Base-specific binding of copper(II) to Z-DNA. The 1.3-A single crystal structure of d(m5CGUAm5CG) in the presence of CuCl2

The single crystal structure of d(m5CGUAm5CG) soaked with copper(II) chloride was solved to atomic (1.3 A) resolution to study the base specificity of copper binding to double-stranded DNA. In the present copper(II) chloride-soaked structure, four crystallographically unique copper(II) complexes were observed bound to five of the six purine bases in the hexamer duplex. Covalent copper(II) binding occurred at N-7 of all four guanine bases and at one of the two adenine bases in the DNA duplex. Copper binding was not observed at the position (Ade4) located in an open solvent channel, whereas the second adenine site (Ade10) shared a complex with a guanine residue (Gua12) of a neighboring symmetry-related hexamer. The coordination geometries and distribution of these copper(II) complexes at the guanine bases in the crystal were comparable to the analogous sites in the isomorphous copper(II) chloride-soaked d(CGCGCG) crystal (Kagawa, T., Geierstanger, B. H., Wang, A. H.-J., and Ho, P.S. (1991) J. Biol. Chem. 266, 20175-20184). Thus, the decreased copper(II) binding affinity for Ade4 was not an artifact of crystal packing, but is intrinsic to the chemical properties of this purine base in duplex DNA. This suggests that the adenine bases in dilute solutions of Z-DNA and more generally other duplex DNA conformations are not susceptible to copper(II) modification. Thus, preferential copper(II) binding at guanine bases over adenine bases in double-stranded DNA may explain the observed specificity of copper(II)-induced oxidative DNA damage near guanine residues (Yamamoto, K., and Kawanishi, S. (1989) J. Biol. Chem. 264, 15435-15440; Sagripanti, J.-L., and Kraemer, K. H. (1989) J. Biol. Chem. 264, 1729-1734). The sharing of a single copper(II) complex by Ade10 and Gua12 of an adjacent hexamer suggests that additional and perhaps specific DNA-DNA interactions, as may be found in the densely packed environment of the nuclear matrix in the cell, may render N-7 of adenine bases prone to copper(II) modification.     

The interactions of ruthenium hexaammine with Z-DNA: crystal structure of a Ru(NH3)6+3 salt of d(CGCGCG) at 1.2 A resolution

A crystal of d(CGCGCG) in the Z-DNA lattice was soaked with ruthenium(III) hexaammine and its structure refined at 1.2 A resolution. Three unique metal complexes were found absorbed to each hexamer duplex. In addition, two symmetry-related binding sites were located, yielding a total of five ruthenium complexes bound to each d(CGCGCG) duplex. One unique site and its symmetry related site are nearly identical to the binding site of cobalt(III) hexaammine on Z-DNA. At that position, the metal complex bridges the convex surfaces of two adjacent Z-DNA strands by hydrogen bonds to the N7 and O6 functional groups of the guanine bases. The remaining three ruthenium three ruthenium(III) hexaammine binding sites are not present in the cobalt(III) hexaammine Z-DNA structure. Of these, two are related by symmetry and span the gap between the convex outer surface of one Z-DNA strand and the helical groove crevice of a neighboring strand. The third ruthenium site has no symmetry mate and involves interactions with only the deep groove. In this interaction, the metal complex hydrogen bonds to both the phosphate backbone and to a set of primary shell water molecules that extend the hydrogen bonding potential of the deep groove crevice out to the surface of the molecule. Solution studies comparing the circular dichroism spectra of low salt poly(dG-dC).poly(dG-dC) samples in the presence of ruthenium(III) and cobalt(III) hexammine show that the ruthenium complex does stabilize Z-DNA in solution, but not as effectively as the cobalt analogue. This suggests that some of the interactions available for the larger ruthenium complex may not be important for stabilization of the left-handed DNA conformation.     

