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Table 7 Average stacking area overlap for dinucleotide steps in crystal structure datasets and fibre models

From: Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps

Dataset/Model

Intra-strand

Cross-strand

Cross-strand

Intra-strand

Total

 

(i1-i2)

(i1-j2)

(j1-i2)

(j1-j2)

 

All

Ring

All

Ring

All

Ring

All

Ring

All-atom

Ring

RR

          

ModelRNA

3.1 (0.7)

2.4 (0.1)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

1.0 (0.0)

0.1 (0.0)

4.1 (0.7)

2.4 (0.1)

freeRNA (347)

3.0 (1.1)

1.9 (0.8)

0.1 (0.3)

0.0 (0.0)

0.2 (0.3)

0.0 (0.0)

0.6 (0.7)

0.1 (0.2)

3.8 (1.1)

2.0 (0.8)

ADNA (94)

3.4 (1.1)

2.0 (1.0)

0.1 (0.2)

0.0 (0.0)

0.1 (0.2)

0.0 (0.0)

0.6 (1.0)

0.1 (0.3)

4.3 (1.0)

2.1 (0.8)

fibre-BDNA

4.4 (0.9)

2.1 (0.1)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

4.8 (1.1)

0.2 (0.0)

9.2 (0.2)

2.3 (0.1)

BDNA (107)

4.2 (1.6)

2.1 (1.3)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

4.6 (1.4)

0.4 (0.5)

8.8 (1.8)

2.5 (1.2)

RY

          

ModelRNA

5.2 (0.9)

3.1 (0.1)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

5.7 (0.9)

3.2 (0.1)

10.9 (1.5)

6.4 (0.1)

freeRNA (210)

5.1 (1.1)

2.9 (0.9)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

5.4 (1.3)

2.7 (1.1)

10.5 (1.5)

5.6 (1.0)

ADNA (42)

5.4 (1.1)

2.9 (1.0)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

6.2 (1.2)

2.7 (1.0)

11.6 (0.9)

5.6 (0.7)

fibre-BDNA

3.0 (0.8)

0.4 (0.0)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

3.6 (1.2)

0.4 (0.0)

6.6 (1.4)

0.9 (0.0)

BDNA (48)

4.2 (2.0)

1.6 (1.1)

0.0 (0.2)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

4.9 (1.6)

1.6 (0.9)

9.1 (2.8)

3.2 (0.7)

YR

          

ModelRNA

0.4 (0.0)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

2.3 (1.1)

0.9 (0.0)

0.4 (0.0)

0.0 (0.0)

3.0 (1.1)

0.9 (0.0)

freeRNA (240)

0.1 (0.2)

0.0 (0.0)

0.8 (1.3)

0.4 (0.6)

2.3 (1.8)

1.0 (0.7)

0.2 (0.3)

0.0 (0.1)

3.4 (0.9)

1.4 (0.4)

ADNA (59)

0.3 (0.5)

0.1 (0.2)

0.2 (0.7)

0.1 (0.3)

3.2 (1.7)

1.2 (0.8)

0.3 (0.4)

0.0 (0.1)

4.0 (0.9)

1.4 (0.6)

fibre-BDNA

1.5 (0.0)

0.0 (0.0)

0.0 (0.0)

0.0 (0.0)

0.2 (0.3)

0.0 (0.0)

1.5 (0.0)

0.0 (0.0)

3.2 (0.3)

0.0 (0.0)

BDNA (57)

2.2 (1.5)

0.1 (0.3)

0.1 (0.2)

0.0 (0.0)

0.2 (0.5)

0.0 (0.0)

2.6 (1.8)

0.2 (0.4)

5.0 (2.0)

0.4 (0.5)

  1. The stacking area overlap was grouped for RR, RY and YR steps in free RNA, ADNA and BDNA datasets and for A and B-form fibre models. Two sets of calculations were carried out by considering: i) all atoms including ring and exocyclic groups in each nucleotide base and ii) only ring atoms. Both intra-strand and cross-strand overlap areas are listed. Units are in Å2. See Figure 4 for the nomenclature used to refer to intra and inter-strand base overlaps.