B-DNA Sequences Research Articles

Enhancing the Features of DNA Mimic Foldamers for Structural Investigations.

DNA mimic foldamers based on aromatic oligoamide helices bearing anionic phosphonate side chains have been shown to bind to DNA-binding proteins sometimes orders of magnitude better than DNA itself. Here, we introduce new features in the DNA mimic foldamers to facilitate structural investigations of their interactions with proteins. Thirteen new foldamer sequences have been synthesized and characterized using NMR, circular dichroism, molecular modeling, and X-ray crystallography. The results show that foldamer helix handedness can be quantitatively biased by means of a single stereogenic center, that the foldamer structure can be made C2-symmetrical as in palindromic B-DNA sequences, and that associations between foldamer helices can be promoted utilizing dedicated C-terminal residues that act as sticky ends in B-DNA structures.

DNA-MBF1 study using molecular dynamics simulations : On the road to understanding the heat stress response in DNA-protein interactions in plants.

Regulatory factor MBF1 is highly conserved between species and has been described as a cofactor and transcription factor. In plants, several reports associate MBF1 with heat stress response. Nevertheless, the specific physical processes involved in the MBF1-DNA interaction are still far from clearly understood. We thus performed extensive molecular dynamics simulations of DNA with a homology-based modethel of the MBF1 protein. Based on recent experimental data, we proposed two B-DNA sequences, analyzing their interaction with our model of the Arabidopsis MBF1c protein (AtMBF1c) at three different temperatures: 293, 300, and 320 K, maintaining a constant pressure of 1 bar. The simulations suggest that MBF1 binds directly to the DNA, supporting the idea of its role as a transcription factor. We identified two different conformations of the MBF1 protein when bound, and characterized the specific groups of amino acids involved in the formation of the DNA-MBF1 complex. These regions of amino acids are bound mostly to the minor groove of DNA by the attraction of positively charged residues and the negatively charged backbone, but subject to the compatibility of shapes, much in the sense of a lock-and-key mechanism. We found that only with a sequence rich in CTAGA motifs at 300 K does MBF1 bind to DNA in the DNA-binding domain Cro/C1-type HTH predicted. In the rest of the systems tested, we observed non-specific DNA-MBF1 interactions. This study complements findings previously reported by others on the role of CTAGA as a DNA-binding element for MBF1c at a heat stress temperature.

Toward a Universal Structural and Energetic Model for Prokaryotic Promoters

With almost no consensus promoter sequence in prokaryotes, recruitment of RNA polymerase (RNAP) to precise transcriptional start sites (TSSs) has remained an unsolved puzzle. Uncovering the underlying mechanism is critical for understanding the principle of gene regulation. We attempted to search the hidden code in ∼16,500 promoters of 12 prokaryotes representing two kingdoms in their structure and energetics. Twenty-eight fundamental parameters of DNA structure including backbone angles, basepair axis, and interbasepair and intrabasepair parameters were used, and information was extracted from x-ray crystallography data. Three parameters (solvation energy, hydrogen-bond energy, and stacking energy) were selected for creating energetics profiles using in-house programs. DNA of promoter regions was found to be inherently designed to undergo a change in every parameter undertaken for the study, in all prokaryotes. The change starts from some distance upstream of TSSs and continues past some distance from TSS, hence giving a signature state to promoter regions. These signature states might be the universal hidden codes recognized by RNAP. This observation was reiterated when randomly selected promoter sequences (with little sequence conservation) were subjected to structure generation; all developed into very similar three-dimensional structures quite distinct from those of conventional B-DNA and coding sequences. Fine structural details at important motifs (viz. −11, −35, and −75 positions relative to TSS) of promoters reveal novel to our knowledge and pointed insights for RNAP interaction at these locations; it could be correlated with how some particular structural changes at the −11 region may allow insertion of RNAP amino acids in interbasepair space as well as facilitate the flipping out of bases from the DNA duplex.

