosome 6. All the results strongly suggest that the telomeric DNA sequences of rice are TTTAGGG or its variant, and the linked satellite DNA TA352 sequences belong to telomere-associated sequences.     

Analysis and location of a rice BAG clone containing telomeric DNA sequences

BAC2, a rice BAC clone containing (TTTAGGG)_n homologous sequences, was analyzed by Southern hybridization and DNA sequencing of its subclones. It was disclosed that there were many tandem repeated satellite DNA sequences, called TA352, as well as simple tandem repeats consisting of TTTAGGG or its variant within the BAC2 insert. A 0. 8 kb (TTTAGGG)_n-containing fragment in BAC2 was mapped in the telomere regions of at least 5 pairs of rice chromosomes by using fluorescencein situ hybridization (FISH). By RFLP analysis of low copy sequences the BAC2 clone was localized in one terminal region of chromosome 6. All the results strongly suggest that the telomeric DNA sequences of rice are TTTAGGG or its variant, and the linked satellite DNA TA352 sequences belong to telomere-associated sequences.     

Synthesis and Properties of Dinucleoside Monophosphates Containing 2-Aminoadenine 8,2′-S- and Uracil 6,2′-O-Cyclonucleosides

Abstract

Two sequence isomers of dinucleoside monophosphates containing 8,2′-anhydro-2,6-diamino-8-mercapto-9-β-D-arabinofuranosylpurine (2NH₂A^s) and 6,-anhydro-6-hydroxy-1-ß-D-arabinofuranosyluracil (U^o), 2NH₂A^s pU^o (1) and U^o p2NH₂A^s (2) were synthesized by the phosphodiester method. Examination of the UV, CD and NMR spectra of these dimers led us to the conclusion that, whereas compound (1) did not take a stacked conformation, compound (2) took a well stacked conformation in which the bases were stacked along a left-handed screw axis. Both the dimers formed a complex with ethidium bromide.     

Static and Dynamic Conformational Properties of AT sequences in B-DNA

Abstract

A theoretical study of the optimal conformations of nucleic acid oligomers containing tracts of AT base pairs is presented. The oligomers are studied in isolation and complexed with netropsin, a minor groove binding ligand. The flexibility of the oligomers and of their complexes is calculated by adiabatic mapping with respect to the total winding angle. The results of this study show that in uncomplexed oligomers the dinucleotide junctions AA, AT and TA have very different structural parameters and different responses to winding stress. The TA junction is clearly the most flexible and is the principal site for accommodating the imposed overwinding. Complexation by netropsin leads to two important effects: firstly, the three junctions adopt more uniform structures, the largest changes again being observed for TA, secondly, the differences in flexibility as a function of sequence are strongly attenuated.     

Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs.

Free energies for stacking of unpaired nucleotides (dangling ends) at the termini of oligoribonucleotide Watson-Crick helixes (DeltaG(0)37,stack) depend on sequence for 3' ends but are always small for 5' ends. Here, these free energies are correlated with stacking at helix termini in a database of 34 RNA structures determined by X-ray crystallography and NMR spectroscopy. Stacking involving GA pairs is considered separately. A base is categorized as stacked by its distance from (相似文献   

A Refined Prediction Method for Gel Retardation of DNA Oligonucleotides from Dinucleotide Step Parameters: Reconciliation of DNA Bending Models with Crystal Structure Data

Abstract

The development and assessment of a prediction method for gel retardation and sequence dependent curvature of DNA based on dinucleotide step parameters are described. The method is formulated using the Babcock-Olson equations for base pair step geometry (1) and employs Monte Carlo simulated annealing for parameter optimization against experimental data. The refined base pair step parameters define a structural construct which, when the width of observed parameter distributions is taken into account, is consistent with the results of DNA oligonucleotide crystal structures. The predictive power of the method is demonstrated and tested via comparisons with DNA bending data on sets of sequences not included in the training set, including A-tracts with and without periodic helix phasing, phased A₄T₄ and T₄A₄ motifs, a sequence with a phased GGGCCC motif, some “unconventional” helix phasing sequences, and three short fragments of kinetoplast DNA from Crithidia fasiculata that exhibit significantly different behavior on non-denaturing polyacrylamide gels. The nature of the structural construct produced by the methodology is discussed with respect to static and dynamic models of structure and representations of bending and bendability. An independent theoretical account of sequence dependent chemical footprinting results is provided. Detailed analysis of sequences with A-tract induced axis bending forms the basis for a critical discussion of the applicability of wedge models, junction models and non A-tract, general sequence models for understanding the origin of DNA curvature at the molecular level.     

Duplex Stabilization by DNA-Hoechst 33258 Conjugates: Effects of Base Pair Mismatches

Abstract

Three types of DNA-Hoechst conjugates are examined for duplex stability in the presence of single-site base pair mismatches. Two of the complexes have the Hoechst ligand tethered to an internal phosphate residue, while the third complex employs terminally labeled conjugate. The presence of the mismatched base pair reduces the T_m values for the non-conjugate duplexes as is expected. Addition of the conjugated Hoechst ligand enhances the T_m values for the mismatched duplexes, but these values remain significantly below that obtained for the native conjugated duplex. While stabilization by the tethered ligand is observed for both cognate and non-cognate sequences, the differences suggest that significant sequence selectivity is still apparent for these conjugates.     

TA-periodic (“601”-like) centromeric nucleosomes of A. thaliana

The bulk of strong nucleosomes (SNs, with visibly periodic DNA sequences) is described by consensus pattern of 5 or 6 base runs of purines alternating with similar runs of pyrimidines – RR/YY SNs. Yet, the strongest known nucleosome positioning sequence, the 601 clone of Lowary and Widom, is rather periodic repetition of TA dinucleotides following one another every 10 bases. We located “601”-like TA-periodic sequences in the genome of A. thaliana. Several families of such sequences are discovered repeating almost exclusively in centromeres. Thus, while A. thaliana SNs of RR/YY type have strong affinity to pericentromeric regions, as it has been previously found, the SNs of TA periodic type concentrate rather in centromeres.