Sequence-dependent binding of metal ion to DNA oligomeres. A comparison of molecular electrostatic potentials with NMR data

Experimentally observed sequence-selective binding of metal ion to DNA oligonucleotides have been compared with variations of electrostatic potential (EP) along the helix. Calculations of EP have been performed for three atomic models of the oligonucleotide duplex [d(CGCGAATTCGCG)2] using several variants of EP calculations, including a solution of non-linear Poisson-Boltzmann equation (NPBE). N7 atom of guanine adjacent to adenine base was identified as a region with the most negative electrostatic potential in the major groove. The EP value for the Me ion binding site surpasses the value for N7 of other guanines by 10-26% depending on particular duplex conformation. Qualitatively, the sequence dependent variations of EP near guanine N7 atoms are in agreement with the sequence-selective behavior of Mn(II) and Zn(II) ions as revealed by NMR experiments. But the difference in EP between the two most negative regions near guanine N7 atoms does not exceed 1.25 kT/e. Simple model suggests that metal ions are capable to form ion-hydrate complexes with G-Pu steps of DNA duplex. These complexes are formed via one Me...G and five Me...water coordination bonds with water molecules hydrogen bonded to two adjacent purine bases in the same chain. We suppose that such a stereospecific structural possibility is the main factor which control the sequence-selectivity in the metal ion binding. A combination of both mechanisms allows to explain sequence specific Mn(II) and Zn(II) binding to a set of oligonucleotides.     

Crystallographic studies of metal ion-DNA interactions: different binding modes of cobalt(II), copper(II) and barium(II) to N7 of guanines in Z-DNA and a drug-DNA complex.

Metal ion coordination to nucleic acids is not only required for charge neutralization, it is also essential for the biological function of nucleic acids. The structural impact of different metal ion coordinations of DNA helices is an open question. We carried out X-ray diffraction analyses of the interactions of the two transition metal ions Co(II) and Cu(II) and an alkaline earth metal ion Ba(II), with DNA of different conformations. In crystals, Co(II) ion binds exclusively at the N7 position of guanine bases by direct coordination. The coordination geometry around Co(II) is octahedral, although some sites have an incomplete hydration shell. The averaged Co-N7 bond distance is 2.3 A. The averaged Co-N7-C8 angle is 121 degrees, significantly smaller than the value of 128 degrees if the Co-N7 vector were to bisect the C5-N7-C8 bond angle. Model building of Co(II) binding to guanine N7 in B-DNA indicates that the coordinated waters in the axial positions would have a van der Waals clash with the neighboring base on the 5' side. In contrast, the major groove of A-DNA does not have enough room to accommodate the entire hydration shell. This suggests that Co(II) binding to either B-DNA or A-DNA may induce significant conformational changes. The Z-DNA structure of Cu(II)-soaked CGCGTG crystal revealed that the Cu(II) ion is bis-coordinated to N7 position of G10 and #G12 (# denotes a symmetry-related position) bases with a trigonal bipyramid geometry, suggesting a possible N7-Cu-N7 crosslinking mechanism. A similar bis-coordination to two guanines has also been seen in the interaction of Cu(II) in m5CGUAm5CG Z-DNA crystal and of Ba(II) with two other Z-DNA crystals.     

Effects of 5-fluorouracil/guanine wobble base pairs in Z-DNA: molecular and crystal structure of d(CGCGFG).

The chemotherapeutic agent 5-fluorouracil is a DNA base analogue which is known to incorporate into DNA in vivo. We have solved the structure of the oligonucleotide d(CGCGFG), where F is 5-fluorouracil (5FU). The DNA hexamer crystallizes in the Z-DNA conformation at two pH values with the 5FU forming a wobble base pair with guanine in both crystal forms. No evidence of the enol or ionized form of 5FU is found under either condition. The crystals diffracted X-rays to a resolution of 1.5 A and their structures have been refined to R-factors of 20.0% and 17.2%, respectively, for the pH = 7.0 and pH = 9.0 forms. By comparing this structure to that of d(CGCGCG) and d(CGCGTG), we were able to demonstrate that the backbone conformation of d(CGCGFG) is similar to that of the archetypal Z-DNA. The two F-G wobble base pairs in the duplex are structurally similar to the T-G base pairs both with respect to the DNA helix itself and its interactions with solvent molecules. In both cases water molecules associated with the wobble base pairs bridge between the bases and stabilize the structure. The fluorine in the 5FU base is hydrophobic and is not hydrogen bonded to any solvent molecules.     

