BIOINORGANIC CHEMISTRY A Short Course Second Edition

266 GROUP I AND II METALS IN BIOLOGICAL SYSTEMS: GROUP II

out at the phosphate 5 ′ to the cleavage site, but this site was at least 20 Å from
the A 9 – G 10.1 Me 2+ binding site. The structure indicated that a destabilized sub-
strate strand might twist to put the cleavage site into position for cleavage of
the scissile phosphate bond.
In the following year, Scott and co - workers solved the X - ray crystallo-
graphic structure of an all - RNA hammerhead ribozyme with a 2 ′ - OCH 3 group
incorporated at the active site cytosine (C 17 ) to prevent cleavage (PDB:
1MME).^35 This structure differed from that of 1HMH in several important
ways: (1) it was an all - RNA ribozyme rather than an RNA – DNA hybrid; (2)
the connectivity of the ribozyme backbone strands was different (for instance

Figure 6.12 Secondary structure of hammerhead ribozyme constructs used for bio-
chemical, spectroscopic, and kinetic studies. (A) the HH α 1 ribozyme and (B) the HH8
ribozyme. (Reprinted with permission from Figure 1B of reference 47 .)

A

U

U

C

U

G

U

U

U

G A

A

A

A

C

U

A

G

U

C

A

G

17

1.5

1.4

1.3

1.2

1.1

2.5

2.4

2.3

2.2

2.1

4

5

6 3

Domain I

G

11.4

11.3

11.2

12

13

14

11.1 G

15.1

15.3

15.4

15.2

10.4

10.3

10.2

10.1

9

8

7

16.2

16.4

16.3

Domain II

scissile bond

C 16.1

G

C

A

A

Helix III

3 ′ 5 ′

5 ′

3 ′

G

Helix I

Helix II

U — A

U — A

A — U

C — G

A

A

A

G

G

15.1

14

9

13

17

6

12

11.1

10.1

—

C

G

—

C

C

G GUCG1.1

CCAGCGG2.1

16.1

C

—

G 43

7

—

8

5

A

G

C

G

G

C C

G

G

A

A

A

C

C

A

B

HH8 hammerhead ribozyme used in biochemical experiments.

G

5'

3'

3'

5'

stem III

stem II

stem I

Hammerhead Ribozyme HHα1, 17 nt ribozyme, 27 nt substrate

Used in biochemical experiments.

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