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Sequence-directed variations in the canonical DNA double helix structure that retain Watson-Crick base-pairing have important roles in DNA recognition, topology and nucleosome positioning. By using nuclear magnetic resonance relaxation dispersion spectroscopy in concert with steered molecular dynamics simulations, we have observed transient sequence-specific excursions away from Watson-Crick base-pairing at CA and TA steps inside canonical duplex DNA towards low-populated and short-lived A•T and G•C Hoogsteen base pairs. The observation of Hoogsteen base pairs in DNA duplexes specifically bound to transcription factors and in damaged DNA sites implies that the DNA double helix intrinsically codes for excited state Hoogsteen base pairs as a means of expanding its structural complexity beyond that which can be achieved based on Watson-Crick base-pairing. The methods presented here provide a new route for characterizing transient low-populated nucleic acid structures, which we predict will be abundant in the genome and constitute a second transient layer of the genetic code.

We report the molecular, cellular, and clinical features of 5 patients from 3 kindreds with biallelic mutations in the autosomal LIG1 gene encoding DNA ligase 1. The patients exhibited hypogammaglobulinemia, lymphopenia, increased proportions of circulating [gamma][delta]T cells, and erythrocyte macrocytosis. Clinical severity ranged from a mild antibody deficiency to a combined immunodeficiency requiring hematopoietic stem cell transplantation. Using engineered LIG1-deficient cell lines, we demonstrated chemical and radiation defects associated with the mutant alleles, which variably impaired the DNA repair pathway. We further showed that these LIG1 mutant alleles are amorphic or hypomorphic, and exhibited variably decreased enzymatic activities, which lead to premature release of unligated adenylated DNA. The variability of the LIG1 genotypes in the patients was consistent with that of their immunological and clinical phenotypes. These data suggest that different forms of autosomal recessive, partial DNA ligase 1 deficiency underlie an immunodeficiency of variable severity., IntroductionThe DNA ligase family is an evolutionarily conserved group of proteins found in both prokaryotic and eukaryotic cells that have previously been implicated in rare immune defects. Substrate dependence divides [...]

We identified dmisteinbergite, the rare trigonal polymorph of CaAl2Si2O8, for the first time in high-grade metamorphic rocks. Dmisteinbergite occurs as a crystallization product of silicate melt inclusions (nanogranitoids) in garnet from three host rocks with different protoliths and re-equilibration conditions, i.e., from 1.0 to 4.5 GPa. Raman spectra and compositions of the dmisteinbergite here investigated are overall identical to those of previously characterized artificial and natural dmisteinbergite. In nanogranitoids, this phase coexists with other metastable polymorphs of feldspar (kumdykolite, kokchetavite) and SiO2 (quartz, cristobalite), recently interpreted as the result of undercooling, supersaturation and rapid crystallization of a silicate melt confined in a micrometric pore. Dmisteinbergite formation likely results from a similar process, and thus it should be regarded as a kinetically controlled phase. Moreover, the investigation of dmisteinbergite as well as of other metastable feldspar polymorphs offers new insights into the behavior of natural materials under non-equilibrium conditions. [ABSTRACT FROM AUTHOR]

The development of a new carbonylation reaction of alkynes with 2-bromophenylboronic acid leading to the formation of indenones is reported. The results suggest that while active site interactions at the leaving group oxygen atom are similar for phosphate and sulfate esters, the interactions with the nonbridging oxygen atom differ significantly.

The DNA repair exhibits an evolvable system, allowing for flexibility in recruiting any enzyme to a new function, so that gene duplication in a redundant DNA repair activity would not be required. Most DNA repair enzymes have broad substrate specificity, enabling an abundant source of enzymes with low promiscuity to simplify DNA repair activity.

Author(s): John M. Pascal [1]; Patrick J. O'Brien [1, 3]; Alan E. Tomkinson [2]; Tom Ellenberger (corresponding author) [1] Shortly after DNA ligases were discovered in the late 1960s, it [...]

Alkaline phosphatase-catalyzed hydrolysis of alkyl phosphates reveal the ionizable groups involved in the binding and catalysis. The enzyme kinetics indicate that the inorganic phosphate dianion seem to bind to the highly charged alkaline phosphatase active site as determined by a new (sup)32P-based assay.

Research shows that Escherichia coli alkaline phosphatase possesses a low level of phosphodiesterase activity. Active site's arginine mutation to serine reduces monoesterase activity without affecting diesterase activity. Results point out to a divergent evolution of phosphodiesterases and phosphomonoesterases in the alkaline phosphatase superfamily.