Dissecting (CAC)5/(GTG)5 multilocus fingerprints from man into individual locus-specific, hypervariable components.

Individual components of multilocus fingerprints from man produced by (CAC)5/(GTG)5 oligonucleotides have been scrutinized to characterize their peculiar properties. Successful cloning and changes occurring during the propagation of recombinant simple repetitive DNA in prokaryotic hosts are described. The isolated locus-specific probes were characterized with respect to their formal (and population genetic) properties and their usefulness for individualization and linkage studies. The localization was determined on chromosomes 8, 9, 11, and 22. Repeat flanking sequences were characterized and analyzed for their coding potential because of significant open reading frames and apparent evolutionary conservation among vertebrates. The organization of the repeats and their flanking regions in the human genome is discussed with respect to the sequence (fine) architecture that developed during evolution. Classical "minisatellite" sequences were not detected near hypervariable (cac)n/(gtg)n repeats. The single-copy probes described herein are a convenient complement to the oligonucleotides employed for multilocus fingerprinting. Many practical applications are apparent.     

Informativeness of human (dC-dA)n · (dG-dT)n polymorphisms

Abundant human interspersed repetitive DNA sequences of the form (dC-dA)_n · (dG-dT)_n have been shown to exhibit length polymorphisms. Examination of over 100 human (dC-dA)_n · (dG-dT)_n sequences revealed that the sequences differed from each other both in numbers of repeats and in repeat sequence type. Using a set of precise classification rules, the sequences were divided into three categories: perfect repeat sequences without interruptions in the runs of CA or GT dinucleotides (64% of total), imperfect repeat sequences with one or more interruptions in the run of repeats (25%), and compound repeat sequences with adjacent tandem simple repeats of a different sequence (11%). Informativeness of (dC-dA)_n · (dG-dT)_n markers in the perfect sequence category was found to increase with increasing average numbers of repeats. PIC values ranged from 0 at about 10 or fewer repeats to above 0.8 for sequences with about 24 or more repeats. (dC-dA)_n · (dG-dT)_n polymorphisms in the imperfect sequence category showed lower informativeness than expected on the basis of the total numbers of repeats. The longest run of uninterrupted CA or GT repeats was found to be the best predictor of informativeness of (dC-dA)_n · (dG-dT)_n polymorphisms regardless of the repeat sequence category.     

The use of microsatellite DNA markers for soybean genotype identification

Conventional morphological and pigementation traits, as well as disease resistance, have been used to distinguish the uniqueness of new soybean cultivars for purposes of plant variety protection. With increasing numbers of cultivars and a finite number of conventional characters, it has become apparent that such traits will not suffice to establish uniqueness. The objective of this work was to provide an initial evaluation of microsatellite or simple-sequence-repeat (SSR) DNA markers to develop unique DNA profiles of soybean genotypes. Microsatellites are DNA sequences such as (AT) _n /(TA) _n and (ATT) _n /(TAA) _n that are composed of tandemly repeated 2–5-basepair DNA core sequences. The DNA sequences flanking microsatellites are generally conserved allowing the selection of polymerase chain reaction (PCR) primers that will amplify the intervening SSR. Variation in the number of tandem repeats, n, results in PCR product length differences. The SSR alleles present at three (AT) _n /(TA) _n and four (ATT) _n /(TAA) _n loci were determined in each of 96 diverse soybean genotypes. Between 11 and 26 alleles were found at each of the seven loci. Only two genotypes had identical SSR allelic profiles and these had very similar pedigrees. The gene diversity for the seven markers averaged 0.87 for all 96 genotypes and 0.74 for a subset of 26 North American cultivars. These are much higher than soybean gene diversity values obtained using RFLP markers, and are similar to the average values obtained for human microsatellite markers. SSR markers provide an excellent complement to the conventional markers that are currently used to characterize soybean genotypes.     

