Molecular structure of cyclic diguanylic acid at 1 A resolution of two crystal forms: self-association, interactions with metal ion/planar dyes and modeling studies

Cyclic ribodiguanylic acid, c-(GpGp), is the endogenous effector regulator of cellulose synthase. Its three dimensional structure from two different crystal forms (tetragonal and trigonal) has been determined by x-ray diffraction analysis at 1 A resolution. Both structures were solved by direct methods and refined by block-matrix least squares refinement to R-factors of 0.112 (tetragonal) and 0.119 (trigonal). In both crystal forms, two independent c-(GpGp) molecules associate with each other to form a self-intercalated dimer. All four c-(GpGp) molecules have very similar backbone conformation. The riboses are in the C3'-endo pucker with pseudorotation angles ranging from -7.2 degrees to 16.5 degrees and the bases have anti glycosyl chi angles (-175.5 degrees to 179.7 degrees). In the tetragonal form, a hydrated cobalt ion is found to coordinate to two N7 atoms of adjacent guanines, forcing these two guanines to destack with a large dihedral angle (33 degrees). This metal coordination mechanism has been noted previously in other Pt- or Co-GMP complexes and may be relevant to the binding of the anticancer drug cisplatin to a GpG sequence in DNA. A model of the adduct between cisplatin and a d(CAATGGATTG) duplex has been constructed in which the induced bending of the DNA helix at the Pt crosslinking site is 33 degrees, consistent with earlier electrophoretic analyses. Moreover, c-(GpGp) exhibits unusual spectral properties not seen in other cyclic dinucleotides. It interacts with planar organic intercalator molecules in ways similar to double helical DNA. We propose a cage-like model consisting of a tetrameric c-(GpGp) aggregate in which a large cavity (host molecule) is generated to afford a binding site for certain planar intercalators (guests molecules). The aggregate likely uses a hydrogen bonding scheme the same as that found in the G-quartet molecules, e.g., telomere DNA. The conformation of c-(GpGp) also suggests that certain nearest-neighbor intercalators may be synthesized on the basis of its unique molecular framework. Modeling studies have been carried out to test this hypothesis.

Minor groove binding of SN6999 to an alkylated DNA: molecular structure of d(CGC[e6G]AATTCGCG)-SN6999 complex

The interaction between a potent synthetic antitumor and antiviral minor groove binding drug 1-methyl-4-[4-[4-(4-(1-methylquinolinium)amino)benzamido]anilino] pyridinium dichloride (SN6999) and an alkylated DNA d(CGC[e6G]AATTCGCG) dodecamer has been studied by X-ray crystallography. The complex forms a new crystal lattice in the space group P2(1)2(1)2(1) with unit cell dimensions of a = 28.48 A, b = 36.11 A, and c = 69.60 A. The structure has been solved by the molecular replacement method and refined to an R-factor of 17.0% at approximately 2.5 A resolution using 1618 reflections. In the complex, the SN6999 covers almost six base pairs in the narrow minor groove with the 1-methylquinolinium (Q) ring near T8-A17 and the 1-methylpyridinium (P) ring near the C3-G22 base pair. The central benzamido (BQ) and anilino (BP) rings are essentially coplanar, with the Q and P rings having large dihedral angles of 38 degrees and 39 degrees, respectively, to the plane of BQ/BP. There is only one direct hydrogen bond between the amide NH of SN6999 to T20O2 of DNA. The drug-DNA interaction is stabilized by stacking interaction of sugar oxygens from T20O4' to BQ and C21O4' to BP. There is charge-induced dipole interaction between the positively charged nitrogen atom of 1-methylquinolinium with C9O4' and that of 1-methylpyridinium with G22O4'. The crystal structure of the complex can be used to explain the NMR results. SN6999 lacks the crescent shape observed in other minor groove binding drugs and distorts the DNA duplex upon binding. The complex packs in the lattice using the G-N2:G-N3 interlocking base pairs at both ends of the helix. As in earlier cases, the two independent e6G:C base pairs adopt different base pairing schemes. The e6G16:C9 base pair adopts a previously observed bifurcated configuration involving three-centered hydrogen bonds and is similar to a Watson-Crick pairing. In contrast, the e6G4:C21 base pair adopts a novel "reverse wobble" configuration with C21 being pushed toward the major groove side. The ethyl group is in the proximal orientation (to N7) in both base pairs. Taken together with the observations found in the same DNA complexed to Hoechst 33258, Hoechst 33342, and retropsin from different crystal lattices, the results suggest that the e6G:C base pairing is weak and polymorphic when compared to a normal G:C base pair and the DNA duplex containing this lesion is readily distorted.

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.

