Strand displacement binding

Cherny D.Y., Belotserkovskii B.P., Frank-Kamenetskii M.D., Egholm M., Buchardt O., Berg R. H., Nielsen, P.E. DNA unwinding upon strand-displacement binding of a thymine-substituted polyamide to double-stranded DNA. Proc. Natl Acad. Sci. USA 1993 90 1667-1670... 

Nielsen P.E., Egholm M., Buchardt O. Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement. J. Md. Recognit. 1994 7 165-170. 

The biochemical process of recombination occurs by breaking and rejoining DNA strands. The key reaction is strand displacement initiated at a nick in the chromosome. Then a protein called RecA (which stands for recombination rec bacteria are unable to recombine their DNA information and therefore are abnormally sensitive to UV radiation) binds to a single-stranded DNA fragment and catalyzer its exchange with the same sequence of the duplex. RecA protein is a strand displacement protein. See Figure 8-16. 

RecA preferentially binds to single-stranded DNA in a cooperative fashion this cooperativity means that RecA will cover an entire single-stranded DNA molecule rather than bind to several molecules partially. Rec A then aligns homologous segments (those with complementary information) to form base pairs. The key reaction of RecA-coated DNA is the movement of the single-stranded regions of the DNA to form a joint molecule—a process called strand displacement. This reaction involves ATP hydrolysis. 

Walker GT, Linn CP, Nadeau JG. DNA detection by strand displacement amplification and fluorescence polarization with signal enhancement using a DNA binding protein. Nucleic Acids Res 1996 24 348-53. 

Replication proceeds via extension of the 3 end. The 5 end is displaced in a rolling circle mechanism and single strand DNA binding proteins attach to the displaced strand. 

Another example of a DNA machine that can easily be triggered by the actions of an aptamer is based on the isothermal strand displacement amplification (Weiz-mann et al., 2006b). In this case, a single-stranded DNA track contains three distinct domains domain I for the binding of a primer DNA to start replication domain II, which can, upon dnplex formation, be recognized by a nicking endonuclease (which cuts one strand of a double-stranded structure) and domain... 

Figure 4.8 DNA machine based on strand displacement amplification. The track consists of a primer binding sequence (black, I), a nicking recognition sequence (green, II), and a template for the product DNA (blue, IE). (1) Binding of the primer starts replication of the entire track by a DNA polymerase. (2) The fully replicated duplex is nicked on the newly formed strand by the nicking enzyme, regenerating the primer site...

Based on the close proximity of the two types of hot spot motifs, it is possible that AID-catalyzed deamination of G residues in WRG could therefore provide a mechanism for loading an EP pol to copy nearby WA motifs. Gonversion of G —> U by AID, followed by U removal by UNG + APE enzymes, results in a nick at the 5 -end of the abasic moiety. If an error-prone repair polymerase (e.g., pol rf) binds and carries out strand displacement synthesis (long-patch BER), then misincorporation of G opposite T (Fig. 3) will yield A —> G transitions in the nontranscribed strand at WA hotspots, in accordance with pol r/ s mutational specificity (Pavlov et al, 2002), as shown (in red) in Fig. 3. 

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