Strand invasion

Bentin, T. and P.E. Nielsen. Superior duplex DNA strand invasion by acridine conjugated peptide nucleic acids. J. Am. Chem. Soc. 2003, 125, 6378-6379. 

Kaihatsu K., Braasch D.A., Cansizo-GLU A., Corey D.R. Enhanced strand invasion by peptide nucleic acid-peptide conjugates. Biochemistry 2002 41 11118-11125. 

Zhang X., Ishihara T, Corey D. R. Strand invasion by mixed base PNAs and a PNA-peptide chimera. Nucleic Acids Res. 2000 28 3332-3338. 

Vickers T.A., Grieeity M.G., Ramasamy K, Risen L.M., Freier S.M. Inhibition of NF-kB specific transcriptional activation by PNA strand invasion. Nucleic Acids Res. 1995 23 3003-3008. 

Peffer, N.J., Hanvey, J.C., Bisi, J.E., Thomson, S.A., Hassman, C.F., Noble, S.A. and Babiss, L.E. (1993) Strand-invasion of duplex DNA by peptidic nucleic acid oligomers. Proceedings of the National Academy of Sciences of the United States of America, 90, 10648-10652. 

Cursory inspection of both the Meselson and Holliday models suggests the need for special enzymes to mediate the recombination process. First an endonuclease is needed to make the initial strand breaks that are required for strand invasion. Second an enzyme is required to mediate formation of the recombination complex. Finally an enzyme is probably required to resolve the recombinant duplexes. 

Figure 7 Repair of the double-strand break by homologous recombination in mammalian cells. In homologous recombination, an intact homologous chromosome is used to retrieve information and repair double-strand breaks in the duplex. The three basic steps of homologous recombination are strand invasion, branch migration, and Holliday junction formation.

Figure 2 Most common DNA/RNA binding modes. Left Strand invasion of homopyrimidine PNA into duplex DNA yields a PNA2-DNA triplex. Right Hybridization of mixed sequence PNA with complementary DNA or RNA produces Watson-Crick base-paired duplex structures.

RecA Can Initiate Recombination by Promoting Strand Invasion... 

ATPase family. To accomplish the exchange, the single-stranded DNA displaces one of the strands of the double helix (Figure 28.48). The resulting three-stranded structure is called a displacement loop or D loop. This process is often referred to as strand invasion. Because a free 3 end is now bound to a contiguous strand of DNA, the 3 end can act as a primer to initiate new DNA synthesis. Strand invasion can initiate many processes, including the repair of double-stranded breaks and the reinitiation of replication after the replication apparatus has come off its template. In the repair of a break, the recombination partner is an intact DNA molecule with an overlapping sequence. 

Recombination is the exchange of segments between two DNA molecules. Recombination is important in some types of DNA repair as well as other processes such as meiosis, the generation of antibody diversity, and the life cycles of some viruses. Some recombination pathways are initialed by strand invasion, in which a single strand at the end of a DNA double helix forms base pairs with one strand of DNA in another double helix and displaces the other strand. A common intermediate formed in other recombination pathways is the Holliday junction, which consists of four strands of DNA that come together to form a crosslike structure. Recoinbinases promote recombination reactions through the introduction of specific DNA breaks and the formation and resolution of junction intermediates. 

An alternative to the inhibition of RNA metabolism by way of an antisense mechanism is to inhibit transcription by interacting with double-stranded DNA in chromatin. Of the two most obvious binding strategies for oligonucleotides binding to double-stranded nucleic acids, strand invasion and triple-strand formation, triple-stranding strategies, until recently, attracted essentially all of the attention. 

Strand invasion, an alternative approach to obstructing transcription by formation of triple strands, has been shown to be feasible if analogs with sufficient affinity can be synthesized. PNAs have been shown to have very hyi affinity and be capable of strand invasion of double-stranded DNA under some conditions (51). Additionally, progress in develop-irg sequence-specific minor groove binders has been reported (52) (for review, see Ref 53). Thus, progress in developing the basic tools with which to evaluate the potential of sequence-specific interactions with DNA has bcai reported, although much remains to be dene. 

If we look in more detail at how homologous recombination is accomplished, we find that it is a complicated process, and not too surprisingly, it presents a number of DNA structural and polarity problems that need to be solved. The two major steps in the reaction are (1) single-strand invasion to promote the formation of an in-... 

Chi - An octanucleotide sequence in E. coli (5 -GCTGGTCC-3 ) recognized by exonuclease V. At this sequence, the exonuclease switches strands and its preferred polarity of DNA degradation. This facilitates the loading of RecA to a free 3 end and initiates strand invasion of a nearby duplex. Figure 25.28... 

Strand Invasion - A process that is postulated to occur in homolous recombination in which an unpaired part of a strand of DNA invades a duplex region of another DNA. 

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