Copper-metformin ternary complexes: Thermal, photochemosensitivity and molecular docking studies

The copper(II) complexes [Cu(Cl)2(met)(o-phen)] (1), [Cu(Cl)2(met)(en)] (2) and [Cu(Cl)2(met)(opda)] (3) (met = metformin, o-phen = ortho-phenanthroline, en = ethylenediamine, opda = ortho-phenylenediamine) were synthesized and characterized by LC-MS, elemental analysis, molar conductance, thermal analysis, infrared spectra, magnetic moment, electronic spectra and XRD studies. The metal center was found in an octahedral geometry. The activation thermodynamic properties were calculated using Coats-Redfern method. Thermal decomposition processes of complexes 1, 2, 3 are non-spontaneous, i.e., the complexes are thermally stable. The positive value of Gibbs free energy of decomposition (ΔG⁎) for the Cu(II) complexes is non-spontaneous processes. UV–Visible absorption, fluorescence, and viscosity measurements have been conducted to assess the interaction of the complexes with CT DNA. The complexes showed absorption hyperchromism in its UV–Vis spectrum with DNA. The binding constants Kb from UV–Vis absorption studies were 4.6 × 105, 1.48 × 105, 2.09 × 105 M−1 for 1, 2, 3 respectively and Stern–Volmer quenching constants (Ksq) from fluorescence studies were 0.636, 0.293, 0.487 for 1, 2, 3 respectively. Finally, viscosity measurements revealed that the binding of the complexes with CT-DNA could be surface binding, mainly due to groove binding. The activity of complexes towards DNA cleavage decreases in the order of 1 > 3 > 2. The complexes were docked in to B-DNA sequence, 5′(D*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)-3′ retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software.

Modeling DNA electronic circular dichroism by QM/MM methods and Frenkel Hamiltonian

We report the modeling of the electronic circular dichroism spectra of different double helix B-DNA sequences. The circular dichroism spectra have been obtained in the framework of the Frenkel excitation theory, while DNA conformational space has been explored using molecular dynamics. Excited states are obtained using hybrid quantum mechanics/molecular mechanics theory at time-dependent density functional theory level. The validity of the effective Frenkel Hamiltonian approach is assessed by comparison with full quantum mechanics treatment of many interacting chromophores. The convergence of the simulated spectra with the number of interacting chromophores is assessed as well as their behavior with respect to experimental results.

CHARMM Drude Polarizable MD Simulations Reproduce Solution X-Ray Diffraction Patterns for B-DNA Sequences and Predict Differential Impact of the Li+, Na+, K+ and Rb+ Ions on DNA Conformational Properties

Recently we have presented the first generation CHARMM Drude polarizable force field for DNA, which is capable of reproducing the main conformational features of DNA in solution, such as A-to-B equilibrium and transitions between BI and BII substates. Our current efforts are directed towards further model improvement, by achieving a proper balance of the interactions among surrounding mobile ions, water and DNA. Compared to the additive (non-polarizable) models, explicit treatment of the electronic polarizability in the Drude model leads to a markedly improved description of the interplay between the ionic atmosphere and DNA conformational behavior. In particular, the Drude model is shown to more accurately reproduce counterion condensation theory predictions of DNA charge neutralization by condensed ions, as well as the experimental data on the competitive binding of Li+, Na+, K+ and Rb+ ions to DNA. The most intriguing results is that the model predicts a differential impact of these seemingly similar monovalent cations on DNA conformational properties - a phenomenon not observed in the state-of-the-art CHARMM36 and AMBER atomistic additive models. In addition, the Drude model reproduces the solution X-ray diffraction patterns for a number of B form DNA sequences at a level of accuracy similar to, or exceeding that of the above mentioned additive models. The obtained results indicate that CHARMM Drude polarizable MD simulations provide a more realistic model of the physical forces involved in the interactions of DNA with its ionic environment, offering the potential to yield new insights into salt-mediated biological processes involving DNA, such as protein-DNA recognition and chromatin folding.

3D molecular assembling of B-DNA sequences using nucleotides as building blocks

Unlike the current atomistic DNA models, this paper proposes a new 3D space-filling model for sequences of DNA base pairs using nucleotides, instead of atoms, as building blocks of DNA molecules. This nucleotide-based model is more scalable than the traditional atomistic model, and has the advantage that easily adapts to any topological conformation of DNA. Interestingly, this model also allows the building of the molecular surface of the DNA, either partly or entirely, as needed for energy computations in molecular applications. Moreover, it allows us to grasp the DNA shape at different levels of shape composition: atom, nucleotide, and DNA macromolecule as a whole.

