6) Conformation of Polynucleotide
Chain (A chain of phosphate group
and sugar)
For assembling DNA/RNA models, the
conformations of DNA-A and DNA-B
Polynucleotide Chain are the basics and
have important meanings.
Make a phoshate group and a sugar into
one pair and prepare polymucletide
chains of DNA-A type conformation
(C3' -endo) and DNA-B type (C2' -endo).
When you think of them as DNA-B type
(C2'-end) in certain cases and as
DNA-Atype (C3'-end) in other cases,
model assembling work will be easier.
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Fig. 18
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Fig. 18 / Fig. 19 / Fig. 20 / Fig. 21
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| 6.1 | A Polynucleotide chain is formed by inserting male end(horn) C5' of Deoxyribose into female bond 05' of phosphate group repeatedly. Fig-18/21 show charateristic forms of one unit Deoxy-ribose and phosphate group of in DNA-A, B, -Z models.
Assemblage will be easier if you enlarge Fig-18/21 with Copying machine and manually color 01', 03', 05'. P etc in red, yellow etc for better understanding.
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| 6.2 | For DNA-Z, prepare polynucletide chains of DNA-A (C3'-end) and DNA-B (C2'-end) each in half quantities. For those for DNA-A type, twist at between C4'-C5', C5'-O5', O5'-P, C3'-O3' referring to colored Fig -20. For those for DNA-B type, twist at between 05'-P(Fid-21 DNA-Z Form-C). Then, the outline of the polynucleotide chains will be obtained.
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Fig. 19
Fig. 20 / Fig. 21
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| 6.3 | For Double helices RNA, conformation of the polynucleotide chain resembles that of DNA-A but is slightly different (Fig-22)
After nearly completing the model, make corrections in accordance with Torsion Angle (ref Sect 6.5 next).
Fig. 22
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| 6.4 | Concerning conformation of polynucleotide chain, angles between atoms are defined and their values are worked out in the Torsion AngleTable.
Fig. 23
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Torsion Angle Table (Reference)
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 |  |  |
 |  |  |
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| A form | 178 | 313 | 275 | 208 | 45 | 83 | 26 |
| B form | 155 | 264 | 314 | 213 | 36 | 152 | 84 |
| Z1 form | C | 266 | 80 | 223 | 221 | 56 | 138 | 21 |
| G | 256 | 291 | 47 | 179 | 191 | 99 | 248 |
RNA-11
(Poly-A, -U) | 208.9
(4.5) | 285.7
(4.7) | 297.9
(5.1) | 179.8
(5.0) | 48.1
(1.8) | 83.2
(- ) | 16.0
(2.8) |
· Backbone conformation in Nucleotides
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| 6.5 | Torsion Angle -Angle phi () between C5and 05
Hold C4and C5in your left hand, bring them to your side and fix them in place. Put P and 05to the other side, holding in your right hand. If C5and 05are rotated clockwise, it is Positive direction.
Protracter: Cut off to bond thickness for easy meaauring of Torsion angles.
Fig. 25
However, when you actually do the above, you will notice it is the same thing to rotate C4and C5clockwise, fixing P and 05in place.
(Positive is to fix your side and to rotate the other side clockwise.)
Fig. 24
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