Binding site selection analysis of protein-DNA interactions via solid phase sequencing of oligonucleotide mixtures.

By combining the concept of degenerate oligonucleotide mutagenesis (1,2,3,4) and the convenience of solid phase chemical DNA sequencing (5), we have developed a rapid procedure for determining the specificity of DNA-binding proteins in vitro. Starting with a degenerate oligonucleotide mixture, the technique assays for alternative nucleotides in fractions that are bound or non-bound to the protein of interest. In contrast to previous approaches using degenerate oligonucleotides, it does not involve cloning but rather employs direct sequencing of the oligonucleotide mixtures after attachment to a solid support. Solid state processing obviates the need for both DNA extractions from polyacrylamide gels and time-consuming ethanol precipitations. Because of its convenience and sensitivity, this binding site selection analysis is well suited to determining rapidly the sequence preference of DNA-binding proteins that are available in small amounts, and complements well established approaches like methylation interference or missing contact assays. The solid phase reaction protocol we propose can also improve these latter approaches.     

An overview of the secondary structure of the V4 region of eukaryotic small-subunit ribosomal RNA.

The V4 region of the small subunit (18S) ribosomal RNA was examined in 72 different sequences representing a broad sample eukaryotic diversity. This domain is the most variable region of the 18S rRNA molecule and ranges in length from ca. 230 to over 500 bases. Based upon comparative analysis, secondary structural models were constructed for all sequences and the resulting generalized model shows that most organisms possess seven helices for this region. The protists and two insects show from one to as many as four helices in addition to the above seven. In this report, we summarize secondary structure information presented elsewhere for the V4 region, describe the general features for helical and apical regions, and identify signature sequences useful in helix identification. Our model generally agrees with other current concepts; however, we propose modifications or alternative structures for the start of the V4 region, the large protist inserts, and the sector that may possibly contain a pseudoknot.     

Maternal cigarette smoking, Down syndrome in live births, and infant race.

Previous studies have suggested that maternal smoking is negatively associated with a Down syndrome live birth. We analyzed the data of the U.S. Perinatal Collaborative Study in a search for racial variation in Down syndrome risk factors. There were 22 cases in 25,346 live births to smoking mothers (4/10,780 blacks, 18/13,320 whites, and 0/1,246 other races) and 42/29,130 live births to nonsmoking mothers (24/14,665 blacks, 14/11,694 whites, and 4/2,771 others). The crude overall rates per 1,000 live births were 0.4 in black smokers and 1.6 in black nonsmokers but 1.4 in white smokers and 1.2 in white non-smokers. Adjusted for maternal age, the summary relative risk for a Down syndrome live birth to a smoking mother was 0.2 in blacks (95% interval 0.1-0.7) but 1.2 in whites (95% interval 0.6-2.5). Stratification on variables associated with socioeconomic status or gestational age at time of entry into the study did not alter the racial difference. A comparison of smokers with those who never smoked revealed essentially the same trends. Among all nonsmokers the ratio of the maternal age-adjusted risks for a Down syndrome live birth in whites compared with blacks was 0.7 (95% interval 0.3-1.3), and among all smokers this ratio was 3.6 (95% interval 1.3-9.9). If the results are not attributable to statistical fluctuation or undetected confounding, then differences in the probability of intrauterine survival of the Down syndrome fetus would appear to be one plausible explanation for the difference.     

Models of multilocus recombination: nonrandomness in chiasma number and crossover positions.

Cytological evidence indicates that genetic interference can be partitioned into two empirical components: nonrandomness in the number of chiasmata that occur and nonrandomness in the locations of multiple chiasmata. Previous studies have incorporated the first effect into genetic models for analyzing multipoint data. An extension to this approach is presented which allows for the second component of interference by modeling the probability density function of the locations of multiple crossovers. Results of reanalyses of multilocus data for the Drosophila X chromosome show that models that incorporate only the first effect give a better fit to these data than do standard mapping functions and that the extended model significantly improved the fit by decreasing the predicted frequency of multiple crossovers in nearby regions. Our results demonstrate that chiasma-based models of multilocus recombination, which are unique in incorporating direct estimates of the frequency of multiple crossovers for a chromosome region, can provide a powerful and realistic means of accounting for genetic interference when applied to the problems of gene localization, locus ordering, and exclusion mapping.     

The Maintenance of Single-Locus Polymorphism. I. Numerical Studies of a Viability Selection Model

The ability of viability selection to maintain single-locus polymorphism is investigated with two models in which the population is bombarded with a series of mutations with random fitnesses. In the first model, the population is allowed to reach equilibrium before mutation resumes; in the second the iterations and mutation occur simultaneously. Monte Carlo simulations of these models show that viability selection is easily able to maintain stable 6- or 7-allele polymorphisms and that monomorphisms and diallelic polymorphisms are uncommon. The question of how monomorphisms arise is also discussed.