Search

We have demonstrated in vitro the existence on the plasmid pBR322 of a promoter signal that is strictly dependent on cAMP and its receptor protein CRP. Transcription initiates with pppG at nucleotide 2270 and proceeds counterclockwise on the standard pBR322 map. DNase protection studies show that CRP selectively binds to the -35 region of the promoter. This region exhibits strong structural homologies to the binding sites of other CRP-dependent promoters.

We have developed a system to study transcriptional regulation of the lambda immunoglobulin gene in a natural setting -- lambda light chain producing lymphoid cells. This assay system has allowed the detection of an enhancer element located 3' of the lambda gene coding sequence. The enhancer can stimulate transcription from the lambda promoter as well as from other immunoglobulin and unrelated promoters. Like all enhancers, the lambda enhancer can function in either orientation with respect to a promoter, but it is significantly more active in one orientation than in the other. The lambda enhancer is unusual in spanning at least 4000 bp of DNA sequence and containing several distinct subelements that have independent enhancer activity. The enhancer is also remarkable because it functions in lambda light chain producing cells but not in kappa chain producing cells. This fact can be interpreted to support a model of immunoglobulin gene rearrangement in which rearrangement follows and depends on transcriptional activation.

The dominant family of interspersed repetitive DNA sequences in the human genome has been termed the Alu family. We have found that more than 75% of the lambda phage in a recombinant library representing an African green monkey genome hybridize with a human Alu sequence under stringent conditions. A group of clones selected from the monkey library with probes other than the Alu sequence were analyzed for the presence and distribution of Alu family sequences. The analyses confirm the abundance of Alu sequences and demonstrate that more than one repeat unit is present in some phages. In the clones studied, the Alu units are separated by an average of 8 kilobase pairs of unrelated sequences. The nucleotide sequence of one monkey Alu sequence is reported and shown to resemble the human Alu sequences closely. Hence, the sequence, dispersion pattern, and copy number of the Alu family members are very similar in the African green monkey and human genomes. Among the clones investigated were two that contain segments of the satellite DNA term alpha-component joined to non alpha-component DNA. The experiments indicate that in the monkey genome Alu sequences can occur close to regions of alpha-component DNA.

We have devised an algorithm for finding partial homologies among a set of nucleotide sequences. The algorithm and other improvements have been incorporated into a commonly used computer program for the analysis of sequence data.

We present a conversational system for the computer analysis of nucleic acid and protein sequences based on the well-known Queen and Korn program (1). The system can be used by persons with only minimal knowledge of computers.

We have developed a versatile program for the analysis of nucleic acid and protein sequences on the IBM Personal Computer. The program is interactive and self-instructing. It contains all the features generally found in sequence analysis programs on large computers, including extensive homology routines, as well as new procedures for the entry of sequence data. The program contains facilities to store and utilize the entire Nucleic Acid Sequence Data Bank. We have devised a new algorithm to find restriction enzyme sites, which allows our microcomputer program to find all sites on a small plasmid for 100 different enzymes in 1 to 2 minutes.