Structural effects of the C2-methylhypoxanthine:cytosine base pair in B-DNA: A combined NMR and X-ray diffraction study of d(CGC[m2I]AATTCGCG)

C2-Methylhypoxanthine (m2I) is a synthetic analog of guanine with the N2-amino group replaced by a methyl group. We have studied the structural consequence of the m2I incorporation in DNA by a combination of X-ray crystallographic, NMR, and enzymatic analyses. The crystal structure of d(CGC[m2I]AATTCGCG) has been solved and refined to an R factor of 20.7% at 2.25-A resolution. In the DNA duplex, the two independent m2I:C base pairs maintain the Watson-Crick scheme. While the C2-methyl group of m2I is in van der Waals contact with the O2 of the base-paired cytosine, it only causes the base pair to have slightly higher propeller twist and buckle angles. Its solution structure was analyzed by the NMR refinement procedure SPEDREF [Robinson, H., & Wang, A. H.-J. (1992) Biochemistry 31, 3524-3533] using 2D nuclear Overhauser effect data. Two starting models, a relaxed fiber model and an X-ray model, were subjected to the NOE-constrained refinement using 1518 NOE cross-peak integrals to arrive at the final models with (NOE) R factors of 13.8% and 14.3%, respectively. The RMSD between the two refined models (all atoms included) is 1.23 A, which presently seems to be near the limit of convergence of NOE-based refinement. The local structures of the two models are in better agreement as measured by the RMSD of the dinucleotide steps, falling in the range 0.54-0.98 A. Both refined solution structures confirm that the m2I dodecamer structure is of the B-DNA type with a narrow minor groove at the AT region, as observed in the crystal. However, significant differences exist between the crystal and solution structures in parameters such as pseudorotation angles, propeller twist angles, etc. The solution structure tends to have a more uniform backbone conformation, an observation consistent with that concluded from the laser Raman study of d(CGCAAATTTGCG) [Benevides, J. M., Wang, A. H.-J., van der Marel, G. A., van Boom, J. H., & Thomas, G. J., J. (1988) Biochemistry 27, 931-938]. Three related dodecamers, d(CGCGAATTCGCG), d(CGC[m2I]AATTCGCG), and d(CGC[e6G]AATTCGCG), were tested as substrates for the restriction endonuclease EcoRI. The m2I dodecamer was active, but the e6G dodecamer was not. Our results illustrate the complementarity in terms of the structural information provided by the two methods, X-ray diffraction and NMR.

NMR studies of pH-dependent conformational polymorphism of alternating (C-T)n sequences

Alternating (C-T)n sequences are involved in the H-DNA structure associated with (GA)n.(CT)n sequences. Low pH values facilitate H-DNA formation. We have undertaken a detailed analysis of the structural consequences of the (C-T)n sequence as a function of pH. The structures of three DNA oligonucleotides, d(CT)4, d(TC)4 and d(TC)15, have been studied by NMR. We found that their conformations are polymorphic and pH dependent. There are at least three major conformational species: an antiparallel-stranded (APS) duplex with entirely C:T base pairs at pH 7, an antiparallel-stranded (APS) duplex with entirely C+:T base pairs at pH 3, and a possible parallel-stranded (PS) duplex with C+:C and T:T base pairs near pH 5. In the intermediate pH range, the APS duplex may have varying numbers of C+:T and C:T base pairs, and there may be a fast exchange going on between APS duplex species involving these two kinds of base pairs. However, the transition between the APS and PS duplexes is slow. Structural refinement of the two octamers, d(TC)4 and d(CT)4, at pH = 6.9 and pH = 3 using 2D-NOE data suggests that the molecules are likely in the duplex form at 5 degrees C. We lack evidence that the structure at pH 3 is a PS structure with T nucleotides residing in the exterior of the helix. Titration of the longer oligonucleotide, d(TC)15, showed a prominent pKa of approximately 6, approaching the value of 7.0 obtained from the titration of poly-(dC).

5'-CGA sequence is a strong motif for homo base-paired parallel-stranded DNA duplex as revealed by NMR analysis

The structure of the non-self-complementary DNA heptamer d(CGACGAC) at low pH has been determined by the quantitative NMR refinement procedure designated SPEDREF (SPEctral-Driven REFinement). Acid-base titration of the molecule indicated a prominent n = 2 pKa near 6.8. In the pH range up to 6.0, the heptamer forms a remarkably stable double helix, which was conclusively shown to be an unusual homobase-paired parallel-stranded double helix (termed II-DNA). In this II-DNA helix, the 5'-CGA trinucleotide is the structural motif that accounts for the stability, with the C+-C hemiprotonated base pair (in which C+ is N3-protonated cytosine) providing for the alignment site and the unusual interstrand G-A base stack in the GpA step furnishing the additional stabilizing forces. The exchangeable proton data from two-dimensional nuclear Overhauser effect spectroscopy are in total agreement with the refined structure. We conclude that the 5'-CGA or other related sequences (e.g., 5'-CCGA) are powerful motifs in promoting the II-DNA or II-RNA conformations that may play certain biological functions.