Biological Macromolecular Dynamics

Abstract

Experimentally observed sequence-selective binding of metal ion to DNA oligonucleotides have been compared with variations of electrostatic potential (EP) along the helix. Calculations of EP have been performed for three atomic models of the oligonucleotide duplex [d(CGCGAATTCGCG)2] using several variants of EP calculations, including a solution of non-linear Poisson-Boltzmann equation (NPBE). N7 atom of guanine adjacent to adenine base was identified as a region with the most negative electrostatic potential in the major groove. The EP value for the Me ion binding site surpasses the value for N7 of other guanines by 10–26% depending on particular duplex conformation. Qualitatively, the sequence dependent variations of EP near guanine N7 atoms are in agreement with the sequence-selective behavior of Mn(II) and Zn(II) ions as revealed by NMR experiments. But the difference in EP between the two most negative regions near guanine N7 atoms does not exceed 1.25 kT/e. Simple model suggests that metal ions are capable to form ion-hydrate complexes with G-Pu steps of DNA duplex. These complexes are formed via one Me…G and five Me…water coordination bonds with water molecules hydrogen bonded to two adjacent purine bases in the same chain. We suppose that such a stereospecific structural possibility is the main factor which control the sequence-selectivity in the metal ion binding. A combination of both mechanisms allows to explain sequence specific Mn(II) and Zn(II) binding to a set of oligonucleotides.     

Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-A resolution.

We describe the three-dimensional X-ray structure of a complex of spermine bound to a Z-DNA duplex, [d(CGCGCG)]2, in the absence of any inorganic polyvalent cations. We have crystallized the DNA hexamer d(CGCGCG) in the exclusion of magnesium and other polyvalent ions and solved its structure at 1.0-A resolution. In the crystal of this pure-spermine form of Z-DNA, the relative orientation, position, and interactions of the DNA differ from the arrangement uniformly observed in over a dozen previously reported Z-DNA hexamers. Moreover, the conformation of the Z-DNA hexamer in this structure varies somewhat from those found in earlier structures. The DNA is compressed along the helical axis, the base pairs are shifted into the major groove, and the minor groove is more narrow. The packing of spermine-DNA complexes in crystals suggests that the molecular basis for the tendency of spermine to stabilize compact DNA structures derives from the capacity of spermine to interact simultaneously with several duplexes. This capacity is maximized by both the polymorphic nature and the length of the spermine cation. The length and flexibility of spermine and the dispersion of charge-charge, hydrogen-bonding, and hydrophobic bonding potential throughout the molecule maximize the ability of spermine to interact simultaneously with different DNA molecules.     

NMR study of hexanucleotide d(CCGCGG)2 containing two triplet repeats of fragile X syndrome

Long repeated stretches of d(CCG) and tri-nucleotide are crucial mutations that cause hereditary forms of mental retardation (fragile X-syndrome). Moreover, the alternating (CG) di-nucleotide is one of the candidates for Z-DNA conformation. Solution NMR structure of d(CCGCGG)(2) has been solved and is discussed. The determined NMR solution structure is a distorted highly bent B-DNA conformation with increased flexibility in both terminal residues. This conformation differs significantly from the Z-DNA tetramer structure reported for the same hexamer in the crystal state at similar ionic strength by Malinina and co-workers. Crystal structure of d(CCGCGG)(2) at high salt concentration includes a central alternating tetramer in Z-DNA conformation, while the initial cytosine swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. In solution, NMR data for sugar ring puckering combined with restrained molecular dynamics simulations starting from a Z-DNA form show that terminal furanose residues could adopt the conformation required for aromatic bases swinging out. Therefore, tetramer formation could be considered possible once the hexanucleotide had previously adopted the Z-DNA form. This work gives some insight into correlations between anomalous crystal structures and their accessibility in the solution state.     

