Tandem DNA Repeats: Generation and Propagation in the Microgene Polymerization Reaction and in Vivo.

Abstract

Short and long-motif periodicities are omnipresent in genomes of both eukaryotes (Britten & Kohne 1968) and prokaryotes (Hofnung & Shapiro, 1999). Repetitive DNA can amount to more than half of higher eukaryotic genomes, specifically in Homo sapience (International Human Genome Consortium, 2001) and Zea mays (Meyers et al., 2001). Even in prokaryotes it can account for about 6% of the total genome, specifically in Mycoplasma pneumoniae (Ruland et al., 1990) and Neisseria meningitides (Parkhill et al., 2000). Two major types of repetitive DNA exist (Dogget, 2000): tandem (head-to-tail contiguous) and interspersed (non-contiguous) with a specific pattern scattered all over the genome and lengths varying up to several hundred nucleotides (nt). Emergence and propagation of interspersed repeats such as REP (Repetitive Extra-genic Palindrome) found in bacteria and Alu repeats that are abundant in the human genome are putatively attributed to reproduction processes mediated by transposons (Gilson et al., 1984) or retroviruses (Ullu & Tschudi, 1984). These are multi-step complex enzymatic processes and will not be considered here. This chapter deals with tandem repeats and their generation in vitro by the Microgene Polymerization Reaction (MPR) (Itsko et al., 2008a; 2008b; 2009), and proposes a mechanism for their in vivo generation as well. Most tandem repetitive DNA sequences in higher eukaryotes are located near the chromosomal telomers or centromers where they play important roles in maintaining genome integrity (Blackburn, 1991) and segregation (Catasti et al., 1994). In addition to this untranscribed but evidently functional repetitive DNA, the human genome contains many apparently non-functional repetitive DNA sequences in the forms of micro-satellites (a variety of di-, tri-, tetra-, and penta-nucleotide tandem repeats) and mini-satellites (30-35 bp long, with variable sequences and conserved cores of 10-15 bp) (Dogget, 2000). The number of repeats is prone to expand during replication because its constituent strands can slide over each other between the multiple complementary regions (Wells, 1996). Thermodynamically unfavorable structures bulging out from DNA duplex that accompany the strand sliding