Perturbation theory analysis for electronic response of DNA base pairs

The electronic responses of duplex B-DNA sequences are investigated using perturbation theory analyses. The electronic polarizability and effective mass are computed for base pair doublets and triplets and the electronic structures are calculated according to density functional theory. High polarizability and a light effective mass are obtained in a sequence such as 5′-GGG-3′. The results indicate that the concentration of GC base pairs causes a high response of the electronic states, and molecular orbitals that are very responsive to the electric field tend to be reactive with other orbitals or conducting hole carriers. Furthermore, the interaction between the electronic states and a positively charged wavepacket is discussed, assuming hole injection in the DNA sequences. The sequence of 5′-GGG-3′ responds sensitively to the external hole approach, which is presumably injected to a guanine site.

Sequence‐Specific Positions of Water Molecules at the Interface between DNA and Minor Groove Binders

Ligands able to specifically recognize DNA sequences are of fundamental interest as transcription-controlling drugs. Herein, we analyze the positions of water molecules relative to B-DNA base pairs in the minor groove of X-ray and NMR protein data bank (PDB) structures. The patterns observed for water molecules at the interface between DNA and a ligand are compared with those obtained for structures without a ligand. Although the ligand end groups are often charged, and therefore highly hydrated, they do not alter the water patterns, which show considerable differences for the AT and CG base pairs. For AT they are much more precise than for CG in both ligand-containing and ligand-free structures. This behavior strongly indicates that the release of water molecules upon ligand binding leads to a gain of entropy and explains why this effect is especially pronounced for A-tract B-DNA sequences.

Design of a New Warhead for the Natural Enediyne Dynemicin A. An Increase of Biological Activity

A concept for designing nontoxic enediyne-based antitumor drugs that was previously suggested (J. Am. Chem. Soc. 2000, 122, 8245) is converted into reality by merging amidines with the natural enediyne dynemicin A. The dynemicin-amidines (DADs) resulting from this combination are biologically not active because they form extremely labile singlet biradicals that can no longer abstract H from DNA. However, if protonated in the acidic environment of the tumor cell, they possess increased biological activity, as is reflected by a lowering of the activation enthalpy for the Bergman cyclization from 16.7 (dynemicin A) to 11-12 kcal/mol (DADs), kinetic stability of the singlet biradicals formed in the cyclization reaction, increased H abstraction ability of the singlet biradicals, and improved docking properties in the minor groove of the duplex 10-mer B-DNA sequence d(CTACTACTGG).d(CCAGTAGTAG) throughout the triggering and Bergman reactions. The implications and the consequences of using DADs to exploit the differences between normal and tumor cells and to design a nontoxic antitumor drugs are discussed.

Docking, Triggering, and Biological Activity of Dynemicin A in DNA: A Computational Study

The triggering and biological activity of the naturally occurring enediyne dynemicin A (1) was investigated, both inside and outside the minor groove of the duplex 10-mer B-DNA sequence d(CTACTACTGG).d(CCAGTAGTAG), using density functional theory (B3LYP with the 3-21G and 6-31G(d) basis set), BD(T)/cc-pVDZ (Brueckner doubles with a perturbative treatment of triple excitations), and the ONIOM approach. Enediyne 1 is triggered by NADPH in a strongly exothermic reaction (-88 kcal/mol), which involves a number of intermediate steps. Untriggered 1 has a high barrier for the Bergman cyclization (52 kcal/mol) that is lowered after triggering to 16.7 kcal/mol due to an epoxide opening and the accompanying strain relief. The Bergman reaction of triggered 1 is slightly exothermic by 2.8 kcal/mol. The singlet biradical formed in this reaction is kinetically stable (activation enthalpies of 19.5 and 21.8 kcal/mol for retro-Bergman reactions) and is as reactive as para-benzyne. The activity-relevant docking mode is an edge-on insertion into the minor groove, whereas the intercalation between base pairs, although leading to larger binding energies, excludes a triggering of 1 and the development of its biological activity. Therefore, an insertion-intercalation model is developed, which can explain all known experimental observations made for 1. On the basis of the insertion-intercalation model it is explained why large intercalation energies suppress the biological activity of dynemicin and why double-strand scission can be achieved only in a two-step mechanism that involves two enediyne molecules, explaining thus the high ratio of single-strand to double-strand scission observed for 1.

