Template directed ligation

Fig. 22 A schematic representation of chiroselective replication cycles. Homochiral peptides Tll and Tdd are produced autocatalytically while the heterochiral peptides TDL and Tdl result from uncatalyzed background reactions. Template-directed ligation reactions proceed through the intermediary of stereospecific noncovalent complexes and pass on stereochemical information from the homochiral products to the substrates, thus resulting in the amplification of homochiral products. Light and dark backgrounds denote regions of the sequence composed of L- and D-amino acids, respectively (Reproduced from [218], Copyright 2001, Nature)...

Fig. 3. A hypothetical ribozyme that can catalyze electron transfer. Aptamers than can bind NAD+ (and, hence, NADH) are selected, and the binding domain is mapped. An oligonucleotide tail that can bind to an unpaired region near the NAD-binding domain is attached to FMN. The bound FMN-oligonucleotide will be adjacent to NADH when it is bound in the active site of the ribozyme. Electron transfer should occur owing to the proximity of the two substrates. The rate of the reaction can be controlled by varying the length of the oligonucleotide tail to vary the distance between NADH and FMN substrate. Although this catalyst is extremely simple (and employs the same principles of catalysis found in nonenzymatic template-directed ligation reactions), it would nevertheless demonstrate the ability of RNA to catalyze reactions other than phosphodiester bond transfers.

Scott GT, deVoe R (1954) The reversible replacement of potassium by rubidium in Ulva lactuca. J Gen Physiol 37 249-253 Seilacher A (2008) Ediacara - Leben wie auf einem anderen Planeten. In Betz O, Kohler H (eds) Die evolution des lebendigen. Attempto, Tubingen, pp 97-115 Seveiin K, Lee DH, Martinez JA, Ghadiii MR (1998) Peptide self-rephcation via template-directed ligation. Chem Eur 3 1017-1024... 

Over the last four decades, synthetic non-enzymatic oligonucleotide ligations have been explored as potential models for the evolution of replicating systems on the early Earth [2-11]. These studies have explored ligation reactions that occur on a template without protein/enzymatic catalysis. Such systems have both provided mechanisms for the early evolution of biopolymer catalysts and placed limits on template directed ligation. More recently, the lure of antisense molecules capable of disrupting specific gene expression has resulted in the exploration of backbone-modified nucleic acids [12-33]. 

Since it has not been possible to cover all the valuable contributions that have been made in these fields of study, we have instead organized the discussion around a minimal scheme for template directed ligation. This minimal scheme will be compared with the autonomous natural genomes that self-replicate via template directed polymerization reactions. The advantages and limitations of each step in the minimal scheme are discussed with respect to the structural diversity in the template that will make it possible to extend these reactions to new materials and new polymerization strategies. 

Figure 5-2 Scheme of template-directed ligation with steps 1, molecular recognition 2, ligation 3, product dissociation. 

Koppitz, M., Nielsen, P.E., Orgel, L.E. (1998). Formation of oligonucleotide-PNA-chimeras by template-directed ligation, J. Am. Chem. Soc., 120 4563... 

Peptide self-replication via template-directed ligation. Chem. Eur. J. 1997, 3, 1017-1023. 

The iEDDA reaction was further employed for template-directed ligation of DNA using fluorescent DNA probes consisting of quenched tetrazine-lluorophore conjugates and methylcyclopropene groups as dienophiles [77]. This method could in principle allow fluorescent detection of specific DNA and RNA sequences in living cells. 

Template-directed ligation of oligonucleotides is accomplished using nucleotide strands with 5 -alkyne and 3 -azide strands to produce DNA strands with an unnatural backbone at the ligation point 2-Propynyl substituted hemicyanine dyes are attached to azide-containing virus molecules... 

Intercalators could have also provided selective pressure toward the formation of a more uniform backbone. As discussed above, non-enzymatic template directed ligation reactions produce a mixture of 2, 5 and 3, 5 linkages, often with enrichment in 2, 5 linkages (65). Recent work in our laboratory has demonstrated that proflavine has a 25-fold higher affinity for 2, 5 -linked versus 3, 5 -linked RNA (66). However, other intercalators, such as ethidium bromide, favor the 3, 5 -linked RNA duplexes (66). It can therefore be postulated that if a given midwife molecule has a preferential association with a 3, 5 -linked RNA... 

---