Interaction between the Z-type DNA duplex and 1,3-propanediamine: crystal structure of d(CACGTG)2 at 1.2 A resolution

The crystal structure of a hexamer duplex d(CACGTG)(2) has been determined and refined to an R-factor of 18.3% using X-ray data up to 1.2 A resolution. The sequence crystallizes as a left-handed Z-form double helix with Watson-Crick base pairing. There is one hexamer duplex, a spermine molecule, 71 water molecules, and an unexpected diamine (Z-5, 1,3-propanediamine, C(3)H(10)N(2)) in the asymmetric unit. This is the high-resolution non-disordered structure of a Z-DNA hexamer containing two AT base pairs in the interior of a duplex with no modifications such as bromination or methylation on cytosine bases. This structure does not possess multivalent cations such as cobalt hexaammine that are known to stabilize Z-DNA. The overall duplex structure and its crystal interactions are similar to those of the pure-spermine form of the d(CGCGCG)(2) structure. The spine of hydration in the minor groove is intact except in the vicinity of the T5A8 base pair. The binding of the Z-5 molecule in the minor grove of the d(CACGTG)(2) duplex appears to have a profound effect in conferring stability to a Z-DNA conformation via electrostatic complementarity and hydrogen bonding interactions. The successive base stacking geometry in d(CACGTG)(2) is similar to the corresponding steps in d(CG)(3). These results suggest that specific polyamines such as Z-5 could serve as powerful inducers of Z-type conformation in unmodified DNA sequences with AT base pairs. This structure provides a molecular basis for stabilizing AT base pairs incorporated into an alternating d(CG) sequence.     

Stabilization of Z-DNA by demethylation of thymine bases: 1.3-A single-crystal structure of d(m5CGUAm5CG)

Methylation of cytosine bases at the C5 position has been known to stabilize Z-DNA. We had previously predicted from calculations of solvent-accessible surfaces that the methyl group at the same position of thymine has a destabilizing effect on Z-DNA. In the current studies, the sequence d(m5CGUAm5CG) has been crystallized and its structure solved as Z-DNA to 1.3-A resolution. A well-defined octahedral hexaaquomagnesium complex was observed to bridge the O4 oxygens of the adjacent uridine bases at the major groove surface, and four well-structured water molecules were found in the minor groove crevice at the d(UA) dinucleotide. These solvent interactions were not observed in the previously published Z-DNA structure of the analogous d(m5CGTAm5CG) sequence. A comparison of the thymine and uridine structures supports our prediction that demethylation of thymine bases helps to stabilize Z-DNA. A comparison of this d(UA)-containing Z-DNA structure with the analogous d(TA) structure shows that access of the O4 position is hindered by the C5 methyl of thymine due to steric and hydrophobic inhibition. In the absence of the methyl group, a magnesium-water complex binds to and slightly affects the structure of the Z-DNA major groove surface. This perturbation of the solvent structure at the major groove surface is translated into a much larger 1.41-A widening of the minor groove crevice, thereby allowing the specific binding of two water molecules at well-defined sites of each internal d(UA) base pair. Possible mechanisms by which modifications at the major groove surface of Z-DNA can affect the solvent properties of the minor groove crevice are discussed.     

