Template switching

DNA adducts most likely reflects increased DNA repair such as nucleotide excision repair and postreplication repair including translesion synthesis, gap filling, and template switching during replication (27,28). 

Fig. 4.1. Schematic representation of die StEP process using two parental DNA sequences. (1) Denatured template DNAs are primed widi defined primers. (2) The partially extended primers produced by very brief annealing/extension randomly reanneal to different parent sequences (template switching). (3) Novel recombinants are created through multiple cycles of annealing/extension and strand switelling, hi principle, StEP is also an error-prone amplification process dial introduces additional point mutations (white circles).

Annealing of fragments and self-priming in PCR leads to fragment extension and incorporation of new mutations, and then template switching... 

Friseia, T. MacGillivray, L. R., Template Switching A Supermolecular Strategy for the Quantitative, Gram-Scale Construction of a Molecular Target in the Solid State. Chem. Commun. 2003, 1306-1307. 

Figure 22.20. Models of two damage tolerance mechanisms. At the lesion site, template switching (the left pathway) uses the newly synthesized daughter strand as the template for DNA synthesis, thus, bypassing the lesion in an error-free manner. In contrast, translesion synthesis (the right pathway) directly copies the damaged site on the template. Consequently, mutations, shown as a square, are often generated opposite the lesion.

Figure 22.24. A molecular switch model for the control of the two pathways of DNA damage tolerance, template switching, and translesion synthesis. The PCNA processivity DNA clamp is shown as a homotrimer. Both SUMO-modification (S) and ubiquitination (U) occur at the K164 position of PCNA. [Adapted from Stelter, P., and Ulrich, H. D. Nature 425,188-191, 2003.]...

Fig. 2. Strategies for uniform labeling of double-stranded DNA. (A) Nick translauon involves the 5 - 3 exonuclease and DNA polymerase functions of E. coli DNA polymerase 1 in the translocation of a single-strand break in a DNA strand. Trcuislocation of the breakpoint occurs in the 5 - 3 direction as a result of concomitant nucleotide hydrolysis and polymerization. (B) Template switching involves the extension of a DNA chain at a single-strand break, in a reaction where DNA is duplicated, rather than replaced as in nick treuislation.

Bohler C, Nielsen PE, Orgel LE, Template switching between PNA and RNA oligonucleotides. Nature 1995 376 578-581. 

DNase I stock solutions are stored at -2O C (1 mg/ml) in 5- xl aliquots (each aliquot is used once). Variation in the activity of DNase I preparations is often observed and the exact amount needed to introduce the desired number of nicks should be determined for each enzyme batch. Sometimes template switches occur which will result in snap-back structures (zero-binding nucleic acid), which remain S, nuclease-resistant upon denaturation. Rigby et al. (1977) suggested that this effect was due to a differential loss of 5 - 3 exonuclease activity upon storage leading to a displacement of the nicked strand and a template switch from the complementary... 

Figure 4-5. In vitro recombination by the staggered extension process (StEP) 11S1. Only one primer and single strands from two parents are shown. Fast annealing and extension cycles during PCR of the parent genes cause template switching of the extending strand. After full-sized recombined genes are synthesized, parent genes are removed by treatment with Dpnl.

Fig. 5. Two alternative models for error-free PRR via recombinational processes. (A) A strand exchange model, and (B) a template switching model. Both models propose that progression of leading strand synthesis in the presence of replicationblocking DNA damage (represented by a triangle) requires the association of the two nascent DNA strands, followed by resolution of the intermediary structure via (A) cleavage of the Holliday junction or (B) reverse branch migration. Adapted from Broomfield et al. (2001).

There is also continued interest in the systematic placement of reactive groups in the solid such that their chemical reactivities are determined by the reactants spatial relationships.This was the original premise of Schmidt s topochemistry and has important implications in modern solventless ("green") synthesisand even mechanochemistry. For example, work by MacGilliv-ray resulted in the solid-phase photochemical synthesis of paracyclophane 12 by a strategy termed "template switching" (Fig. 

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