X-RAY STRUCTURAL STUDIES ON 3 ANALOGS OF THE ALPHA-ANOMER OF THE ANTITUMOR ANTIBIOTIC SHOWDOMYCIN - DIFFERENTIAL RING-PUCKERING EFFECTS OF HYDROXYL SUGAR SUBSTITUENTS IN LYXO AND ARABINO CONFIGURATIONS

The crystal structures of three a-analogues of the anititumour antibiotic showdomycin (1) have been determined at room temperature. They are 2-(a-D-2'- deoxyribofuranosyl)maleimide (2), 2-(a-D-arabinofuranosyl) maleimide (3) and 2-(a-D-lyxofuranosyl)- maleimide (4). The structures were refined to R factors of 0-039, 0-042 and 0-029 for 971, 1025 and 716 observed reflections. The conformational properties of the sugar rings are discussed in detail, in relation to the differing hydroxyl group substitutions. Compounds (2) and (3) have CY-endo, C4"-exo and CY-endo ring puckers, whereas (3) has C2"-endo, C l'-exo puckers. Compound (3) has an intramolecular hydrogen bond between the 05' and 02' hydroxyl groups. This and the sugar pucker difference are in accord with NMR chemical shift data for the O5' and O2' protons. Crystal data: compound (2), C9H11NOs, orthorhombic, P212~21, a = 5-916 (1), b = 8-191 (1), c = 19.691 (3) A, Z = 4; compound (3), C9HIINO6, orthorhombic, P212121, a = 6.785 (1), b = 8.006 (1), c = 17.564 (2) A, Z= 4; compound (4), C9HI1NO6, monoclinic, P2~, a = 8.681 (1), b = 5.135 (1), c= 11-364 (1) A, Z= 2

CRYSTAL AND MOLECULAR-STRUCTURE OF 2',3',5'-TRI-O-ACETYL-6-O-(MESITYLENESULPHONYL)GUANOSINE

The structure of a 6-O-mesitylenesulphonyl derivative of 2',3',5'-tri-O-acetylguanosine, C 24 H 29 N50 10 S, has been determined by X-ray diffraction. Crystals are monoclinic, a = 26.370 (4), b = 8.200 (2), c = 17.991 (3) A, fl = 132.77 (4) o. The solution of the structure in space group C2 was not straightforward and is described in detail. Refinement converged at R = 0.110 for 1102 observed reflections. The guanine base displays some deviations from its usual geometry due to the loss of C(6)-O(6) double-bond character. The ribose sugar is C(2')-endo puckered

Diffraction in low-energy electron scattering from DNA: bridging gas phase and solid state theory

Using high-quality gas phase electron scattering calculations and multiple scattering theory, we attempt to gain insights on the radiation damage to DNA induced by secondary low-energy electrons in the condensed phase, and to bridge the existing gap with the gas phase theory and experiments. The origin of different resonant features (arising from single molecules or diffraction) is discussed and the calculations are compared to existing experiments in thin films.Comment: 40 pages preprint, 12 figures, submitted to J. Chem. Phy

A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer

We report here that a tetra-substituted naphthalene-diimide derivative (MM41) has significant in vivo anti-tumour activity against the MIA PaCa-2 pancreatic cancer xenograft model. IV administration with a twice-weekly 15 mg/kg dose produces ca 80% tumour growth decrease in a group of tumour-bearing animals. Two animals survived tumour-free after 279 days. High levels of MM41 are rapidly transported into cell nuclei and were found to accumulate in the tumour. MM41 is a quadruplex-interactive compound which binds strongly to the quadruplexes encoded in the promoter sequences of the BCL-2 and k-RAS genes, both of which are dis-regulated in many human pancreatic cancers. Levels of BCL-2 were reduced by ca 40% in tumours from MM41-treated animals relative to controls, consistent with BCL-2 being a target for MM41. Molecular modelling suggests that MM41 binds to a BCL-2 quadruplex in a manner resembling that previously observed in co-crystal structures with human telomeric quadruplexes. This supports the concept that MM41 (and by implication other quadruplex-targeting small molecules) can bind to quadruplex-forming promoter regions in a number of genes and down-regulate their transcription. We suggest that quadruplexes within those master genes that are up-regulated drivers for particular cancers, may be selective targets for compounds such as MM41

Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation

DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn-syn, water mediated anti-syn and syn-syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5' intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation

Modelling the regulation of telomere length: the effects of telomerase and G-quadruplex stabilising drugs

Telomeres are guanine-rich sequences at the end of chromosomes which shorten during each replication event and trigger cell cycle arrest and/or controlled death (apoptosis) when reaching a threshold length. The enzyme telomerase replenishes the ends of telomeres and thus prolongs the life span of cells, but also causes cellular immortalisation in human cancer. G-quadruplex (G4) stabilising drugs are a potential anticancer treatment which work by changing the molecular structure of telomeres to inhibit the activity of telomerase. We investigate the dynamics of telomere length in different conformational states, namely t-loops, G-quadruplex structures and those being elongated by telomerase. By formulating deterministic differential equation models we study the effects of various levels of both telomerase and concentrations of a G4-stabilising drug on the distribution of telomere lengths, and analyse how these effects evolve over large numbers of cell generations. As well as calculating numerical solutions, we use quasicontinuum methods to approximate the behaviour of the system over time, and predict the shape of the telomere length distribution. We find those telomerase and G4-concentrations where telomere length maintenance is successfully regulated. Excessively high levels of telomerase lead to continuous telomere lengthening, whereas large concentrations of the drug lead to progressive telomere erosion. Furthermore, our models predict a positively skewed distribution of telomere lengths, that is, telomeres accumulate over lengths shorter than the mean telomere length at equilibrium. Our model results for telomere length distributions of telomerase-positive cells in drug-free assays are in good agreement with the limited amount of experimental data available

Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction

The use of a small molecule compound to reduce toxic repeat RNA transcripts or their translated aberrant proteins to target repeat-expanded RNA/DNA with a G4C2 motif is a promising strategy to treat C9orf72-linked disorders. In this study, the crystal structures of DNA and RNA-DNA hybrid duplexes with the -GGGCCG- region as a G4C2 repeat motif were solved. Unusual groove widening and sharper bending of the G4C2 DNA duplex A-DNA conformation with B-form characteristics inside was observed. The G4C2 RNA-DNA hybrid duplex adopts a more typical rigid A form structure. Detailed structural analysis revealed that the G4C2 repeat motif of the DNA duplex exhibits a hydration shell and greater flexibility and serves as a 'hot-spot' for binding of the anthracene-based nickel complex, NiII(Chro)2 (Chro = Chromomycin A3). In addition to the original GGCC recognition site, NiII(Chro)2 has extended specificity and binds the flanked G:C base pairs of the GGCC core, resulting in minor groove contraction and straightening of the DNA backbone. We have also shown that Chro-metal complexes inhibit neuronal toxicity and suppresses locomotor deficits in a Drosophila model of C9orf72-associated ALS. The approach represents a new direction for drug discovery against ALS and FTD diseases by targeting G4C2 repeat motif DNA

Phase transition of a single star polymer: a Wang-Landau sampling study

Star polymer is a typical nonlinear macromolecule possessing special thermodynamic behaviors for the existence of a jointing point. The thermodynamic transitions of a single star polymer are systematically studied with bond fluctuation model using Wang-Landau sampling technique. A new analysis method applying the shape factor is proposed to determine coil-globule (CG) and liquid-crystal (LC) transitions, which shows higher efficiency and precision than canonical specific heat function. It is found that the LC transition of star polymer at lower temperature obeys the identical scaling law as linear polymer. With the increase of the arm density of star polymer, however, the CG transition point, corresponding to {\theta} temperature, shifts towards the LC transition and the reason comes from the high density arms of star polymer, which requires the lower temperature for attracting force to overcome the volume excluding effects of chain. This work clearly demonstrates that the distinction of linear and star polymers in structures only affects CG transition and has no influence on LC transition.Comment: 30 pages, 10 figures, submit to JC