DNA-copper (II) complex and the DNA conformation

Spectrophotometric, sedimentation, infrared, optical rotatory dispersion (ORD), and circular dichroism (CD) methods have been used to demonstrate the structural changes in DNA induced by the interaction of copper(II) with bases and to elucidate the complex binding sites. As shown by the electrolyte-induced reversion (addition of salts) of temperature-denatured copper DNA the effectiveness of re-formation of the double-stranded structure depends on the temperature, copper(II) ion concentration, and on the base composition of the DNA. Exposure of heat-denatured copper DNA to higher temperatures decreases the reversion effect on addition of electrolyte. The results indicate that a greater fraction with a cooperative transition appears on heating DNA to 80 or 100°C at a Cu²⁺/DNA-P ratio of 2 : 1 than at a Cu²⁺/DNA-P ratio of 1 : 1. With AT-rich copper DNA, reversion to the native DNA structure was not observed. Selective methylation of guanine residues in DNA also affects the electrolyte-induced reversion, indicating the importance of GC pairs for copper(II) binding and the reversion to the native structure. Temperature-denatured copper DNA shows an increased sedimentation coefficient Which decreases again after electrolyte-induced reversion. This change in s is reduced by selective methylation of DNA. Complex formation between copper(II) and the bases is accompanied by a conformational change of the DNA double-helical structure as demonstrated by ORD and CD experiments. The ORD profile of GC-rich DNA is much more affected by copper(II) than that of AT-rich ones. Even at very low copper(II) concentrations, e.g., at 0.02 and 0.2 Cu²⁺/DNA-P, the ORD and CD measurements exhibit conformational changes of the DNA secondary structure at room temperature. By comparing the infrared spectra of deoxynucleosides with that of DNA of different GC content it has been shown that both guanine and cytosine are involved in the formation of the complex of copper(II) with DNA. N-7 and O at C-6 in guanine and N-3 as well as O of C-2 in cytosine are discussed as the most probable binding sites in DNA. A binding model for the coordination of the copper(II) ion between guanine and cytosine of the opposite strands is suggested. The results are in good agreement with the assumptions and predictions made by Eichhorn and Clark about the complexing of copper(II) with DNA. The recent proposal made by Schreiber and Daune about an interaction of the type guanine–Cu²⁺–guanine cannot be excluded as an additional kind of coordination of copper(II) in DNA.     

Crystal structure of d(GCGCGCG) with 5''-overhang G residues.

The crystal structure of the DNA heptamer d(GCGCGCG) has been solved at 1.65 A resolution by the molecular replacement method and refined to an R-value of 0.184 for 3598 reflections. The heptamer forms a Z-DNA d(CGCGCG)2 with 5'-overhang G residues instead of an A-DNA d(GCGCGC)2 with 3'-overhang G residues. The overhang G residues from parallel strands of two adjacent duplexes form a trans reverse Hoogsteen G x G basepair that stacks on the six Z-DNA basepairs to produce a pseudocontinuous helix. The reverse Hoogsteen G x G basepair is unusual in that the displacement of one G base relative to the other allows them to participate in a bifurcated (G1)N2 . . . N7(G8) and an enhanced (G8)C8-H . . . O6(G1) hydrogen bond, in addition to the two usual hydrogen bonds. The 5'-overhang G residues are anti and C2'-endo while the 3'-terminal G residues are syn and C2'-endo. The conformations of both G residues are different from the syn/C3'-endo for the guanosine in a standard Z-DNA. The two cobalt hexammine ions bind to the phosphate groups in both GpC and CpG steps in Z(I) and Z(II) conformations. The water structure motif is similar to the other Z-DNA structures.     

NMR solution structure of a DNA dodecamer containing a transplatin interstrand GN7-CN3 cross-link.

The DNA duplex d(CTCTCG*AGTCTC).d(GAGAC-TC*GAGAG) containing a single trans- diammine-dichloroplatinum(II) interstrand cross-link (where G* and C* represent the platinated bases) has been studied by two-dimensional NMR. All the exchangeable and non-exchangeable proton resonance lines were assigned (except H5'/H5") and the NOE intensities were transformed into distances via the RELAZ program. By combining the NOESY and COSY data (330 constraints) and NMR-constrained molecular mechanics using JUMNA, a solution structure of the cross-linked duplex has been determined. The duplex is distorted over two base pairs on each side of the interstrand cross-link and exhibits a slight bending of its axis ( approximately 20 degrees ) towards the minor groove. The platinated guanine G* adopts a syn conformation. The rotation results in a Hoogsteen-type pairing between the complementary G(6)* and C(19)* residues which is mediated by the platinum moiety and is stabilized by a hydrogen bond between O6(G(6)*) and N4H(C(19)*). The rise between the cross-linked residues and the adjacent residues is increased owing to the interaction between these adjacent residues and the ammine groups of the platinum moiety. These results are discussed in relation to the slow rate of closure of the monofunctional adducts into interstrand cross-links.     