Simultaneous incorporations of two anticancer drugs into DNA. The structures of formaldehyde-cross-linked adducts of daunorubicin-d(CG(araC)GCG) and doxorubicin-d(CA(araC)GTG) complexes at high resolution

Anthracycline antibiotics (notably daunorubicin (DAU) and doxorubicin (DOX)) and nucleoside analog arabinosylcytosine (araC or aC) are important anticancer drugs. They are sometimes used together in the treatment of certain cancers. Both classes of compounds act by blocking DNA replication and transcription. To probe whether both drugs can be incorporated simultaneously into DNA and the possible structural consequences, we carried out x-ray diffraction analyses of the complexes between DAU/DOX and araC-containing DNA hexamers cross-linked with formaldehyde. The crystal structures were determined to high resolution (DAU-CGaCGCG, 1.2 A, space group P4(1)2(1)2, R = 0.182, 3275 reflections; DOX-CAaCGTG, 1.5 A, space group C2, R = 0.175, 3359 reflections), and they are similar to those of the previously studied DAU- and DOX-DNA complexes, despite different crystal packings. Two DAU/DOX molecules intercalate at both ends of the helix with their amino sugars in the minor groove. As in the structure of DAU-CGCGCG (Wang, A.H.-J., Gao, Y.-G., Liaw, Y.-C., and Li, Y.K. (1991) Biochemistry 30, 3812-3815), a covalent methylene bridge (from formaldehyde) between the N3' of daunosamine and the N2 of the guanine is formed in both adducts. In DOX-CAaCGTG, the two halves are slightly different with a root-mean-square deviation of 0.322 A between them. The O14 hydroxyls of the intercalated DOXs are within hydrogen bond distances to the O2P atoms of the A2p(aC3) and A8p(AC9) steps. The O2'-hydroxyl group from araC does not affect the binding of DAU-DOX or the conformation of the drug-DNA complexes. The results suggest that three major drug modifications on DNA, i.e., intercalation, covalent bond formation, and nucleoside analog incorporation, can coexist in the same DNA molecule without difficulty. When they occur in close proximity in DNA, they may provide an additive inhibitory effect for the target enzymes.

Structural influence of RNA incorporation in DNA: quantitative nuclear magnetic resonance refinement of d(CG)r(CG)d(CG) and d(CG)r(C)d(TAGCG)

RNA and DNA adopt different types of conformations, i.e., A-type with C3'-endo sugar pucker for RNA and B-type with C2'-endo sugar pucker for DNA, respectively. The structural influence of the incorporation of RNA nucleotides into DNA is less understood. In this paper, we present the three-dimensional structures of two RNA-containing oligonucleotides, d(CG)r(CG)d(CG) and d(CG)r(C)d-(TAGCG), as determined by the NMR refinement procedure, and assess the possible structural perturbation of DNA induced by RNA. With a single RNA insertion into an octamer DNA, its overall conformation remains as the canonical B-DNA, except that the sugar pucker of the rC3 residue is C3'-endo (pseudorotation angle P = 3.6 degrees). In contrast, the hybrid hexamer is neither the pure B-DNA nor the pure A-DNA conformation. Instead, we propose a model in which the DNA parts adopt B conformation, whereas the RNA part adopts A conformation, with the overall conformation closer to A-DNA. To ensure an exhaustive search of the conformational space, the model was subjected to 100-ps simulated annealing with slow cooling or 100-ps molecular dynamics with subsequent quenching. Models obtained at different time points of the trajectories were further subjected to the SPEDREF NOE refinement [Robinson & Wang (1992) Biochemistry 31, 3524] and they appeared to arrive at a convergent model (< 0.5 A RMSD for the central four base pairs). The consensus hexamer structure contains a significant discontinuity at the (rG4)p(dC5) step with a base pair tilt angle of 6.7 degrees and roll angle of 11.5 degrees.(ABSTRACT TRUNCATED AT 250 WORDS)

Functional analysis of matrix proteins expressed from cloned genes of measles virus variants that cause subacute sclerosing panencephalitis reveals a common defect in nucleocapsid binding

We have developed an in vitro nucleocapsid-binding assay for studying the function of the matrix (M) protein of measles virus (MV) (A. Hirano, A. H. Wang, A. F. Gombart, and T. C. Wong, Proc. Natl. Acad. Sci. USA, 89:8745-8749, 1992). In this communication we show that the M proteins of three MV strains that cause acute infection (Nagahata, Edmonston, and YN) bind efficiently to the viral nucleocapsids whereas the M proteins of four MV strains isolated from patients with subacute sclerosing panencephalitis (SSPE) (Biken, IP-3, Niigata, and Yamagata) fail to bind to the viral nucleocapsids. MV Biken (an SSPE-related virus) produces variant M sequences which encode two antigenically distinct forms of M protein. A serine-versus-leucine difference is responsible for the antigenic variation. MV IP-3 (an SSPE-related virus) also produces variant M sequences, some of which have been postulated to encode a functional M protein responsible for the production of an infectious revertant virus. However, the variant M proteins of Biken and IP-3 strains show no nucleocapsid-binding activity. These results demonstrate that the nucleocapsid-binding function is conserved in the M proteins of MV strains that cause acute infection and that the M proteins of MV strains that cause SSPE exhibit a common defect in this function. Analysis of chimeric M proteins indicates that mutations in the amino-terminal, carboxy-proximal, or carboxy-terminal region of the M protein all abrogate nucleocapsid binding, suggesting that the M protein conformation is important for interaction with the viral nucleocapsid.

