Ramified rolling circle amplification for synthesis of nucleosomal DNA sequences

Nucleosomes are a crucial platform for the recruitment and assembly of protein complexes that process the DNA. Mechanistic and structural in vitro studies typically rely on recombinant nucleosomes that are reconstituted using artificial, strong-positioning DNA sequences. To facilitate such studies on native, genomic nucleosomes, there is a need for methods to produce any desired DNA sequence in an efficient manner. The current methods either do not offer much flexibility in choice of sequence or are less efficient in yield and labor. Here, we show that ramified rolling circle amplification (RCA) can be used to produce milligram amounts of a genomic nucleosomal DNA fragment in a scalable, one-pot reaction overnight. The protocol is efficient and flexible in choice of DNA sequence. It yields 10-fold more product than PCR, and rivals production using plasmids. We demonstrate the approach by producing the genomic DNA from the human LIN28B locus and show that it forms functional nucleosomes capable of binding pioneer transcription factor Oct4

Ratios of bottom meson branching fractions involving J/psi mesons and determination of b quark fragmentation fractions

We report a measurement of the ratios of the decay rates of the B^+, B^0 and B^0_s mesons into exclusive final states containing a J/psi meson. The final states were selected from 19.6 pb^{-1} of p-pbar collisions recorded by the Collider Detector at Fermilab. These data are interpreted to determine the bquark fragmentation fractions f_u, f_d and f_s. We also determine the branching fractions for the decay modes B^+ --> J/psi K^+, B^+ --> J/psi K^*(892)^+, B^0 --> J/psi K^0, B^0 --> J/psi K^*(892)^0 and B_s^0 --> J/psi phi(1020). We discuss the implications of these measurements to B meson decay models.Comment: 40 pages with 5 figures. Submitted to Phys. Rev. D. PostScript also available at http://www-cdf.fnal.gov/physics/pub96/cdf3609_bfrag_br_prd.p