Intrinsic Bent DNA Sites in the Developmentally Amplified C3-22 Gene Promoter of Rhynchosciara americana (Diptera: Sciaridae)

The Rhynchosciara americana C3-22 gene is located in an amplified domain and is developmentally expressed. The aim of the present work was to identify intrinsically bent DNA sites in a segment containing the gene promoter and downstream sequence. The results indicated that this gene is flanked by intrinsically bent DNA sites. Three bent DNA sites (b^?3, b^?2, and b^?1) were localized in the promoter, and one was localized downstream of the gene (b⁺¹). These sites had helical parameters that confirmed the curved structure, as well as segments with left-handed superhelical writhe. In silico analysis of the promoters of four other insect genes, which encode secreted polypeptides, showed that they all had curved structures and similar helical parameters. Correlation with other results indicates that the detected intrinsically bent DNA sites that flank the C3-22 gene might be a consensus feature of the gene structure in the amplified domains.     

Electrostatic calculations and model-building suggest that DNA bound to CAP is sharply bent

Two observations suggest that DNA, upon binding to E. coli catabolite gene activator protein (CAP), is sharply bent by a total angle of at least 100-150 degrees: (1) The electrostatic potential field of CAP shows regions of positive potential that form a ramp on 3 sides of the protein. (2) The DNA binding site size as determined by DNA ethylation interference with binding, (Majors: "Control of the E. coli Lac Operon at the Molecular Level." Ph.D. Thesis, Harvard University, Cambridge, 1977) and by relative affinities of DNA fragments of various lengths (Liu-Johnson et al.: Cell 47:995-1005, 1986) requires severe bending of the DNA to maintain its favorable electrostatic contact with the protein.     

Induction of developmental toxicity in mice treated with Alstonia scholaris (Sapthaparna) In utero

BACKGROUND: The teratogenic effect of hydroalcoholic extract of Alstonia scholaris (ASE) was studied in the pregnant Swiss albino mice administered with 0, 60, 120, 240, 360, and 480 mg/kg ASE on Day 11 of gestation. METHODS: Females were allowed to complete the term and parturiate. The litters were monitored regularly for mortality, growth retardation, congenital malformations, and appearance of physiological markers up to 7 weeks post‐parturition (p.p.). RESULTS: The administration of 60, 120, 180, and 240 mg/kg ASE to the pregnant mice on Day 11 did not induce mortality, congenital malformations, or alter the normal growth patterns. A further increase in the herbal extract dose up to 360 or 480 mg/kg resulted in a dose dependent increase in the mortality, growth retardation, and congenital malformations, characterized mainly by bent tails and syndactyly. The administration of higher doses (360 or 480 mg) of ASE also caused a significant delay in the morphological parameters such as fur development, eye opening, pinna detachment, and vaginal opening. The incisor eruption and testes decent were found to be delayed in litters born to the mothers treated with 240–480 mg/kg ASE. CONCLUSIONS: Our study indicates clearly that ASE treatment caused teratogenic effect only at doses above 240 mg/kg (>20% of LD₅₀). Lower doses had no developmental toxicity. Birth Defects Res B 68:472–478, 2003. © 2003 Wiley‐Liss, Inc.     

Scaffold/matrix attachment regions and intrinsic DNA curvature

Recent approaches have failed to detect nucleotide sequence motifs in Scaffold/Matrix Attachment Regions (S/MARs). The lack of any known motifs, together with the confirmation that some S/MARs are not associated to any peculiar sequence, indicates that some structural elements, such as DNA curvature, have a role in chromatin organization and on their efficiency in protein binding. Similar to DNA curvature, S/MARs are located close to promoters, replication origins, and multiple nuclear processes like recombination and breakpoint sites. The chromatin structure in these regulatory regions is important to chromosome organization for accurate regulation of nuclear processes. In this article we review the biological importance of the co-localization between bent DNA sites and S/MARs. Published in Russian in Biokhimiya, 2006, Vol. 71, No. 5, pp. 598–606.     