Nonbonded bivalence approach to cell-permeable molecules that target DNA sequences

Polyamides such as the natural antibiotic distamycin A can form binary or ternary complexes with B-DNA. The driving forces and advantages for forming the ternary complexes are not fully understood. The computational studies reported herein suggest that three- and four-ring polyamides have a propensity for forming the same dimer conformations in water as those in their ternary complexes. The pre-dimerization of a polyamide in water facilitates the formation of the ternary complex, making the polyamide more selective, and tighter binding to the minor groove whose minimal width is predetermined by the B-DNA sequence. Relative to the dimer tethered with covalent bonds, the smaller, monomeric polyamide available from reversible dimerization in water makes the molecule inherently more cell permeable. A nonbonded bivalence approach that dimerizes molecules by intermolecular interactions is proposed for improving affinity, selectivity, and cell permeability.

Local sequential minimization of double stranded B-DNA using Monte Carlo annealing.

A software algorithm has been developed to investigate the folding process in B-DNA structures in vacuum under a simple and accurate force field. This algorithm models linear double stranded B-DNA sequences based on a local, sequential minimization procedure. The original B-DNA structures were modeled using initial nucleotide structures taken from the Brookhaven database. The models contain information at the atomic level allowing one to investigate as accurately as possible the structure and characteristics of the resulting DNA structures. A variety of DNA sequences and sizes were investigated containing coding and non-coding, random and real, homogeneous or heterogeneous sequences in the range of 2 to 40 base pairs. The force field contains terms such as angle bend, Lennard-Jones, electrostatic interactions and hydrogen bonding which are set up using the Dreiding II force field and defined to account for the helical parameters such as twist, tilt and rise. A close comparison was made between this local minimization algorithm and a global one (previously published) in order to find out advantages and disadvantages of the different methods. From the comparison, this algorithm gives better and faster results than the previous method, allowing one to minimize larger DNA segments. DNA segments with a length of 40 bases need approximately 4 h, while 2.5 weeks are needed with the previous method. After each minimization the angles between phosphate-oxygen-carbon A1, the oxygen-phosphate-oxygen A2 and the average helical twists were calculated. From the generated fragments it was found that the bond angles are A1=150 degrees +/-2 degrees and A2=130 degrees +/-10 degrees, while the helical twist is 36.6 degrees +/-2 degrees in the A strand and A1=150 degrees +/-6 degrees and A2=130+/-6 degrees with helical twist 39.6 degrees +/-2 degrees in the B strand for the DNA segment with the same sequence as the Dickerson dodecamer.

Characteristics of migration patterns of DNA oligomers in gels and the relationship to the question of intrinsic DNA bending.

We have developed a methodology that is capable of quantitatively describing the electrophoretic mobility patterns of oligomeric B-DNA through polyacrylamide gels (PAG) in the presence of varying concentration of the organic solvent 2-methyl-2,4-pentanediol (MPD), used routinely to induce DNA crystallization. The model includes the ion atmosphere and its polarization, electrostatic excluded volume, hydrodynamic interactions, and fluctuation effects that characterize the overall size of the migrating polyion. Using this model, and by critically examining the mobility patterns of linear random-sequence B-DNA molecules in PAG as a function of MPD, we address the question of the discrepancy between current models used to explain the molecular origins of A-tract-induced DNA bending. Direct analysis of the mobility of B-DNA oligomers on PAG, and comparison to the mobility of A-tract-containing oligomers, shows a significant apparent effect of MPD on the mobility of generic B-DNA sequences, which is larger than the effect on A-tract-containing oligomers. The effect is chain-length dependent, especially at lower MPD concentration. Thus, the apparent reduction in gel mobility, as a function of MPD, is not unique to A-tract regions or A-tract-containing molecules. However, our analysis suggests that MPD molecules are probably excluded from the surface of both B-DNA and A-tract molecules. This is supported by circular dichroism studies on A-tract and B-DNA molecules in solutions containing various MPD concentrations.

