Duplex invasion

Fig. 4.4 Double duplex invasion of pseudo complementary PNAs. In order to obtain efficient binding, the target (and thus the PNAs) should contain at least 50% AT (no other sequence constraints), and in the PNA oligomers all A/T base pairs are substituted with...

Triplex Triplex Invasion Duplex Invasion Double Duplex Invasion Tail-Ciamp... 

PNA targeting of duplex DNA is not limited to homopurine sequences. Under special circumstances (high negative superhelical stress) mixed purine-pyrimidine PNA-peptide conjugates can bind by duplex invasion (Fig. 4.7) [31], but such complexes are of limited stability. However, using a set of pseudo-complementary PNAs containing diaminopurine-thiouracil substitutions, very stable double duplex invasion complexes can be formed (Fig. 4.4) and the only sequence requirement is about 50% AT content. Very recently, it was also demonstrated that reasonably stable helix invasion complexes can be obtained with tail-clamp PNA comprising a short (>six bases) homopyrimidine bis-PNA clamp and a mixed sequence tail extension [32] (Fig. 4.7). 

Bentin T, Nielsen P.E. Combined tri-plex/duplex invasion of double-stranded DNA by Tail-Clamp peptide nucleic acids (PNA). (Submitted)... 

Lohse j., Dahl O., Nielsen P.E. Double duplex invasion by peptide nucleic acid a general principle for sequence-specific... 

Lohse J, Dahl O, Neilsen PE (1999) Double duplex invasion by peptide nucleic acid a general principle for sequence-specific targeting of double stranded DNA. Proc Natl Acad Sci USA 96 11804-11808 Lonn U, Lonn S, Nylen U, Windblad G (1990) Bleomycin-induced DNA lesions are dependent on nucleosome repeat length. Biochem Pharmacol 39(1) 101-107 Lopez-Larraza DM, Bianchi NO (1993) DNA response to bleomycin in mammalian cells with variable degrees of chromatin condensation. Environ Mol Mutagen 21(3) 258—264 Lopez-Larraza DM, Padron J, Rond NE, Vidal Rioja LA (2006) Chromatin condensation and differential sensitivity of mammalian and insect cells to DNA strand breaks induced by bleomycin. Mutat Res 16 April [Epub ahead of print]... 

Lohse, J., Dahl, O. and Nielsen, P.E. (1999). Double duplex invasion by peptide nucleic acid a general principle for sequence-specific targeting of double-stranded DNA. Proc. Natl. Acad. Sci. USA, 96, 11804-11808. 

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. 

Duplex ultrasonography is the most commonly used test to diagnosis DVT. It is a non-invasive test that can measure the rate and direction of blood flow and visualize clot formation in proximal veins of the legs. It cannot reliably detect small blood clots in distal veins. Coupled with a careful clinical assessment, it can rule in or out (include or exclude) the diagnosis in the majority of cases. 

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. 

For the present site-selective scission of double-stranded DNA, both pcPNA additives must have flanking portions so that gap-like structures are formed in the double-stranded DNA. Thus, no site-selective scission was observed when pcPNA 3 and pcPNA 4 were combined as additives [Figure 7.10(a), lane 4], These two pcPNAs are completely complementary (their duplex is not much formed due to mutual steric repulsion under the conditions employed), and thus no gap-like structures are produced in the invasion complex [see structure at the bottom of Figure 7.9(a)], No scission occurred in the absence of pcPNA additives, as expected (lane 2). 

Although duplex sonography is non-invasive and widely available, there are some difficulties that any ultrasound service must deal with (Box 12.1). Nonetheless, with stringent quality control and ideally with confirmation of stenosis by an independent observer, duplex sonography is now the most common way that carotid stenosis severe enough to warrant surgery is diagnosed (Chappell et al. 2006). 

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.

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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