Solution structure of the sequence-specific HMG box of the lymphocyte transcriptional activator Sox-4.

Two groups of HMG box proteins are distinguished. Proteins in the first group contain multiple HMG boxes, are non-sequence-specific, and recognize structural features as found in cruciform DNA and cross-over DNA. The abundant chromosomal protein HMG-1 belongs to this subgroup. Proteins in the second group carry a single HMG box with affinity for the minor groove of the heptamer motif AACAAAG or variations thereof. A solution structure for the non-sequence-specific C-terminal HMG box of HMG-1 has recently been proposed. Now, we report the solution structure of the sequence-specific HMG-box of the SRY-related protein Sox-4. NMR analysis demonstrated the presence of three alpha-helices (Val10-Gln22, Glu30-Leu41 and Phe50-Tyr65) connected by loop regions (Ser23-Ala49 and Leu42-Pro49). Helices I and II are positioned in an antiparallel mode and form one arm of the HMG box. Helix III is less rigid, makes an average angle of about 90 degrees with helices I and II, and constitutes the other arm of the molecule. As in HMG1B, the overall structure of the Sox-4 HMG box is L-shaped and is maintained by a cluster of conserved, mainly aromatic residues.

The solution structure of a DNA duplex containing the cis-Pt(NH3)2[d(-GTG-)-N7(G),N7(G)] adduct, as determined with high-field NMR and molecular mechanics/dynamics.

The solution structure of the cis-Pt-GTG adduct in the double-stranded oligomer d(CTCTAGTGCTCAC).td(GTGAGCACTAGAG) was studied with high-resolution NMR techniques. For model building, the distance information obtained from two-dimensional NOE experiments was used in molecular mechanic computations and molecular dynamic structure refinements. The structural distortion upon platination appears to be restricted to the base pairs Pt-G6.C21 and T7.A20; Pt-G8.C19 forms a normal Watson-Crick base pair. T7 is positioned in the minor groove and stacks with the highly propeller-twisted Pt-G6. There is no hydrogen bonding between T7 and A20. The complementary strand is undistorted; A20 stacks with its flanking cytidines (C19 and C21) as in regular B-DNA. The duplex is locally unwound (from base pair A5.T22 to G8.C19: 19 degrees) and is slightly kinked (20 degrees) at the platination site. The platinum coordination distorts the DNA structure at the 5' side of the platinated-GTG-sequence and changes the minor groove face.

The antitumor drug nogalamycin forms two different intercalation complexes with d(GCGT).d(ACGC).

The structures of the physical complex of d(GCGT).d(ACGC) with the anthracycline antitumor drug nogalamycin were studied in order to determine the sequence specificity and the drug orientation at the symmetric d(C2G3).d(C6G7) binding site of this oligonucleotide. For this purpose, one- and two-dimensional NMR techniques were used in combination with molecular mechanics and molecular dynamics computations. Analysis of the NMR spectra reveals that nogalamycin forms two different intercalation complexes with d(GCGT).d(ACGC). These complexes are called complex I and complex II and are present in a ratio of 0.45:0.55. In both complexes the nogalamycin is intercalated at the d(C2G3).d(C6G7) sequence with the bicyclic and nogalose sugars residing in the major and minor groove, respectively. This results in a buckling of the flanking base pairs and a doubling of the inter-base-pair distances at the intercalation site. In complex I, the aglycon ring of the drug stacks with the C6-G7 bases, and the sugars are directed to the G1.C8 end; while in the case of complex II the anthraquinone ring system is stacked with C2-G3 bases, and the sugars are pointed to the T4.A5 base pair end. The two nogalamycin-d(GCGT).d(ACGC) structures are stabilized by intra- and intermolecular hydrogen bonds, electrostatic interactions, and van der Waals contacts. Comparison of different nogalamycin-oligonucleotide structures reveals a nogalamycin binding specificity to the 3'-side of the cytosine base in cytosine-purine sequences in double-stranded DNA.

A circular dichroism study on the conformation of d(CGT) modified with N-acetyl-2-aminofluorene or 2-aminofluorene.

The trinucleotide d(CGT) was modified by covalent binding of the carcinogen N-acetyl-2-aminofluorene (AAF) or 2-aminofluorene (AF) at the C8 position of the guanine base. The conformations of d(CGT)-AAF and -AF were studied by comparing the absorption and circular dichroism properties with those of dCMP + dGMP-AAF or -AF + dTMP in a molar ratio of 1:1:1 and AAF- and AF-containing dGMP. For both AAF- and AF-d(CGT) complexes the results show significant stacking interactions between the fluorene residue and the base(s) and are discussed in terms of the conformation of d(CGT)-AAF and -AF. In d(CGT)-AF we observe a clear interaction between AF and thymine, whereas the C-G stack is still intact. In the case of d(CGT)-AAF the C-G stack is weakened and the glycosidic rotation angle of dGuo-C8-AAF is most probably syn. The specific fluorene-base interactions persist at elevated temperatures. The carcinogen-base interactions are stronger in the AAF-carrying d(CGT) than in the case of the deacetylated complex. This is consistent with the higher mobility of the AF-adduct and its conformationally heterogeneous appearance in DNA.

The fluorescence emission properties of dGuo-C8-AAF, dGuo-C8-AF and the imidazole ring-opened products of dGuo-C8-AF indicate a different dynamic structure for the various compounds.