Z-DNA is formed by poly (dC-dG) and poly (dm5C-dG) at micro or nanomolar concentrations of some zinc(II) and copper(II) complexes

We report studies on the interaction of some zinc(II) and copper(II) complexes of amines and amino acids with poly(dC-dG) and poly(dm5C-dG). Of the zinc complexes the species zinc-tris(2-aminoethyl) amine is found to be the most efficient for inducing Z-DNA giving a mid point at low ionic strength of 1.4 microM (poly(dC-dG] and 44nM (poly(dm5C-dG). While an antagonistic effect on raising the ionic strength is observed, the transition occurs at only 2 microM for poly(dm5C-dG) at 150mM NaCl. The most efficient copper(II) complex is that of diethylene triamine, though copper(II) complexes are generally less efficient than zinc(II) complexes. We also report kinetic and thermodynamic studies upon the B-Z transition induced by these complexes. A model is proposed for the interaction of one of the zinc complexes which involves not only direct zinc-DNA binding but also the formation of hydrogen bonds between the metal bond amine groups and the residues adjacent to the coordination site.     

Z-DNA crystallography

We review the effect of sequence on the structure of left-handed Z-DNA in single crystals. The various substituent groups that define a nucleotide base as guanine, cytosine, thymine, or adenine affect both the DNA conformation and the organization of solvent around the duplex. These are discussed in terms of their effect on the ability of sequences to adopt the unusual Z-DNA structure. In addition, the experimental and theoretical methods used to treat DNA hydration are discussed as they relate to the stability of Z-DNA. Finally, we argue that Z-DNA, as defined by the crystal conformation, is sufficient in itself to account for the physical properties of left-handed conformations observed in polymers and in genomic sequences. © 1997 John Wiley & Sons, Inc. Biopoly 44: 65–90, 1997     

The Interactions of Ruthenium Hexaammine with Z-DNA: Crystal Structure of a RU(NH3)+3 6 Salt of d(CGCGCG) at 1.2 Å Resolution

Abstract

Acrystalofd(CGCGCG)in the Z-DNA lattice was soaked with ruthenium(III) hexaammine and its structure refined at 1.2 Å resolution. Three unique metal complexes were found adsorbed to each hexamer duplex. In addition, two symmetry-related binding sites were located, yielding a total of five ruthenium complexes bound to each d(CGCGCG) duplex. One unique site and its symmetry related site are nearly identical to the binding site of cobalt(III) hexaammine on Z-DNA. At that position, the metal complex bridges the convex surfaces of two adjacent Z-DNA strands by hydrogen bonds to the N7 and 06 functional groups of the guanine bases. The remaining three ruthenium(III) hexaammine binding sites are not present in the cobalt(III) hexaammine Z-DNA structure. Of these, two are related by symmetry and span the gap between the convex outer surface of one Z-DNA strand and the helical groove crevice of a neighboring strand. The third ruthenium site has no symmetry mate and involves interactions with only the deep groove. In this interaction, the metal complex hydrogen bonds to both the phosphate backbone and to a set of primary shell water molecules that extend the hydrogen bonding potential of the deep groove crevice out to the surface of the molecule. Solution studies comparing the circular dichroism spectra of low salt poly(dG-dC) · poly(dG-dC) samples in the presence of ruthenium(III) and cobalt(III) hexaammine show that the ruthenium complex does stabilize Z-DNA in solution, but not as effectively as the cobalt analogue. This suggests that some of the interactions available for the larger ruthenium complex may not be important for stabilization of the left-handed DNA conformation.     