Molecular and crystal structures of ecteinascidins: potent antitumor compounds from the Caribbean tunicate Ecteinascidia turbinata

Some members of marine alkaloid ecteinascidins (Et's), isolated from the Caribbean tunicate Ecteinascidia turbinata, exhibit potent anticancer activity. The three dimensional structures of the N12-formyl derivative of Et729 1a and the natural N12-oxide of Et743 2 have been determined by x-ray crystallography at 0.9 A resolution. Compounds 1a and 2 crystallize in the space groups P2(1)2(1)2(1) (a = 23.214(9) A, b = 28.541(10) A and c = 13.303(9) A) and P2(1) (a = 11.720(5) A, b = 13.230(4) A, c = 28.557(5) A, beta = 90.22(2) degrees), respectively. Their crystal structures have been solved by the Patterson search method, which located the sulfur atoms permitting the phase extension. The final crystallographic R-factors are 0.059 and 0.069 for 1a and 2, respectively. There are two independent molecules, associated as a dimer, in the asymmetric unit of crystals of both 1a and 2. The structure determination allows an unequivocal assignment of the relative configuration of all the chiral centers. Assuming that ecteinascidins and safracin C (whose absolute configuration is known) have the same absolute configuration at C1 position, then the absolute configurations of various chiral positions in Ets are C1(R), N2(R), C3(R), C4(R), C11(R), C13(S), C21(S) and C22(R), respectively. The four independent Et molecules adopt two conformations in which the position of ring C relative to rings A & B is different. The molecules have a compact shape and they are conformationally strained due to a severe van der Waals clash between the sulfur atom and the aromatic ring A. By analogy to the related saframycin, the potent biological activity of Et's may be associated with their ability to form a covalent adduct to DNA using the reactive carbinolamine group. The covalent binding interaction between the Et and the N2 of guanine in the minor groove of the DNA double helix has been studied by computer modelling which suggests that rings A and B "stack" against the DNA backbone. While the bulky drug molecule makes numerous contacts with DNA, it does not significantly distort the conformation of the DNA double helix.

Demonstration of Z-d(5BrCGAT5BrCG) and B-d(CGCGATCGCG) form crystal structures in DNA-cobalt hexammine complexes by Kr 647.1 nm excitation of Raman spectra

Cobalt hexammine [Co(NH3)6(3+)] is an efficient DNA complexing agent which significantly perturbs nucleic acid secondary structure. We have employed red excitation (647.1 nm) from a krypton laser to obtain Raman spectra of the highly colored complexes formed between cobalt hexammine and crystals of the DNA oligomers, d(5BrCGAT5BrCG) and d(CGCGATCGCG), both of which incorporate out-of-alternation pyrimidine/purine sequences. The Co(NH3)6(3+) complex of d(5BrCGAT5BrCG) exhibits a typical Z-form Raman signature, similar to that reported previously for the alternating d(CGCGCG) sequence. Comparison of the Raman bands of d(5BrCGAT5BrCG) with those of other oligonucleotide and polynucleotide structures suggests that C3'-endo/syn and C3'-endo/anti thymidines may exhibit distinctive nucleoside conformation markers, and tentative assignments are proposed. The Raman markers for C2'-endo/anti adenosine in this Z-DNA are consistent with those reported previously for B-DNA crystals containing C2'-endo/anti dA. Raman bands of the cobalt hexammine complex of d(CGCGATCGCG) are those of B-DNA, but with significant differences from the previously characterized B-DNA dodecamer, d(CGCAAATTTGCG). The observed differences suggest an unusual deoxyguanosine conformer, possibly related to a previously characterized structural intermediate in the B-->Z transition. The present results show that crystallization of d(CGCGATCGCG) in the presence of cobalt hexammine is not alone sufficient to induce the left-handed Z-DNA conformation. This investigation represents the first application of off-resonance Raman spectroscopy for characterization of highly chromophoric DNA and illustrates the feasibility of the Raman method for investigating other structurally perturbed states of DNA-cobalt hexammine complexes.

Z-DNA structure of a modified DNA hexamer at 1.4-A resolution: aminohexyl-5'-d(pCpGp[br5C]pGpCpG)

Oligonucleotides with modification at the 5'-end have been used for various biochemical applications. As a first step to better assess the effects of those modifications on DNA conformation, we determined at 1.4-A resolution the left-handed Z-DNA structure of a DNA hexamer, aminohexyl-5'-d(pCpGp[br5C]pGpCpG), by X-ray diffraction analysis. This hexamer was crystallized in the monoclinic C2 (a = 51.13 A, b = 18.44 A, c = 34.67 A, and beta = 120.9 degrees) space group. Its structure has been refined by the restrained least-squares refinement to a final R factor of 0.164 using 3727 [> 2.0 sigma (F)] observed reflections. The overall conformation of the double helix resembles that of the canonical Z-DNA. The terminal 5'-phosphate groups of the dC residues adopt conformations (beta approximately 180 degrees and gamma approximately 60 degrees) similar to phosphodiester's conformation of the internal dC residues. Two types of interhelical stackings are observed, one of which may serve as a model for a single-strand nick in the backbone of DNA double helix. A barium ion is found to bridge two side-by-side Z-DNA helices by coordinating to the O6 and N7 atoms of two guanines simultaneously. This "cross-linking" ability of barium ion may be a useful property in promoting the reversible aggregation of nucleic acids.