Full-strand Minimization of Single and Double Stranded B-DNA Using Monte-Carlo Annealing

A new algorithm is developed which implements the Monte Carlo annealing method and is used to model and minimize linear, single and double stranded B-DNA sequences. The preliminary B-DNA structures are modeled using initial structures obtained from the Brookhaven database. The model contains structural details at the atomic level and is therefore more elaborate and accurate than the pseudo-atomic and elastomechanical models. The minimization concerns the entire chain length and not only local nucleotide complexes. A variety of DNA sequences (coding or non-coding, random or real, homogeneous or heterogeneous) are investigated in the range of 20-40 base pairs. The potential energy function is written in terms of a set of internal coordinates defined to account for the helical parameters such as twist, tilt and rise, which are important parameters for the description of the global shape of any type of DNA or RNA molecule. The force field used is composed of a limited number of bonded and non-bonded interactions such as bond stretch, angle bend and Lennard-Jones interactions with the Dreiding II force field parameter set used for these interactions. From the minimized structures the angles between Phosphate-Oxygen-Carbon " A 1 " and Oxygen-Phosphate-Oxygen " A 2 " and the average helical twist were calculated. For single strands it is shown that the bond angles are A 1 =107 - 1° and A 2 =122 - 1°, while the helical twist is 37.8 - 1°. For double stranded DNA our model predicts the helical twist of h =35.5 - 2° well, in the A strand, while the prediction is less accurate, h =47 - 2° for the complementary strand B. The average values for the angles A 1 and A 2 are 130 - 1° and 150 - 3° for strand A and 102 - 4° and 123 - 5° for strand B. The reason for this discrepancy is attributed to the different conformations initially adopted by the sugars in the A and B strands.

Sequence Directed Flexibility of DNA and the Role of Cross-strand Hydrogen Bonds

Persistence length and torsional rigidity for different B-DNA sequences have been calculated by analysing crystal structure database. The values of these parameters for mixed sequence DNA are in good agreement with those estimated by others. Persistence lengths for the homopolymeric sequences, namely poly(dA)·poly(dT) and poly(dG)·poly(dC), are significantly large compared to those of others as expected from the inability of these sequences to form nucleosome under normal conditions. The heteropolymeric sequences poly(dA-dC)·poly(dG-dT) and poly(dG-dC)·poly(dG-dC), on the other hand, have smaller persistence lengths. This implies larger flexibility of the d(AC)·d(GT), d(CA)·d(TG), d(GC)·d(GC) and d(CG)·d(CG) doublets, some of which constitute the genetic disease forming triplet repeats d(CTG)·d(CAG) and d(CGG)·d(CCG). Thus it is expected that these triplet repeat sequences are also flexible and wrap around the histone octamer efficiently. Persistence length calculations also indicate larger flexibility for these triplet repeat sequences. Furthermore, our computations reveal that the rigidity of a given DNA sequence is controlled by its ability to form cross-strand bifurcated hydrogen bonds between the successive base pairs. Molecular orbital calculations suggest that these hydrogen bonds are generally extended with bond lengths around 3Å.

Non-B-DNA structures on the interferon-β promoter?

The high mobility group (HMG) 1 protein intervenes as an essential factor during the virus induced expression of the interferon-β (IFN-β) gene. It is a non-histone chromatine associated protein that has the dual capacity of binding to a non-B-DNA structure such as cruciform-DNA as well as to AT rich B-DNA sequences. In this work we compare the binding affinity of HMG1 for a synthetic cruciform-DNA to its binding affinity for the HMGI-binding site present in the positive regulatory domain II (PRDII) of the IFN-β promoter. Using gel retardation experiments, we show that HMGI protein binds with at least ten times more affinity to the synthetic cruciform-DNA structure than to the PRDII B-DNA sequence. DNA hairpin sequences are present in both the human and the murine PRDII-DNAs. We discuss in this work the presence of yet putative, non-B-DNA structures in the IFN-β promoter.