The effect of HCl on the solution structure of calf thymus DNA: A comparative study of DNA denaturation by proton and metal cations using fourier transform IR difference spectroscopy

The interaction of HCl with calf thymus DNA was investigated in aqueous solution at pH 7-2 with H⁺/DNA(P)(P:phosphate) molar ratios (r) of 1/80, 1/40, 1/20, 1/10, 1/4, 1/2, and 1, using Fourier Transform (FTIR) difference spectroscopy. Correlations between spectral changes, proton binding mode, DNA denaturation, and conformational variations are established. A comparison was also made between their spectra of denaturated DNA, in the presence of proton and Cu ions with similar cation concentrations. The FTIR difference spectroscopic results have shown that at low proton concentrations of r = 1/80 and 1/40 (pH 7–5), no major spectral changes occur for DNA, and the presence of H⁺ results in an increased base-stacking interaction and helical stability. At higher proton concentrations of r > 1/40, the proton binding to the cytosine and adenine bases begins with major destabilization of the helical duplex. As base protonation progresses, a B to C conformational conversion occurs with major DNA spectral changes. Protonation of guanine bases occurs at a high cation concentration r > 1/2 (pH < 3) with a major increase in the intensity of several DNA in-plane vibrations. Copper ion complexation with DNA exhibits marked similarities with proton at high cation concentrations (r > 1/10), whereas at low metal ion concentrations, copper–PO₂ and copper–guanine N-7 bindings are predominant. No major DNA conformational transition was observed on copper ion complexation. © 1995 John Wiley & Sons, Inc.     

Structural features and hydration of d(C-G-C-G-A-A-T-T-A-G-C-G); a double helix containing two G.A mispairs

Single crystal X-ray diffraction techniques have been used to characterise the molecular structure of the title compound to 2.5A resolution. The structure consists of ten standard Watson-Crick base pairs and two G.A mismatched base pairs. The purine-purine mismatches have guanine in the usual anti orientation with respect to the sugar and adenine in syn orientation. There are two hydrogen bonds formed between the mismatch bases, N-1 and O-6 of guanine with N-7 and N-6 of adenine respectively. The bulky purine-purine mismatches are accommodated with minor perturbation of the sugar-phosphate backbone. There is a slight improvement in base pair overlap at the mismatch sites. Details of the backbone conformation, base stacking interactions and hydration are presented and compared with those of the parent compound d(C-G-C-G-A-A-T-T-C-G-C-G).     

Stacking interaction of guanine with netropsin in the minor groove of d(CGTATATACG)2

We present the structure of the decanucleotide d(CGTATATACG) determined by single crystal X-ray diffraction at 1.58 A resolution. A netropsin drug is found in the minor groove with guanine stacked on a pyrrole ring of the drug, a feature described here for the first time. The stacked guanine is an extra-helical base coming from the end of a neighbour oligonucleotide. This observation may open the way to the development of minor groove binding drugs with a higher sequence selectivity. The oligonucleotide is in the B-conformation, but the terminal base-pairs are disrupted: the cytosine residues are disordered while the guanine residues penetrate into the minor groove of neighbouring duplexes. Four hydrated Ni ions with octahedral co-ordination are found associated with the N7 atoms of each guanine. The high affinity of these ions with guanine suggests that they may be used as probes for specific guanine residues.     

An FTIR Spectroscopic Study of Calf-thymus DNA Complexation with Al(III) and Ga(III) Cations

Abstract

The interaction of calf-thymus DNA with trivalent Al and Ga cations, in aqueous solution at pH =6–7 with cation/DNA(P) (P=phosphate) molar ratios (r) 1/80, 1/40, 1/20, 1/10, 1/4 and 1/2 was characterized by Fourier Transform infrared (FTIR) difference spectroscopy.

Spectroscopic results show the formation of several types of cation-DNA complexes. At low metal ion concentration (r=l/80, 1/40), both cations bind mainly to the backbone PO₂ group and the guanine N-7 site of the G-C base pairs (chelation). Evidence for cation chelate formation comes from major shifting and intensity increase of the phosphate antisymmetric stretch at 1222 cm-¹ and the mainly guanine band at 1717 cm¹. The perturbations of A-T base pairs occur at high cation concentration with major helix destabilization. Evidence for cation binding to A-T bases comes from major spectral changes of the bands at 1663 and 1609 cm-¹ related mainly to the thymine and adenine in-plane vibrations. A major reduction of the B-DNA structure occurs in favor of A-DNA upon trivalent cation coordination.