Coribozymes cofactorassisted ribozymes

Aptamers are capable of recognizing targets as small as metal ions (most RNA enzymes are metallo-ribozymes using metal as cofactors). They can interact with a wide variety of molecules that are important for metabolism, including amino acids, porphyrins, nucleotide factors, coenzymes, small peptides, and short oligonucleotides (Illangasekare and Yarus, 1997; Jadhav and Yarus, 2002a; Joyce, 2002; McGinness et al., 2002; Reader and Joyce, 2002) (Table 3.5).

The first aptamer selected for a biological cofactor was an ATP-binding RNA (Sassanfar and Szostak, 1993; Fig. 3.8) showing a change in the conformation of the RNA and number of close contacts between the ATP and RNA.

Since the ATP motif also binds adenosine and NAD+, the idea was that it could serve to bind adenosine-derived cofactors as well. The presence of adenosine in many common biological cofactors (ATP, CoA, FAD, NAD+, SAM, coenzyme B12) has been postulated to reflect an evolutionary origin for modern metabolism. It is even possible to consider that catalytic groups that were part of nucleic enzymes were incorporated in specific amino acids rather than being "retained" as coenzymes. This could be the case for imidazole, the functional group of his-tidine, whose present synthesis in the cell is triggered by a nucleotide (Maurel and Ninio, 1987; Benner et al., 1989; Maurel, 1992). Further, the use of organic cofactors was illustrated by a DNA enzyme that requires histidine as a cofactor during RNA cleavage (Szazani et al., 2004).

A small aptamer recognizing anionic moieties has also been obtained by Szostak and co-workers (Szazadni et al., 2004). In this case the significant interactions are with the phosphate of ATP (Kd of 5 mmol/L compared with the AMP Kd of 5.5

Table 3.5 Small targets of RNA aptamers

Target

Minimal size

Kd (mmol/L)

Reference

Adenine

-

10

Meli et al., 2002

Guanine

32

1.3

Kiga et al., 1998

Guanosine

-

32

Connell and Yarus, 1994

l-Adenosine

58

1.7

Klussmann et al., 1996

Theophylline

38

0.1

Jenison et al., 1994

Caffeine

-

3 500

Jenison et al., 1994

Riboflavin

35

0.5

Burgstaller and Famulok, 1994

NMN/NAD

-

2.5

Lauhon and Szostak, 1995

d-ATP

40

14

Sassanfar et al., 1993

Cyanocobalamin

35

88nmol/L

Lorsch and Szostak, 1994

l-Valine

-

12 000

Majerfeld and Yarus, 1994

l-Citrulline

44

65

Famulok, 1994

i-Arginine

-

0.33

Geiger et al., 1996

d-Arginine

38

135

Nolte et al., 1996

Biotin

31

6

Wilson et al., 1998

HO OH

NNNNN NNNNnn

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