The reactive metabolites of the carcinogenic N-acetyl-2-aminofluorene (AAF) form adducts with the guanine base of DNA. The fluorescence emission characteristics of N-(deoxy-guanosin-8-yl)-N-acetyl-2-aminofluorene (dGuo-C8-AAF), N-(deoxyguanosin-8-yl)-2-aminofluorene (dGuo-C8-AF) and the two N7 = C8 imidazole ring-opened products of dGuo-C8-AF (ro-dGuo-C8-AF I + II) were investigated and related to their conformational properties. The dGuo-C8-AF adduct (phi F congruent to 4-5 X 10(-4) shows a broad and structureless emission band, which is attributed to the formation of an excited-state complex. In contrast, the emission spectra of dGuo-C8-AAF (phi F congruent to 1.10(-4] and both ro-dGuo-C8-AF compounds [phi F(ro-dGuo-C8-AF I) congruent to 4.10(-3); phi F(ro-dGuo-C8-AF II) congruent to 4.10(-4)] are narrow. This indicates that dGuo-C8-AAF and ro-dGuo-C8-AF I + II do not decay into an exciplex as occurs in dGuo-C8-AF. The spectroscopic features are discussed in terms of the differences in the dynamic structure of the various compounds.

Excited state properties of the N-(deoxyguanosin-8-yl)-2-aminofluorene adducts.

The spectroscopic characteristics of adducts derived from the covalent binding of the carcinogen 2-aminofluorene to the C8 position of deoxyguanosine [N-(deoxyguanosin-8-yl)-2-amino-fluorene, dGuo-C8-AF], and from an adduct of similar structure formed with the synthetic polynucleotide poly(dG-dC).poly(dG-dC), were investigated. At 77 K both adducts are characterized by well-defined and rather narrow fluorescence emission spectra with maxima at 370 and 390 nm characteristic of the aromatic, monomolecular 2-aminofluorene (AF) residue. In contrast, at room temperature, the fluorescence is characterized by a broad, structureless emission band with a maximum at 460 nm in aqueous mixtures, shifting to 415 nm in solvents of lower polarity (100% propanol); the maxima are located at intermediate wavelengths in solutions of different propanol/water compositions, and this emission is attributed to an excited state complex (exciplex). The fluorescence quantum yield decreases when either the solvent polarity or the temperature are increased, varying from 5.4% (100% propanol) to 0.04-0.05% (100% H2O). The fluorescence decay profiles of dGuo-C8-AF adducts (measured at the National Synchrotron Light Source facility at the Brookhaven National Laboratory) can be roughly, but not exactly, modeled in terms of two exponential decay components in the range of about 0.3-1.0 ns with the propanol concentration greater than 60%; at lower propanol concentrations, a single short lifetime is observed and in 100% water solutions its value is 0.08 ns. The shorter lifetime, favored in solvent mixtures of higher polarities, is attributed to an exciplex with significant charge-transfer character.(ABSTRACT TRUNCATED AT 250 WORDS)

A spectroscopic study of the conformation of poly d(G-C).poly d(G-C) modified with the carcinogenic 2-aminofluorene.

The conformational properties of both the B- and Z-form helix of the 2-aminofluorene (AF) modified synthetic polynucleotide poly d(G-C).poly d(G-C) were extensively studied with a variety of optical techniques (UV absorbance, linear dichroism, circular dichroism and fluorescence spectroscopy). The spectroscopic results show, that: (i) the presence of the AF adduct in poly d(G-C).poly d(G-C) facilitates the conversion of the right-handed B-form polynucleotide to the left-handed Z-type poly d(G-C).poly d(G-C) duplex; (ii) in B- as well as in Z-form poly d(G-C).poly d(G-C)-AF the carcinogenic residue is situated in a specific and ordered complex with the DNA, in which the AF chromophore is significantly immobilized and the long axis of the fluorene ring system is positioned in a parallel mode to the DNA base planes; (iii) in B-type poly d(G-C).poly d(G-C)-AF the carcinogenic residue exhibits strong stacking interactions with the adjacent DNA bases, which are coupled to an important destabilization of the AF-containing B-duplex; (iv) in contrast to the B-form complex, the AF-containing Z-type DNA is highly stabilized and a remarkable reduction of the AF-base interactions is observed; (v) in Z-form poly d(G-C).poly d(G-C)-AF the AF chromophore resides at a medium-exposed position. The combined data support a conformational model, in which the planar AF is inserted in the B-type polynucleotide helix, while the carcinogenic residue in the Z-form poly d(G-C).poly d(G-C)-AF structure is placed in an outside position.

An optical study of the conformation of the aminofluorene-DNA complex.

Calf thymus DNA was modified with 2-aminofluorene (AF) to different extents by treatment with N-hydroxy-2-aminofluorene. The AF-modified DNAs together with free AF, the AF-modified guanine (Gua-C8-AF) and the AF-modified deoxyguanosine (dGuo-C8-AF) were subsequently studied by u.v. absorbance, linear dichroism and fluorescence spectroscopy. The emission and absorption properties of double-stranded DNA-AF and single-stranded DNA-AF closely resemble those of dGuo-C8-AF. The emission spectra of these three compounds show a broad, red-shifted emission, characteristic for exciplex formation. The linear dichroism and circular dichroism spectra of double-stranded DNA-AF show that the AF moiety forms a well-defined, regular structure. The dichroic ratio in the 310-340 nm region is constant, which indicates the presence of only one type of adduct. The long-wavelength transition moment of this adduct makes an angle of 72-74 degrees with the DNA helix axis. The binding of AF to double-stranded is DNA is accompanied by a destabilization of the DNA helix structure, a strong quenching of the AF emission quantum yield, intense AF circular dichroism and an apparent immobilization of the dGuo-C8-AF complex. In single-stranded DNA-AF, the AF conformation appears more random, although the interactions between AF and the surrounding bases persist. The strong interactions between AF and the surrounding bases which dominate the optical properties of the studied complexes, the significant destabilization of the DNA double helix after modification with AF, and the relatively small angle between AF and the base planes support a model in which the adduct is inserted into the DNA helix.