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Table 2 Conditions of 3×pen aRNA cleavage evaluated during optimization of the reaction yield.

From: DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli

Reaction No. [3×pen aRNA]
(μM)*
Molar ratio 3×pen aRNA: Pen17zyme1/1B/1C: Pen17zyme2 Additional components
in the annealing buffer
[Mn2+] (mM)* Reaction
T (°C)
Time Additional Cycles
1 0.25 1:0:1 N/A 0 23 10 min 0
2 0.25 1:0:1 N/A 7.5 23 10 min 0
3 0.25 1:0:1 N/A 15 23 10 min 0
4 0.25 1:0:1 N/A 45 23 10 min 0
5 0.25 1:0:1 N/A 15 23 100 min 0
6 0.25 1:1(Pen17zyme1):0 N/A 15 23 100 min 0
7 0.25 1:1(Pen17zyme1B):0 N/A 15 23 100 min 0
8 0.25 1:1(Pen17zyme1C):0 N/A 15 23 100 min 0
9 0.25 1:5(Pen17zyme1B):0 N/A 15 23 100 min 0
10 0.25 1:1(Pen17zyme1B):0 N/A 15 23 17 h 0
11 0.25 1:1(Pen17zyme1B):0 N/A 15 40 100 min 0
12 0.25 1:1(Pen17zyme1B):0 10%EtOH 15 23 100 min 0
13 0.25 1:5(Pen17zyme1B):0 0.3 M KCl, 1.2 M NaCl 15 23 17 h 0
14 0.25 1:5(Pen17zyme1B):0 20% PEG 8000 15 23 17 h 0
15 0.25 1:5(Pen17zyme1B):0 500 μM spermine 15 23 17 h 0
16 0.25 1:5(Pen17zyme1B):0 N/A 15 23 17 h 50
17 0.25 1:5(Pen17zyme1B):0 2.2 M potassium acetate 15 23 17 h 0
18 0.25 1:5(Pen17zyme1B):0 3 M LiCl 15 23 17 h 0
19 0.80 1:1(Pen17zyme1B):1 500 μM spermine 15 23 17 h 0
20 0.80 1:10(Pen17zyme1B):1 500 μM spermine 15 23 17 h 0
21 0.80 1:20(Pen17zyme1B):2 500 μM spermine 15 23 17 h 0
22 0.80 1:10(Pen17zyme1B):10 500 μM spermine 15 23 17 h 0
23 0.80 1:10(Pen17zyme1B):10 500 μM spermine 15 23 17 h 6
24 0.80 1:10(Pen17zyme1B):10 500 μM spermine 15 23 40 h 0
25 0.80 1:10(Pen17zyme1B):10 500 μM spermine 15 23 72 h 0
26 0.80 1:10(bioPen17zyme1B):10(biopen17zyme2) 500 μM spermine 15 23 72 h 0
  1. * The value corresponds to the final concentration of the indicated component in the reaction mixture.