Bending and curvature calculations in B-DNA.

A simple program, BEND, has been written to calculate the magnitude of local bending and macroscopic curvature at each point along an arbitrary B-DNA sequence, using any desired bending model that specifies values of twist, roll and tilt as a function of sequence. The program has been used to evaluate six different DNA bending models in three categories. Two are bent non-A-tract models: (a) A new model based on the nucleosome positioning data of Satchwell et al 1986 (J. Mol. Biol. 191, 659-675), (b) The model of Calladine et al 1988 (J. Mol. Biol. 201, 127-137). Three are bent A-tract models: (c) The wedge model of Bolshoy et al 1991 (Proc. Natl. Acad. Sci. USA 88, 2312-2316), (d) The model of Cacchione et al 1989 (Biochem. 28, 8706-8713), (e) A reversed version of model (b). The last is a junction model: (f) The model of Koo & Crothers 1988 (Proc. Natl. Acad. Sci. USA 85, 1763-1767). Although they have widely different assumptions and values for twist, roll and tilt, all six models correctly predict experimental A-tract curvature as measured by gel retardation and cyclization kinetics, but only the new nucleosome positioning model is successful in predicting curvature in regions containing phased GGGCCC sequences. This model--showing local bending at mixed sequence DNA, strong bends at the sequence GGC, and straight, rigid A-tracts--is the only model consistent with both solution data from gel retardation and cyclization kinetics and structural data from x-ray crystallography.

Adenine and guanine 8CH exchange in nucleic acids: Resolution and measurement by Raman optical multichannel analysis

Deuterium exchange of 8C protons of adenine and guanine in nucleic acids is conveniently monitored by laser Raman spectrophotometry, and the average exchange rate so determined [kA + kG] can be exploited as a dynamic probe of the secondary structure of DNA or RNA [J. M. Benevides and G. J. Thomas, Jr. (1985) Biopolymers 24, 667-682]. The present work describes a rapid Raman procedure, based upon optical multichannel analysis, which permits discrimination of the different 8CH exchange rates, kA of adenine and kG of guanine, in a single experimental protocol. For this procedure, simultaneous measurements are made of the intensity decay or frequency shift in separately resolved Raman bands of adenine and guanine, each of which is sensitive only to 8C deuteration of its respective purine. Resolution of the rates kA and kG is demonstrated for the mononucleotide mixtures, 5'-rAMP + 5'-rGMP and 5'-dAMP + 5'-dGMP, for the polynucleotides poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC), for calf thymus DNA, and for the 17 base-pair operator OR3. We show that the different exchange rates of adenine and guanine, in nucleotide mixtures and in DNA, may also be calculated independently from intensity decay of the composite 1481-cm-1 band, comprising overlapped adenine and guanine components, over a time domain that encompasses two distinct regimes: (1) a relatively more rapid exchange of guanine, and (2) a concurrent slower exchange of adenine. Both methods developed here yield consistent results. We find, first, that exchange of guanine is approximately twofold more rapid than that of adenine when both purines are present in the same structure and solvent environment, presumably a consequence of the greater basicity of the 7N site of guanine. Second, we find that adenine suffers greater retardation of exchange than guanine when both purines are incorporated into a "classical" B-DNA secondary structure, such as that of calf thymus DNA. This finding suggests different microenvironments at the 7N-8C loci of adenine and guanine in aqueous B-DNA. We also confirm that adenine residues of B-form poly(dA-dT).poly(dA-dT) exchange much more slowly than those of other B-DNA sequences, implying a secondary structure for the alternating-AT sequence with unusual stereochemistry in the major groove. The greater resistance of adenine than guanine to 8CH exchange in the B-DNA secondary structure is more evident in high molecular weight calf thymus DNA and in the alternating AT and GC copolymer duplexes than in the smaller 17 base-pair operator OR3.(ABSTRACT TRUNCATED AT 400 WORDS)

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.