G.A. van der Marel

Molecular structure of a left-handed double helical DNA fragment at atomic resolution.

The DNA fragment d(CpGpCpGpCpG) crystallises as a left-handed double helical molecule with Watson–Crick base pairs and an antiparallel organisation of the sugar phosphate chains. The helix has two nucleotides in the asymmetric unit and contains twelve base pairs per turn. It differs significantly from right-handed B-DNA.

Iterative procedure for structure determination from proton-proton NOEs using a full relaxation matrix approach. Application to a DNA octamer

Abstract A method is proposed, called the iterative relaxation matrix approach (IRMA), for the structure determination of biomolecules in solution based on 2D NOE data. Proton-proton distances are determined in a way in which indirect magnetization transfer (spin diffusion) is taken fully into account. In this method experimental NOEs are combined with calculated NOE values based on a molecular model. Back-transformation of this mixed NOE matrix gives a relaxation matrix which provides a better estimation of the cross-relaxation rates than can be obtained directly from the NOE cross peaks. From the cross-relaxation rates distance constraints can be derived, which are used in restrained molecular dynamics calculations to obtain an improved molecular model. The iteration cycle can be repeated until all experimental NOE values are satisfactorily explained. The method was tested with a DNA octamer, d(GCGTTGCG)·d(CGCAACGC).

Molecular Structure of the Netropsin-d(CGCGATATCGCG) Complex: DNA Conformation in an Alternating AT Segment

The molecular structure of the complex between a minor groove binding drug (netropsin) and the DNA dodecamer d(CGCGATATCGCG) has been solved and refined by single-crystal X-ray diffraction analysis to a final R factor of 20.0% to 2.4-A resolution. The crystal is similar to that of the other related dodecamers with unit cell dimensions of a = 25.48 A, b = 41.26 A, and c = 66.88 A in the space group P2(1)2(1)2(1). In the complex, netropsin binds to the central ATAT tetranucleotide segment in the narrow minor groove of the dodecamer B-DNA double helix as expected. However, in the structural refinement the drug is found to fit the electron density in two orientations equally well, suggesting the disordered model. This agrees with the results from solution studies (chemical footprinting and NMR) of the interactions between minor groove binding drugs (e.g., netropsin and distamycin A) and DNA. The stabilizing forces between drug and DNA are provided by a combination of ionic, van der Waals, and hydrogen-bonding interactions. No bifurcated hydrogen bond is found between netropsin and DNA in this complex due to the unique dispositions of the hydrogen-bond acceptors (N3 of adenine and O2 of thymine) on the floor of the DNA minor groove. Two of the four AT base pairs in the ATAT stretch have low propeller twist angles, even though the DNA has a narrow minor groove. Alternating helical twist angles are observed in the ATAT stretch with lower twist in the ApT steps than in the TpA step.

A new approach to the synthesis of phosphotriester intermediates of nucleosides and nucleic acids

Abstract Aryl phosphorodichloridates can be converted by means of 1-hydroxybenzotriazole into an effective phosphorylating agent, which can be applied to the synthesis of phosphotriester intermediates of nucleic acids.

A convenient and general approach to the synthesis of properly protected d-nucleoside-3′-hydrogenphosphonates via phosphite intermediates

Abstract Evidence will be presented to show that the monofunctional phosphitylating reagents bis(N,N-di-ethylamino)chlorophosphine and salicylchlorophosphine are very effective for the preparation of 5′-0,N-protected d-nucleoside-3′-hydrogenphosphonates.

Structure, kinetics and thermodynamics of DNA hairpin fragments in solution.

The hairpin-to-coil equilibrium of the hexadecadeoxynucleotide d(ATCCTATTTTTAGGAT) was extensively studied by means of NMR, T-jump and UV. The thermodynamic and kinetic parameters for this equilibrium were determined, yielding a consistent picture of the dynamical behavior of this hairpin structure, which is shown to be a clear example of a situation in which the linebroadening of the imino proton resonances is not determined by the lifetime of the double helix. A comparative study of the homologous hairpins in which the size of the loop was elongated from 4 to 7 thymidine residues shows a monotonous decrease in Tm for the hairpin-to-coil transitions. This finding is in contrast with the view that the stability of hairpins reaches a maximum with a loop size of 6-7 residues. The NMR results indicate that the accessibility of the thymine bases in the loop towards solvent molecules or complementary nucleotides greatly depends on the size of the loop.

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)

Structures of mismatched base pairs in DNA and their recognition by the Escherichia coli mismatch repair system.

The Escherichia coli mismatch repair system does not recognize and/or repair all mismatched base pairs with equal efficiency: whereas transition mismatches (G X T and A X C) are well repaired, the repair of some transversion mismatches (e.g. A X G or C X T) appears to depend on their position in heteroduplex DNA of phage lambda. Undecamers were synthesized and annealed to form heteroduplexes with a single base‐pair mismatch in the centre and with the five base pairs flanking each side corresponding to either repaired or unrepaired heteroduplexes of lambda DNA. Nuclear magnetic resonance (n.m.r.) studies show that a G X A mismatch gives rise to an equilibrium between fully helical and a looped‐out structure. In the unrepaired G X A mismatch duplex the latter predominates, while the helical structure is predominant in the case of repaired G X A and G X T mismatches. It appears that the E. coli mismatch repair enzymes recognize and repair intrahelical mismatched bases, but not the extrahelical bases in the looped‐out structures.

Synthesis of 1-O-(1,2-di-O-palmitoyl-sn-glycero-3-phospho)-d-myo-inositol 4,5-bisphosphate: an analogue of naturally occurring (ptd)Ins(4,5)P2

Abstract Optically active 2,3,6-tri-O-benzyl-4,5-di-O-(trans-prop-1-enyl)-D-myo-inositol and 1,2-di-O-palmitoyl-sn-glycerol were coupled using mono- and bifunctional phosphitylating reagents to yield, after final removal of all benzyl-protecting groups the chiral title compound.

Peptides containing a sulfinamide or a sulfonamide moiety: new transition-state analogues

A versatile synthesis of two new types of transition-state analogues of the amide bond hydrolysis is described: the sulfinamide and the sulfonamide moiety. These transition-state analogues are part of peptides which will be used for the generation of catalytic antibodies as well as for development of protease inhibitors.