Interruptions of (CG)n sequences by GG, TG and CA need not prevent B to Z transition in solution

Oligonucleotides containing alternating purines-pyrimidines with AT base pairs have been shown to exist in the Z-form preferably in solid state. We report that oligodeoxyribonucleotides with GG, TG and CA interruptions in their alternating CG sequences can undergo B to Z transition in solution in the absence of any chemical modification or topological constraint. The sequences, d(CGCGCGGCGCGC) and d(CGTGCGCACG) have been synthesised and shown to adopt Z- conformation in presence of millimolar concentrations of Ni2+ under low water activity conditions. Significance of GG, TG and CA interruptions in the B to Z transition is discussed.

Distribution of simple repetitive (TG/CA)n and (CT/AG)n sequences in human and rodent genomes

Sixteen million nucleotide sequence of genome of various organisms have been analysed to detect and study the extent of occurrence of simple repetitive sequences. Two sequence motifs (TG/CA)n and (CT/AG)n capable of adopting unusual DNA structures, left handed Z-conformation and triple-helical conformation respectively, are found to be abundant in rodent and human genomes, but almost completely absent in bacterial genome. (TG/CA)n and (CT/AG)n sequences are present mostly in the intron or 5'/3' flanking regions of the genes. The presence of such repeat motifs in genomic sequence of higher eukaryotes has been correlated with their possible functional significance in nucleosome organization, recombination and gene expression.

Thermal decomposition of zirconyl oxalates I. Barium zirconyl oxalate

Conditions for the preparation of stoichiometric barium zirconyl oxalate heptahydrate (BZO) have been standardized. The thermal decomposition of BZO has been investigated employing TG, DTG and DTA techniques and chemical and gas analysis. The decomposition proceeds through four steps and is not affected much by the surrounding gas atmosphere. Both dehydration and oxalate decomposition take place in two steps. The formation of a transient intermediate containing both oxalate and carbonate groups is inferred. The decomposition of oxalate groups results in a carbonate of composition Ba2Zr2O5CO3, which decomposes between 600 and 800° and yields barium zirconate. Chemical analysis, IR spectra and X-ray powder diffraction data support the identity of the intermediate as a separate entity.Die Bedingungen für die Herstellung von stöchiometrischem Barium-zirconyl-oxalat Heptahydrat (BZO) wurden standardisiert. Die thermische Zersetzung von BZO wurde unter Einsatz der TG-, DTG- und DTA, sowie der chemischen und Gasanalyse untersucht. Die Zersetzung verläuft über vier Stufen und wird von der umgebenden Gasathmosphäre nicht besonders beeinflusst. Sowohl die Dehydratisierung als auch die Oxalatzersetzung erfolgt in zwei Stufen. Die Bildung einer intermediären Übergangsverbindung mit sowohl Oxalat- als auch Carbonatgruppen wirken hierbei mit. Die Zersetzung der Oxalatgruppen ergibt ein Carbonat der Zusammensetzung Ba2Zr2O5CO3, das zwischen 600 und 800° zersetzt wird und Bariumzirconat ergibt. Die Angaben der chemischen Analyse, der IR-Spekren und der Röntgen-Pulver-Diffraktion unterstützen die Identität der Intermediärverbindung als eine separate Einheit.On a standardisé les conditions de préparation de l'oxalate heptahydraté de zirconyle et de baryum (BZO) stoechiométrique. On a étudié la décomposition thermique de BZO par TG, TGD et ATD ainsi que par analyses chimiques et analyses des gaz. La décomposition a lieu en quatre étapes et n'est pas trop influencée par l'atmosphère ambiante. La déshydratation et la décomposition de l'oxalate ont lieu en deux étapes. Il se forme un composé intermédiaire de transition contenant à la fois les groupes oxalate et carbonate. La décomposition des groupes oxalate fournit un carbonate de composition Ba2Zr2O5CO3 qui se décompose entre 600 et 800° pour fournir du zirconate de baryum. L'analyse chimique, les spectres IR et la diffraction des rayons X sur poudre, apportent les preuves de l'existence d'un composé intermédiaire comme entité séparée.

CA/TG sequence at the 5' end of oligo(A)-tracts strongly modulates DNA curvature

An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5' end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAACCCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5' and 3' ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing of the sequences with AC/GT and CA/TG doublet junctions gives a similar cutting pattern in the A-tracts, which is quite different from that in the C-tracts, indicating that the oligo(A)-tracts have similar structures in the two oligomers. KMnO4 probing shows that the oligomer with a CA/TG doublet junction forms a kink that is responsible for its inherent curvature and unusual electrophoretic mobility. UV melting shows a reduced thermal stability of the duplex with CA/TG doublet junction, and circular dichroism (CD) studies indicate that a premelting transition occurs in the oligomer with CA/TG doublet step before global melting but not in the oligomer with AC/GT doublet step, which may correspond to thermally induced unbending of the oligomer. These observations indicate that the CA/TG doublet junction at the 5' end of the oligo(A)-tract has a crucial role in modulating the overall curvature in DNA.

CA\TG Sequence at the 5'end of Oligo(A)-tracts Strongly Modulates DNA Curvature

An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5' end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAACCCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5' and 3' ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing of the sequences with AC/GT and CA/TG doublet junctions gives a similar cutting pattern in the A-tracts, which is quite different from that in the C-tracts, indicating that the oligo(A)-tracts have similar structures in the two oligomers. KMnO4 probing shows that the oligomer with a CA/TG doublet junction forms a kink that is responsible for its inherent curvature and unusual electrophoretic mobility. UV melting shows a reduced thermal stability of the duplex with CA/TG doublet junction, and circular dichroism (CD) studies indicate that a premelting transition occurs in the oligomer with CA/TG doublet step before global melting but not in the oligomer with AC/GT doublet step, which may correspond to thermally induced unbending of the oligomer. These observations indicate that the CA/TG doublet junction at the 5' end of the oligo(A)-tract has a crucial role in modulating the overall curvature in DNA.