A family of related sequences associated with (TTTAGGG)n repeats are located in the interstitial regions of wheat chromosomes

A family of related sequences associated with (TTTAGGG) _n repeats has been cloned from the wheat cultivar Chinese Spring. These sequences reveal a high level of polymorphism between wheat varieties when used as restriction fragment length polymorphism (RFLP) probes. Although this family of sequences contains motifs homologous to the repeats in the telomeres of wheat, they are located at interstitial sites on wheat chromosomes.     

A novel intramolecular G-quartet-containing fold of single-stranded d(GT)8 and d(GT)16 oligonucleotides

Human genome is shown to be enriched with (GT)_n stretches of lengths from 8 to 20 dinucleotides. Low temperature (T ≤ 10 °C) conformations of d(GT)_n oligonucleotides (n = 7, 8, 12, 16, 20) were studied by means of circular dichroism (CD), thermal melting, ethidium bromide (EtBr) probing and single nucleotide substitutions. Rotational relaxation times for EtBr:d(GT)_n complexes confirmed a monomolecular state of the oligonucleotides. CD spectra indicated involvement of all guanines of d(GT)₈ and d(GT)₁₆ in G-quartets, while dT(GT)₇, d(GT)₁₂ and d(GT)₂₀ were shown to be only partially ordered. The schemes of the d(GT)₈ and d(GT)₁₆ folds are suggested.     

Isolation, characterization and transposition of an (IS2)2 intermediate

We have isolated and characterized a dimer derivative of the extensively studiedEscherichia coli insertion sequence IS2. The dimer structure — called (IS2)₂ — consists of two IS2 elements arranged as a direct repeat, separated by 1 bp. The junction between the (IS2)₂ dimer and target sequences is located at various positions in independent isolates; however, one position was preferred. The transposition of (IS2)₂ into a target plasmid resulted in cointegrate-type structures. The transposition frequency of the (IS2)₂ dimer itself was significantly higher than that of the isogenic monomer IS2 insertion. The poor stability and high activity of (IS2)₂ indicates that this is an active transposition intermediate. The mode of transposition of (IS2)₂ is analogous to the joined dimer model described in the case of (IS21)₂ and (IS30)₂.     

Synthesis and structure of an organosamarium aryloxide complex, (C5 Me5)2 Sm(OC6HMe4-2,3,5,6)

Bis(pentamethylcyclopentadienyl)samarium bis- (tetrahydrofuranate), (C₅Me₅)₂Sm(THF)₂, reacts with 2,3,5,6-tetramethylphenol in toluene to yield (C₅Me₅)₂Sm(OC₆HMe₄-2,3,5,6). The compound crystallizes in the space group P2₁/c with a = 8.725(3) Å, b=18.821(6) Å, c=18.461(6) Å, β= 111.17(2)°, V = 2827(2) ų and D_c=1.340 g cm⁻³ for Z = 4. Molecules of the aryloxide complex are monomeric and exhibit a bent metallocene structure with a nearly linear Sm---O---C(aryloxide) linkage: Sm---O = 2.13(1) Å, O---C = 1.29(2) Å, and Sm---O---C = 172.3(13)°. Reaction of the samarium complex with phenyllithium produces the previously- characterized species (C₅Me₅)₂Sm(C₆H₅)(THF).     

Length-dependent structure formation in Friedreich ataxia (GAA)n*(TTC)n repeats at neutral pH