Structural consequences of a carcinogenic alkylation lesion on DNA: effect of O6-ethylguanine on the molecular structure of the d(CGC[e6G]AATTCGCG)-netropsin complex

Exposure of cells to alkylating agents produces DNA lesions, most of which are repaired. However some alkyl lesions persist and play a role in inducing point mutations and the subsequent carcinogenic conversion. O6-Ethylguanine (e6G) is a relatively persistent alkylation lesion caused by the exposure of DNA to N-ethyl-N-nitrosourea. We study the consequence of the e6G incorporation in DNA by X-ray crystallography. We have obtained crystals of the modified DNA dodecamer d(CGC[e6G]AATTCGCG) and the unmodified d(CGCGAATTCGCG), complexed to the minor groove binding drug netropsin. The space group of both crystals is P2(1)2(1)2(1), isomorphous to other related dodecamer DNA crystals. The structures have been solved by the molecular replacement method and refined by the constrained least-squares procedure to R-factors of approximately 16% at resolution of approximately 2.5 A. The two independent e6G-C base pairs in the DNA duplex adopt different base-pairing schemes. The e6G4-C21 base pair has a configuration similar to a normal Watson-Crick base pair, except with one three-centered hydrogen bond pair and one direct hydrogen bond between e6G4 and C21. In contrast, the e6G16-C9 base pair adopts a wobble configuration. The ethyl group is in the proximal orientation (to N7) in both base pairs. These observations enrich and support those found in the crystal structure of d(CGC[e6G]AATTCGCG), complexed to minor groove binding drugs Hoechst 33258 and Hoechst 33342 [Sriram et al. (1992) EMBO J. 11, 225-232]. We suggest that a dynamic equilibrium between these two configurations for the e6G-C base pair is likely and would present an ambiguous signal to the cellular transcription, replication, or repair mechanisms. In contrast, thymine can pair with e6G in only one way, albeit imperfect, mimicking a Watson-Crick base pair. This may be a plausible explanation of why thymine is found preferentially incorporated across the e6G during replication. In addition, we analyze the influence of the alkylation lesion on DNA and the molecular details of netropsin-DNA interaction. In the present two new netropsin complexes, the netropsin spans across five base pairs (starting halfway between C3-G22 and e6G4-C21 base pairs and ending at T8-A17 base pair) in the narrow minor groove. This is in contrast to the earlier crystal structure of netropsin complexed with another DNA dodecamer having the same AATT central core sequence, d(CGCGAATT[br5C]GCG) [Kopka et al. (1985) J. Mol. Biol. 272, 390-395]. In the latter structure, the netropsin lies between G4-br5C21 and br5C9-G16 base pairs.(ABSTRACT TRUNCATED AT 400 WORDS)

Additional antitumor ecteinascidins from a Caribbean tunicate: crystal structures and activities in vivo

Ecteinascidins (Ets), isolated from the Caribbean tunicate Ecteinascidia turbinata, protect mice in vivo against P388 lymphoma, B16 melanoma, M5076 ovarian sarcoma, Lewis lung carcinoma, and the LX-1 human lung and MX-1 human mammary carcinoma xenografts. Crystal structures of two tris(tetrahydroisoquinoline) Ets were investigated with single crystals of the 21-O-methyl-N12-formyl derivative of Et 729 and the natural N12-oxide of Et 743. Representatives of an additional class of Ets, Et 722 and Et 736, isolated from the same organism, were assigned tetrahydro-beta-carboline-substituted bis(tetrahydroisoquinoline) structures by NMR and fast atom bombardment MS spectra.

Unusual DNA conformation at low pH revealed by NMR: parallel-stranded DNA duplex with homo base pairs

We have investigated the conformational potentials of several DNA oligonucleotides containing sequences related to 5'-CGA in neutral pH and low pH (< 5.0) conditions. One-dimensional proton NMR spectra show that d(CGATCG), d(TCGATCGA), and d(CGATCGATCG) exhibit new sets of resonances at low pH (approximately 3.8-4.4), when compared to those from the neutral pH samples. The low pH form and the neutral pH form are in slow equilibrium. Analyses of the data suggest that these sequences under low pH conditions adopt structures distinct from B-DNA. Two-dimensional nuclear Overhauser effect spectroscopy (2D NOESY) data from the DNA hexamer d(CGATCG) of the neutral and low pH samples were used to analyze their respective structures in solution. An iterative NOE spectral-driven refinement procedure, SPEDREF [Robinson, H., & Wang, A. H.-J. (1992) Biochemistry 31, 3524-3533], was used to show that the neutral pH structure is close to canonical B-DNA. In contrast, analysis of the low pH form using the 2D NOESY data suggests that its structure is consistent with a right-handed parallel-stranded (PS) double helix with symmetrical non-Watson-Crick (C+:C, G:G, A:A, T:T) homo base pairs. Supporting evidence for the PS helix includes the asymmetric inversion-recovery relaxation times associated with the two ends of the helix. The structure is favored by the 5'-CGA sequence in which the cytosines provide the C+:C pairing for the nucleation step and the GpA step is significantly stabilized by the interstrand G-A stacking interactions.(ABSTRACT TRUNCATED AT 250 WORDS)

Conformational perturbation of the anticancer nucleotide arabinosylcytosine on Z-DNA: molecular structure of (araC-dG)3 at 1.3 A resolution

