Ligation, nucleic acids

Seckute J, Yang J, Devaraj NK (2013) Rapid oligonucleotide-templated fluorogenic tetrazine ligations. Nucleic Acids Res 41(15) el48. doi 10.1093/nar/gkt540... 

The use of click chemistry is a promising strategy as a postsynthetic ligation for nucleic acids in order to circumvent the time-consuming synthesis of phosphoramidites as DNA building blocks [31, 32]. This is particularly relevant for several fluorophores that are unstable under the acidic, oxidative, or basic conditions of automated DNA phosphoramidite chemistry and DNA workup. 

In addition, Dose and Seitz (2005) employed native chemical ligation to synthesize peptide nucleic acids (PNAs) by linking shorter segments of PNAs to make long contiguous strands, which could not be made through typical oligo synthesis procedures. 

Dose, C., and Seitz, O. (2005) Convergent synthesis of peptide nucleic acids by native chemical ligation. Org. Lett. 7(20), 4365-4368. 

Figure 10.13 Phosphoryl-transfer reactions. The figure shows (a) nucleotide polymerization, (b) nucleic acid hydrolysis, (c) first cleavage of an exon-intron junction by group I ribozyme (d) and by a group II ribozyme, (e) strand transfer during transposition and (f) exon ligation during RNA splicing. (From Yang et al., 2006. Copyright 2006, with permission from Elsevier.)...

Levy, M. and Ellington, A. D. (2003). Peptide-template nucleic acid ligation, / Mol Evol, 56, 607-15. 

Gel purification is a rapid and efficient way of isolating nucleic acids of the appropriate size from syntheses, PCR reactions, ligations, or tethered product-binding reactions. For preparative separation of random libraries (—150 bases) the following two types of polyacrylamide gels are used ... 

Another issue that should be considered carefully is the purity of nucleic acids used at each step. Since it is known that RNA can self-cleave and ligate, DNA produced from PCR that is entering the next cycle of selection should be size-purified by native PAGE (Section 8.3.1.5). Finally, all solutions should be prepared from DNase/RNase-free reagents in DEPC H20, 0.2 pm filtered, and stored at 4 °C (buffers) or —20 °C (especially nucleotide solutions). 

Buzayan, J.M., Hampel, A. and Bruening, G. (1986) Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA. Nucleic Acids Res., 14, 9729-9743. 

Bain, J. D., and Switzer, C. (1992). Regioselective ligation of oligoribonucleotides using DNA splints. Nucleic Acids Res. 20, 4372. 

Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 2002 30(12) e57. 

Also, template controlled ligation of peptide nucleic acids is possible using EDC in an imidazole buffer. The highest selectivity is obtained using a peptide condensation that forms an abasic site. An example is the following reaction which produces the peptide 673. 

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