Intrinsically bent DNA sites in the <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> third chromosome amplified domain

Bent DNA sites promote the curvature of DNA in both eukaryotic and prokaryotic chromosomes. Here, we investigate the localization and structure of intrinsically bent DNA sites in the extensively characterized Drosophila melanogaster third chromosome DAFC-66D segment (Drosophila amplicon in the follicle cells). This region contains the amplification control element ACE3, which is a replication enhancer that acts in cis to activate the major replication origin ori-β. Through both electrophoretic and in silico analysis, we have identified three major bent DNA sites in DAFC-66D. The bent DNA site (b1) is localized in the ACE3 element, whereas the other two bent DNA sites (b2 and b3) are localized in the ori-β region. Four additional bent DNA sites were identified in the intron of the S18 gene and near the TATA box of the S15, S19, and S16 genes. The identification of DNA bent sites in genomic regions previously characterized as functionally relevant for DNA amplification further supports a function for DNA bent sites in DNA replication in eukaryotes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Intrinsic chiral domains enantioselectively segregated from twisted nematic cells of bent-core mesogens

Enantioselective segregation has been attained in the Bx phase of a novel substituted oxadiazole achiral banana-shaped liquid crystal (LC) without introducing any chiral species. This bent-core molecule exhibits LC polymorphism; the higher temperature nematic (N) phase and the lower temperature banana smectic phase (Bx phase), in which spontaneous chiral segregation with (+) and (-) chiral domains occurs with equal probabilities. In twisted cell geometries, extrinsically induced twisted N structures are formed and result in intrinsically chiral conglomerate when the temperature is decreased from N to Bx. The observed optical activity in homochiral Bx phase is comparable to those theoretically predicted and is proportional to the cell thickness.     

Availability of fluoride to plants grown in contaminated soils

Two pot experiments were carried out to study uptake of fluoride (F) in clover and grasses from soil. Fluoride concentrations in t Trifolium repens (white clover) and t Lolium multiflorium (ryegrass) were highly correlated with the amounts of H₂O– and 0.01 t M CaCl₂–extractable F in soil when increasing amounts of NaF were added to two uncontaminated soils (r=0.95–0.98, t p<0.001). The amounts of H₂O– or 0.01 t M CaCl₂–extractable F did not explain the F concentrations to a similar extent in t Agrostis capillaris (common bent) grown in 12 soils (Cambic Arenosols) collected from areas around the Al smelters at Å: rdal and Sunndal in Western Norway (r=0.68–0.78). This may be due to variation in soil pH and other soil properties in the 12 soils. Soil extraction with 1 t M HCl did not estimate plant–available F in the soil as well as extraction with H₂O or 0.01 t M CaCl₂. Fluoride and Al concentrations in the plant material were positively correlated in most cases. Fluoride and Ca concentrations in the plant material were negatively correlated in the first experiment. No consistent effects were found on the K or Mg concentrations in the plant material. The F accumulation in clover was higher than in the grasses. The uptake from soil by grasses was relatively low compared to the possible uptake from air around the Al smelters. The uptake of F in common bent did not exceed the recommended limit for F contents in pasture grass (30 mg kg^–1) from soil with 0.5–28 mg F(H₂O) kg^–1 soil. The concentration in ryegrass was about 50 mg F kg^–1 when grown in a highly polluted soil (28 mg F(H₂O) kg^–1 soil). Concentrations in clover exceeded 30 mg F kg^–1 even in moderately polluted soil (1.3–7 mg F(H₂O) kg^–1 soil). Liming resulted in slightly lower F concentrations in the plant material.     

Base triplet nonisomorphism strongly influences DNA triplex conformation: effect of nonisomorphic G* GC and A* AT triplets and bending of DNA triplexes

Structural understanding of DNA triplexes is grossly inadequate despite their efficacy as therapeutic agents. Lack of structural similarity (isomorphism) of base triplets that figure in different DNA triplexes brings in an added complexity. Recently, we have shown that the residual twist (Deltat degrees ) and the radial difference (Deltar A) adequately define base triplet nonisomorphism in structural terms and allow assessment of their role in conferring stability as well as sequence-dependent structural variations in DNA triplexes. To further corroborate these, molecular dynamics (MD) simulations are carried out on DNA triplexes comprising nonisomorphic G* GC and A* AT base triplets under different sequential contexts. Base triplet nonisomorphism between G* GC and A* AT triplets is dominated by Deltat degrees (9.8 degrees ), in view of small Deltar (0.2 A), and is in contrast to G* GC and T* AT triplets where both Deltat degrees (10.6 degrees ) and Deltar (1.1A) are prominent. Results show that Deltat degrees alone enforces mechanistic influence on the triplex-forming purine strand so as to favor a zigzag conformation with alternating conformational features that include high (40 degrees ) and low (20 degrees ) helical twists, and high anti(G) and anti(A) glycosyl conformation. Higher thermal stability of this triplex compared to that formed with G* GC and T* AT triplets can be traced to enhanced base-stacking and counterion interactions. Surprisingly, it is found for the first time that the presence of a nonisomorphic G* GC or A* AT base triplet interrupting an otherwise mini A* AT or G* GC isomorphic triplex can induce a bend/curvature in a DNA triplex. These observations should prove useful in the design of triplex-forming oligonucleotides and in the understanding the binding affinities of this triplex with proteins.