The left-handed Z-DNA structure of an araC-containing (where araC stands for arabinosylcytosine) hexamer, (araC-dG)3, has been solved by x-ray diffraction analysis at 1.3 A resolution. This hexamer was crystallized in the hexagonal P6(5)22 (a = b = 17.96 A, c = 43.22 A) space group in which the hexamers have statistically disordered packing arrangement along the 6(5) screw axis, yet the crystals diffract x-rays to high resolution. Its structure has been refined by the constrained least square refinement to a final R factor of 0.287 using 737 [> 3.0 sigma(F)] observed reflections. The asymmetric unit of the unit cell contains only a dinucleotide, 5'-p (araC)p(dG). The overall conformation resembles that of the canonical Z-DNA, but with some differences in details. The O2' hydroxyl groups of the araC residues form intramolecular hydrogen bonds with N2 of the 5'-guanine residues. In the deep groove of Z-DNA, these hydroxy groups replace the bridging water molecules that stabilize the guanine in the syn conformation. The results reinforce the earlier observation made by the structural analysis of another hexamer, d(CG[araC]GCG), with a mono-substitution of araC [M.-K. Teng, Y.-C. Liaw, G. A. van der Marel, J. H. van Boom, and A. H.-J. Wang (1989) Biochemistry, vol. 28, pp. 4923-4928]. These two structures show that araC residue can be incorporated readily into the Z structure and probably facilitates the B to Z transition, as supported by uv absorption spectroscopic studies in a number of araC-containing oligonucleotides. The potential biological roles of the araC-modified Z-DNA are discussed.

The matrix proteins of neurovirulent subacute sclerosing panencephalitis virus and its acute measles virus progenitor are functionally different

Persistence of measles virus in the brains of patients with subacute sclerosing panencephalitis (SSPE) is accompanied by changes in the viral matrix (M) protein. To understand the significance of these changes, cell culture and cell-free assays were developed to compare the functions of the M proteins of an SSPE virus Biken strain and its acute measles virus progenitor Nagahata strain. The Nagahata viral M protein is associated with the intracellular viral nucleocapsids and the plasma membrane, whereas the Biken viral M protein is localized mainly in the cytosol. The lack of M protein in the Biken viral nucleocapsids is due to a failure of the Biken M protein to bind to the viral nucleocapsids. The Biken M protein also fails to bind to the Nagahata viral nucleocapsids. Conversely, the Nagahata M protein can bind to the Biken viral nucleocapsids, although this association is not as stable at physiological salt concentration. These results offer concrete evidence that the M protein of an SSPE virus is functionally different from that of its progenitor acute measles virus.

A simple spectral-driven procedure for the refinement of DNA structures by NMR spectroscopy

We have developed a simple and quantitative procedure (SPEDREF) for the refinement of DNA structures using experimental two-dimensional nuclear Overhauser effect (2D NOE) data. The procedure calculates the simulated 2D NOE spectrum using the full matrix relaxation method on the basis of a molecular model. The volume of all NOE peaks is measured and compared between the experimental and the calculated spectra. The difference of the experimental and simulated volumes is minimized by a conjugated gradient procedure to adjust the interproton distances in the model. An agreement factor (analogous to the crystallographic R-factor) is used to monitor the progress of the refinement. The procedure is an The agreement is considered to be complete when several parameters, including the R-factor, the energy associated with the molecule, the local conformation (as judged by the sugar pseudorotation), and the global conformation (as judged by the helical x-displacement), are refined to their respective convergence. With the B-DNA structure of d(CGATCG) as an example, we show that DNA structure may be refined to produce calculated NOE spectra that are in excellent agreement with the experimental 2D NOE spectra. This is judged to be effective by the low R-factor of approximately 15%. Moreover, we demonstrate that not only are NOE data very powerful in providing details of the local structure but, with appropriate weighting of the NOE constraints, the global structure of the DNA double helix can also be determined, even when starting with a grossly different model. The reliability and limitations of a DNA structure as determined by NMR spectroscopy are discussed.

Molecular structures of two new anti-HIV nucleoside analogs: 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine and 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)hypoxanthine

The x-ray crystal structures of two new anti-HIV compounds, 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine (2'-F-dd-araA) and 9-(2,3-dideoxy-2-fluoro-beta-D-threo- pentofuranosyl)hypoxanthine (2'-F-dd-aral), have been determined at two temperatures. Both crystals are in the space group P2(1)2(1)2(1), and their structures were solved by direct methods. Least-squares refinement produced final R-factors of 0.027 for the 2'-F-dd-araA structure and of 0.044 for the 2'-F-dd-aral structure, respectively. The latter structure contains a two-fold disordered conformation of the sugar moiety. All three conformers (one for 2'-F-dd-araA and two for 2'-F-dd-aral) adopt an anti chi CN glycosyl torsion angle. The sugar in the 2'-F-dd-araA structure has a C2'-endo pucker conformation, whereas the sugar in the 2'-F-dd-aral structure has a mixture of C2'-endo and C3'-endo pucker conformations. When the sugar adopts the C2'-endo conformation, the torsion angle about the C4'-C5' bond is in a transgauche+ conformation. In contrast, when the sugar adopts the C3'-endo conformation, the torsion angle about the C4'-C5' bond is in a gauche(+)-gauche- conformation. The C2'-F bond distance is 1.406(3) A, similar to that found in other aliphatic C-F bonds. The results suggest that the 2'-fluoro-2',3'-dideoxyarabinosyl nucleosides do not have a strong preference for either C2'-endo or C3'-endo sugar pucker.