More than 15 human genetic diseases have been associated with the expansion of trinucleotide DNA repeats, which may involve the formation of non-duplex DNA structures. The slipped-strand nucleation of duplex DNA within GC-rich trinucleotide repeats may result in the changes of repeat length; however, such a mechanism seems less likely for the AT-rich (GAA)_n·(TTC)_n repeats. Using two-dimensional agarose gels, chemical probing and atomic force microscopy, we characterized the formation of non-B-DNA structures in the Friedreich ataxia-associated (GAA)_n·(TTC)_n repeats from the FRDA gene that were cloned with flanking genomic sequences into plasmids. For the normal genomic repeat length (n = 9) our data are consistent with the formation of a very stable protonated intramolecular triplex (H-DNA). Its stability at pH 7.4 is likely due to the high proportion of the T·A·T triads which form within the repeats as well as in the immediately adjacent AT-rich sequences with a homopurine· homopyrimidine bias. At the long normal repeat length (n = 23), a family of H-DNAs of slightly different sizes has been detected. At the premutation repeat length (n = 42) and higher negative supercoiling, the formation of a single H-DNA structure becomes less favorable and the data are consistent with the formation of a bi-triplex structure.     

Synthesis of bent titanocene metalloligands with the (diphenylphosphino)tetramethylcyclopentadienyl moiety. X-ray structure of [(η-C5Me4 2)2TiCl2]Mo(CO)4

The reactions of lithium(diphenylphosphino)tetramethylcyclopentadienide with CpTiCl₃ and secondly with TiCl₃ followed by CCl₄ oxidation lead to the formation of two titanocene phosphines: (η⁵-C₅H₅)[η⁵-C₅Me₄P(C₆H₅)₂]TiCl₂ (2) and [η⁵-C₅Me₄P(C₆H₅)₂]₂TiCl₂ (3), respectively. The metalloligand 3 reacts readily with Mo(CO)₄cod, Mo(CO)₅THF and Mo(CO)₆ to give in each case [(η⁵-C₅Me₄ o(CO)₄ (6) as a sole product. The structure of 6 has been determined by X-ray diffraction. Crystal data: P , a = 11.716(1), b = 11.753(2), c = 16.110(2) Å, α = 99.06(1), β = 92.61(1), γ = 104.20(1)°, Z = 2. The molybdenum-titanium distance of 5.194(1) Å rules out any metal-metal interaction. The chlorine substitution reactions by CO in 2 and 3 and by thiolate group (pH₃C-C₆H₄-S) in 16 are reported.     

Differential genotoxic effects of antitumor trans-[PtCl2(E-iminoether)2] and cisplatin in Escherichia coli

In the present work, we measured survival and the platinum on the genome after treatment of repair-proficient or repair-deficient Escherichia coli strains with trans-[PtCl₂(E-iminoether)₂] and compared these results with the effects of “classical” cisplatin. We found that toxicity of antitumor trans-[PtCl₂(E-iminoether)₂] in repair-deficient trains was much less than that of cisplatin. This markedly reduced toxicity was not a consequence of the reduced uptake or low levels of DNA binding in the bacteria cells but rather appeared to reflect DNA binding mode of this trans-platinum drug different from that of cisplatin.     

Synthesis and crystal structure of the MgCl2(CH3COOC2H5)2· (CH3COOC2H5) adduct

The reaction of α-MgCl₂ with boiling ethyl acetate affords MgCI₂(CH₃COOC₂H₅)₂· (CH₃COOC₂H₅), which is obtained as crystals suitable for X-ray analysis only from the mother liquor. M=315.5, orthorhombic, space group P2₁22₁ (No. 18), a=25.077(3), b=8.616(1), c=7.345(1) Å, V=1587.0(3) ų, Z=4, D_x=1.32 g cm⁻³,λ A(Mo Kα)=0.71069 Å, μ=4.17 cm⁻¹, F(000)=664, T=298 K, observed reflections: 1667, R=0.059 and R_w=0.069. The structure is composed of polymeric chains of MgCl₂(CH₃COOC₂H₅₎₂ and the ethyl acetate molecules occupy a mutually trans position.     

