Abstract: A computational method has been developed to detect the conditions whereby gene expression control mechanisms will stop the transcription of RNA that would otherwise be used to form a connectron.

Abstract: A computer method for the determination of the interaction between transient and permanent connectrons, interference RNA and small temporal RNA.

Abstract: An algorithm has been developed to identify four DNA sequences of 20 bases or more that form a structure called a connectron. Two sequences C1 and C2 are adjacent to each other. These sequences are expressed as RNA in the 3′UTR of some genes in many prokaryotic, archea and eukaryotic genomes. The other half of a connectron is two DNA sequences T1 and T2 that are on the same chromosome and range in distance from each other by about 1 kb to 105 kb. The C1 sequence is identical to the T1 sequence and the C2 sequence is identical to the T2 sequence. C1/C2 and T1-T2 can be on different chromosomes. The C1/C2 RNA sequence of the gene transcript finds the two double-stranded DNA sequences T1 and T2. The single-stranded RNA and double-stranded DNA then form a triple-stranded Hoogsteen helix of the RNA/DNA/DNA variety. Because the C1 sequence is adjacent to the C2 sequence, the T1 sequence is made spatially adjacent to the T2 sequence in a compact X-shaped structure.

Abstract: The invention is directed to the design of DNA-binding proteins (DBP's) with capabilities of binding to any predetermined target double-stranded DNA sequence. Disclosed are the rules for design of the proteins; an algorithm for screening for the optimal DBP's; a computer system employing the rules and the algorithm; general formulae encompassing the proteins; and methods of use of the proteins.