Unusual conformational flexibility in N1-substituted uncommon purine nucleosides. Crystal structure of 1-allyl-isoguanosine and 1-allyl-xanthosine

Several new N1-substituted uncommon purine nucleosides, including doridosine (1-methyl-isoguanosine; m-iG), 1-allyl-isoguanosine (a-iG) and 1-allyl-xanthosine (a-X), have been synthesized and tested as agonists for the adenosine receptors. Some have smooth muscle relaxant or negative chronotropic activities. The X-ray crystal structure of these compounds has been determined at atomic resolution in order to understand the structure-activity relationship. The structures were solved by direct methods and refined by full-matrix least-squares refinement procedure. The crystallographic parameters are: a-iG, space group P2(1), a = 10.573 (1) A, b = 21.955 (2) A, c = 14.360 (1) A, beta = 110.65 (1) degree, no. of 3 sigma Fo's = 4585, R = 0.047; a-X, space group P2(1)2(1)2(1), a = 16.015 (2) A, b = 16.239 (1) A, (1) A, c = 5.3723 (5) A, no. of 3 sigma Fo's = 1169, R = 0.031. In the a-iG crystal, there are 4 independent molecules (with different conformation) per asymmetric unit. While all 4 molecules adopt anti chi CN glycosyl torsion angle, their riboses have 3 distinct puckers (C2'-exo, C2'-endo and C1'-exo). In contrast, the a-X structure adopts a syn chi CN glycosyl torsion angle, which is stabilized by an intramolecular hydrogen bond between the N3 of purine base and the O5' of the ribose (in C2'-endo pucker). Both purine bases (a-iG and a-X) are mainly in the keto tautomer form. For the isoguanine base, the averaged N1-C2 bond distance (1.42 A) is significantly longer than that (1.375 A) of the guanine base. For the xanthine base, N3 nitrogen has an imino proton attached which is unambiguously located in the electron density map. The surprising flexibility in the ribose ring of these N1-substituted uncommon purine nucleosides suggests that the ribose moiety may not participate in the binding of nucleoside to the adenosine receptors.

Conformation of B-DNA containing O6-ethyl-G-C base pairs stabilized by minor groove binding drugs: molecular structure of d(CGC[e6G]AATTCGCG complexed with Hoechst 33258 or Hoechst 33342

O6-ethyl-G (e6G) is an important DNA lesion, caused by the exposure of cells to alkylating agents such as N-ethyl-N-nitrosourea. A strong correlation exists between persistence of e6G lesion and subsequent carcinogenic conversion. We have determined the three-dimensional structure of a DNA molecule incorporating the e6G lesion by X-ray crystallography. The DNA dodecamer d(CGC[e6G]AATTCGCG), complexed to minor groove binding drugs Hoechst 33258 or Hoechst 33342, has been crystallized in the space group P212121, isomorphous to other related dodecamer DNA crystals. In addition, the native dodecamer d(CGCGAATTCGCG) was crystallized with Hoechst 33342. All three new structures were solved by the molecular replacement method and refined by the constrained least squares procedure to R-factors of approximately 16% at approximately 2.0 A resolution. In the structure of three Hoechst drug-dodecamer complexes in addition to the one published earlier [Teng et al. (1988) Nucleic Acids Res., 16, 2671-2690], the Hoechst molecule lies squarely at the central AATT site with the ends approaching the G4-C21 and the G16-C9 base pairs, consistent with other spectroscopic data, but not with another crystal structure reported [Pjura et al. (1987) J. Mol. Biol., 197, 257-271]. The two independent e6G-C base pairs in the DNA duplex adopt different base pairing schemes. The e6G4-C21 base pair has a configuration similar to a normal Watson-Crick base pair, except with bifurcated hydrogen bonds between e6G4 and C21, and the ethyl group is in the proximal orientation. In contrast, the e6G16-C9 base pair adopts a wobble configuration and the ethyl group is in the distal orientation.(ABSTRACT TRUNCATED AT 250 WORDS)

Covalent modification of guanine bases in double-stranded DNA. The 1.2-A Z-DNA structure of d(CGCGCG) in the presence of CuCl2

We have solved the single crystal structure to 1.2-A resolution of the Z-DNA sequence d(CGCGCG) soaked with copper(II) chloride. This structure allows us to elucidate the structural properties of copper in a model that mimics a physiologically relevant environment. A copper(II) cation was observed to form a covalent coordinate bond to N-7 of each guanine base along the hexamer duplex. The occurrence of copper bound at each site was dependent on the exposure of the bases and the packing of the hexamers in the crystal. The copper at the highest occupied site was observed to form a regular octahedral complex, with four water ligands in the equatorial plane and a fifth water along with N-7 of the purine base at the axial positions. All other copper complexes appear to be variations of this structure. By using the octahedral complex as the prototype for copper(II) binding to guanine bases in the Z-DNA crystal, model structures were built showing that duplex B-DNA can accommodate octahedral copper(II) complexes at the guanine bases as well as copper complexes bridged at adjacent guanine residues by a reactive dioxygen species. The increased susceptibility to oxidative DNA cleavage induced by copper(II) ions in solution of the bases located 5' to one or more adjacent guanine residues can thus be explained in terms of the cation and DNA structures described by these models.