Supramolecular assemblies of new 2-D complexes: Syntheses, crystal structures, spectroscopic and magnetic properties of {[MnAu2(CN)4(NITpPy)2(H2O)2]}n and {[Co(N(CN)2)2(NITpPy)2(H2O)2]}n

Two new complexes, {[MnAu₂(CN)₄(NITpPy)₂(H₂O)₂]}_n (1) and {[Co(N(CN)₂)₂(NITpPy)₂(H₂O)₂]}_n (2), have been synthesized and characterized. The single-crystal X-ray analysis for the complexes 1 and 2 demonstrates that each M(II) (M = Mn or Co) ion assumes a distorted octahedral MN₄O₂ coordination polyhedron. Four nitrogen atoms come from the cyanide groups and the pyridyl rings in a common plane, and two oxygen atoms come from the H₂O molecules in trans-positions. The structures of complexes 1 and 2 illustrate that aurophilicity and/or hydrogen bonding interactions play important roles in increasing dimensionality. Magnetic investigations on complexes 1 and 2 show the presence of weak antiferromagnetic interactions.     

1-D coordination chains of Cu(hfac)2 and Mn(hfac)2 bridged by phenyl-nitronylnitroxide derivatives

Two alternating 1-D metal-radical linear [L:Cu(hfac)₂]_n and zig-zag [L:Mn(hfac)₂]_n chains (where L = 4-trimethylsilylethynyl-1-(4,4,5,5-tetramethyl-3-oxylimidazoline-1-oxide)benzene) and hfac = hexafluoroacetylacetonate) are described and characterized by X-ray diffraction of their crystals. Bulk magnetic measurements of L:Cu(hfac)₂ indicated a ferromagnetic interaction with J = 6 cm⁻¹ and L:Mn(hfac)₂ yielded ferrimagnetic interactions with J = −95 cm⁻¹. For the latter, a strong increase of their magnetic moment at lowest temperatures was observed only at very low static magnetic field, while for H_dc > 0.05 T saturation effect led to a downward slope after reaching a maximum.     

Binuclear complexes of a new hexadentate macrocyclic ligand. The crystal and molecular structure of [LCu2(CH3CO2)2](ClO4)2·5H2O

The 30-membered hexaaza macrocylic ligand, L (L=3,7,11,18,22,26-hexaazatricyclo-[26.2.2.2^13,16]tetratriaconta-1(31),13(33),14,16(34),28(32),29-hexaene), is capable of forming binuclear complexes with the divalent transition metal ions Ni, Cu and Zn. The two metal ions are bound by the two dipropylenetriamine units of the macrocycle. Extra coordination sites on the metal ions can be occupied by exogenous ligands such as acetate, chloride and thiocyanate. The crystal structure of one of the di-copper complexes is described: [LCu₂(CH₃CO₂)₂](ClO₄)₂·5H₂O crystallizes in the monoclinic space group P2₁/c (No. 14), with a=9.369(2), b=17.644(3), c= 27.466(3) Å, β=92.90(1)°, U=4534.7 ų and Z=4. The Cu1···Cu2 separation is 8.40(3) Å. The access for potential exogenous bridging ligands, to the cavity between the copper ions, is somewhat restricted by the two phenyl units of the macrocycle which appear almost parallel in the structure. The redox potential of the couple L(Cu²⁺)₂/L(Cu⁺)₂, recorded by cyclic voltammetry for the chloride adduct, [LCu₂Cl₂]Cl₂·5H₂O, is −0.061 V versus SCE in DMF.     

Genomic Organization and Chromosomal Assignment of the Human Voltage-Gated Na Channel β1 Subunit Gene (SCN1B)

