BIOINORGANIC CHEMISTRY A Short Course Second Edition

MAGNESIUM AND CATALYTIC RNA 265

The structure showed that the three base - paired stems I, II, and III form type
A - DNA helices and that the core contained the two conserved structural
domains described in the previous paragraph. A single Me 2+ ion was bound in
close proximity to the pro - R p oxygen of A 9 ’ s phosphate and the N 7 position
of G 10.1. The phosphodiester backbone of the DNA inhibitor strand was splayed

Figure 6.11 Secondary structure of the HH16 hammerhead ribozyme used for bio-
chemical, spectroscopic, and kinetic studies.

Conserved residues underlined italicized.

Figure Key

Enzyme residues in bold and larger font size.
Substrate residues in plain text and smaller font size.
Cleavage site nucleotide, C17, in a dashed box.
Scissle C17-G1.1 phosphate bond marked
with arrow.

noncanonical bases

single hydrogen bonds between bases

and backbone riboses

single hydrogen bonds between these bases

C A A A A A

L2.1

U

U

C

C

C

A U16.1

C

UC UC C

CA U A CC

C 3

U 4

U 7 A 6

A 9

C G GG

1.11.2 1.31.4 1.5 1.6

G G

2.1 2.2 2.32.42.52.6

G 5

G 8

G G10.1

A 13 A^14

11.1G^12

15.1

17

10.4C C

10.3

G

11.4

G

11.3

C

11.2

G

G

G

15.2 G

15.3

15.4

16.2

16.3

16.4

15.5 16.5

L2.2 G 10.2

L2.3

L2.4

Cleavage Site

3'

5'

3' 5'

Hammerhead ribozyme HH16, 38 nt ribozyme, 17 nt substrate.

Used in biochemical experiments. Two representational methods shown.

C

A

U

U

G

U

U A

A

C

C

C

A

C

A

C

C

C

A A

A

G C

G C

C G

G A

A

A

C

A

C

G

U

C

U

U

C

C

G

U

G

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

G

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

16.1

G

G

G

G

G

G

5'

3'

stem (helix) I

stem (helix) II

L2.4

L2.3 L2.2

L2.1

stem (helix) III

3' 5'