Molecular structure of a DNA decamber containing an anticancer nucleoside arabinosylcytosine: conformational perturbation by arabinosylcytosine in B-DNA

Arabinosylcytosine (araC) is an important anticancer drug that has been shown to be misincorporated into DNA double helix. The incorporation of araC into DNA may have significant conformational consequences that could affect the function of DNA. In this paper, we present the high-resolution 3D structure of an araC-containing decamer d[CCAGGC(araC)TGG], as determined by X-ray diffraction analysis, and assess the possible DNA structural perturbation induced by araC. The modified decamer was crystallized in the monoclinic C2 (a = 31.97 A, b = 25.56 A, c = 34.62 A and beta = 114.50 degrees) space group, the same as that from d(CCAGGCCTGG) [Heinemann, U., & Alings, C. (1989) J. Mol. Biol. 210, 369]. The structure of the araC-containing decamer was solved by the molecular replacement method and refined by the constrained least-squares refinement procedure to obtain a final R factor of 0.187 using 2349 [greater than 2.0 sigma(F)] observed reflections to a resolution of 1.6 A. The overall conformation resembles that of the canonical decamer DNA structure, but with significant differences in regions close to the araC site. The O2' hydroxyl groups of the araC residues lie in the major groove of the helix, and they are in close contact with the C5 methyl and C6 H6 atoms of the thymine on the 3'-side. This creates a higher buckle in the araC7-G14 base pair (14 degrees), as compared to that found in the canonical decamer (9 degrees). This may slightly destabilize B-DNA. No direct intramolecular hydrogen bond is formed, in contrast to the situation when araC is incorporated into Z-DNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular structure of antitumor drug steffimycin and modelling of its binding to DNA

The molecular and crystal structure of steffimycin have been determined by single crystal X-ray diffraction to 0.9 angstrom resolution. The triclinic crystals are in the space group P1, with the unit cell dimensions of a = 8.606(3) angstrom, b = 22.168(7) angstrom, c = 8.448(2) angstrom, alpha = 97.56(3) degrees, beta = 95.97(2) degrees, gamma = 87.94(3) degrees, Z = 2. The structure was solved by direct methods and refined by the full-matrix least-squares method to a final R value of 0.065 with 3405 (Inet greater than 2.0 sigma (Inet] observed reflections using the NRCVAX software package. The crystal lattice includes 2 independent steffimycin, 3 water and one 2-methyl-2,4-pentanediol molecules. The conformation of steffimycin is grossly similar to other anthracycline antibiotics including daunorubicin. The crystal packing interactions of steffimycin suggest a preferred stacking of the aglycone chromophore of the antibiotic which resembles the intercalative interactions seen in the daunorubicin-d(CGTACG) (Wang et al., Biochemistry 26, 1152 (1987] and nogalamycin-d(CGT(pS)ACG) (Liaw et al., Biochemistry 28, 9913 (1989] complexes. The atomic coordinates data from these complexes were used to model the intercalative binding of steffimycin to DNA. The models were then stereochemically idealized by the constraint refinement program NUCLSQ. Subsequently XPLOR software package was used for energy minimization of these models in vacuo. The model building studies suggest that steffimycin has a higher CpG base sequence specificity over the TpA step, similar to that of daunorubicin and nogalamycin.

Influence of aglycone modifications on the binding of anthracycline drugs to DNA: the molecular structure of idarubicin and 4-O-demethyl-11-deoxydoxorubicin complexed to d(CGATCG)

X-ray diffraction analyses of the complexes between two anthracycline antitumor compounds, idarubicin (IDR) and 4-O-demethyl-11-deoxydoxorubicin (ddDOX), with the DNA hexamer d(CGATCG) provided the detailed three-dimensional molecular structures at 1.7 A and 1.8 A resolution, respectively. Their structures have been refined with the constrained refinement procedure to final R-factors of 0.188 (1724 reflections for IDR) and 0.179 (1247 reflections for ddDOX). The overall structures of both complexes are similar to those of the previously studied DAU- and DOX-DNA complexes. In both complexes, two IDR (and ddDOX) molecules bind to the DNA hexamer double helix with the elongated aglycone chromophore intercalated between the CpG steps at both ends of the helix. The aglycone chromophore spans the GC Watson-Crick base pairs with its amino sugar lying in the minor groove where little structural difference is seen, compared with the daunorubicin-d(CGATCG) and doxorubicin-d(CGATCG) complexes. In contrast, the missing C4 methoxy of IDR and the missing methyl group at the O4 position of ddDOX result in a different binding surface in the major groove. The O4 hydroxyl group is capable of receiving and/or donating a hydrogen bond to proteins that bind to the drug-DNA complex. The missing O11 hydroxyl group in ring B creates an empty space in the intercalation cavity between the two GC base pairs, which appears to affect the stacking interactions between the aglycone and the DNA base pairs. Those structural changes in the major groove of the drug-DNA complexes due to the modifications of the aglycone chromophore may be responsible in part for the difference in their biological activities.