Voltage-gated sodium (Na⁺) channels are essential for the generation and propagation of action potentials in striated muscle and neuronal tissues. Biochemically, Na⁺ channels consist of a large α subunit and one or two smaller β subunits. The α subunit alone can exhibit all of the functional attributes of a voltage-gated Na⁺ channel, but requires a β₁ subunit for normal inactivation kinetics. While genetic mutations in the skeletal muscle Na⁺ channel α-subunit gene can cause human disease, it is not known whether hereditary defects in the β₁ subunit underlie any inherited syndromes. To help explore this further, we have carried out an analysis of the detailed structure of the human β₁ subunit gene (SCN1B) including the delineation of intron-exon boundaries hy genomic DNA cloning and sequence analysis. The complete coding region of SCN1B is found in 9.0 kb of genomic DNA and consists of five exons (72 to 749 bp) and four introns (90 bp to 5.5 kb). Using a 15.9-kb genomic SCN1B clone, we assigned the gene to the long arm of chromosome 19 (19q13.1-q13.2) by fluorescence in situ hybridization. An intragenic polymorphic (TTA)_n repeat that is positioned between two tandem Alu repetitive sequences was also characterized. The (TTA)_n repeat exhibits 5 distinct alleles and a heterozygosity index of 0.59. This information should be useful in evaluating SCN1B as a candidate gene for hereditary disorders affecting membrane excitability.     

Small ligands that neither bind to nor alter the structure of d(GA·TC)n sequences in DNA

Three minor-groove binding ligands have been used to study the characteristics of two d(GA·CT)_n DNAs embedded in longer DNA fragments. The binding of mithramycin, netropsin or Thia-Net to these sequences has been studied using DNAse I footprinting. None of these ligands appeared to bind to d(GA·CT)₅ nor to d(GA·CT)₂₂ extensively, although with mithramycin some protected bonds were detected at the very edge of these sequences. In general, these small ligands did not enhance the DNAse I cleavage patterns at the alternating d(GA·CT)_n flanking sequences located near DNA regions where the drug was bound. The d(GA·CT)_n sequences could act as a rigid block in which it is not easy to propagate structural changes, whereas other sequences flanking the binding sites showed cleavage enhancements.     

New precursors in the chemistry of IVB transition metal alkoxides V. Synthesis and molecular structure of Zr3Fe(μ4-O)(μ2-OC3H7)6-(OC3H7)4(acac)3

The reaction of iron(III) acetylacetonate with zirconium(IV) n-propanolate in n-propanol leads to a tetranuclear species Zr₃FeO(OC₃H₇)₁₀(acac)₃. This compound crystallizes in the triclinic system (space group P ): a = 12.426(2), b = 12.977(2), c = 20.129(4) Å, α = 91.55(1), β = 97.90(1), γ = 100.53(1)°. The structure consists of discrete tetranuclear molecules. The metal atoms design an almost perfect tetrahedron around a four-fold coordinated oxygen atom. The zirconium atoms are in a seven-fold coordination and the iron atom in a five-fold coordination.     

Creation of a SINE enriched library for the isolation of polymorphic (AGC)n microsatellite markers in the bovine genome

Trinucleotide (AGC)_n microsatellites are found as 3′ tails of the artiodactyl short interspersed nuclear element (SINE) A-dimer. We describe a polymerase chain reaction (PCR)-based method for the construction of a plasmid library enriched for SINE (AGC)_n microsatellites. By amplifying Sau3AI inserts with a conserved SINE primer and a flanking vector primer, a 35-fold enrichment of (AGC)_n microsatellites over a conventional genomic library was obtained. The SINE primer was used for both sequencing of AGC-containing inserts and analysis of polymorphism. Twenty-three unique reverse primers were synthesized and used on bovine genomic DNA, 21 producing PCR products of expected size. Five polymorphic (AGC)_n microsatellites with 2–4 alleles each were characterized. Allele sizes differed by a 3 bp motif and lacked the stutter bands associated with dinucleotide repeats. A tendency of increased polymorphism for longer AGC repeat arrays was observed. High stringency selection for positive clones containing eight or more AGC repeats can thus facilitate the isolation of polymorphic (AGC)_n microsatellites, Enrichment for (AGC), microsatellites by SINE-vector PCR can be applied to other bovidae species, such as sheep or goat, containing the artiodactyl SINE elements.