Covalent strategy

Molecular Design of Artificial Restriction Enzymes (Covalent vs. Non-Covalent Strategy) 161... 

Covalent Strategy for the First-generation of Artificial Restriction Enzymes... 

This covalent" strategy is very successful for site-selective DNA scission. However, the scission is not sufficiently efficient and must be promoted for practical applica-... 

Figure 7.1 Site-selective hydrolysis of DNA using (a) covalent and (b) non-covalent strategies.

To accomplish site-selective DNA scission using the non-covalent strategy, we need both (i) molecular scissors that show sufficiently high substrate-specificity and (ii) hot spots" that are formed at predetermined positions in substrate DNA and are hydrolyzed preferentially by these molecular scissors. 

Non-covalent strategy has been used also for site-selective scission of RNA (a) D. Hiisken, G. Goodall, M. J. J. Blommers, W. Jahnke,... 

Non-covalent Strategy for the Second-generation of Artificial Restriction Enzymes 162... 

Evidence for the hydrolytic scission of 11. Covalent strategy for site-selective scission of ... 

Fig. 16. Two strategies for site-selective scission of DNA and RNA (A) covalent strategy in which lanthanide complexes are covalently linked near the target phosphodiester linkages by using oligonucleotides that are complementary with the DNA and RNA substrates, and (B) non-covalent strategy , in which the target phosphodiester linkage is activated by some non-covalent interactions and dilferentiated from the others in the substrate in terms of intrinsic reactivity. The black ribbons show the oligonucleotides (or their equivalents) used for the artificial enzymes...

Hybridization of covalent and non-covalent strategies for improved site-selective DNA scission (Arishima etal, 2003)... 

Fig. 22. Combination of non-covalent and covalent strategies for improved site-selective DNA scission. Lane 1,5-base gap without ethylenediamine-A, triacetate groups lane 2,1-base gap with two ethylenediaminetriacetate groups at the gap site lane 3,1-base gap with four ethylenediaminetriacetate groups at the gap site lane 4,1-base gap with six ethylenediaminetriacetate groups at the gap site. The systems are schematically depicted in (B). The residue X is a derivative...

Fig. 25. Structures of the type-I RNA-activators (A) and the type-II RNA-activators (B) for non-covalent strategy ...

Fig. 27. Site-selective RNA scission by non-covalent strategy (A) the system composed of the type-I activator (DNApi -Aor) and Lu(III) and (B) the system composed of the type II activator (DNAl, -Acr + DNAr, ) and Lu(III).

Fig. 29. Effect of the sequence of target site on the site-selective RNA scission by non-covalent strategy . Lane 1, Lu(III) only lane 2, DNAF2-Acr/Lu(III) lane 3, DNApi-Acr/Lu(III) lane 4, DNAp3-Acr/Lu(III). At pH 8.0 and 37 °C for 2 h [RNAiJo = 1, [modified oligonucleotidejo = 10, and [LuCl3]o = 100 pM [NaCl]o...

By extending the non-covalent strategy described in sect. 14.1, new RNA cntters which selectively cut RNA substrates at two designated sites were prepared. With these tools, any portion of fragment ean be elipped ont of RNA substrates (fig. 31). These RNA cutters were prepared... 

Fig. 31. Two-site RNA cutters based on non-covalent strategy for clipping selected fragment from the RNA substrate. The two phosphodiester linkages in front of the two acridines are simultaneously activated and selectively hydrolyzed by lanthanide ions.

Covalent strategy enamine catalysis Intramolecular process Hajos-Parrish-Eder-Sauer-Wiechert reaction... 

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