Answers.Body: <p>Not quite sure what you're asking, but I have found the Wikipedia page on <a href="https://en.wikipedia.org/wiki/Nucleic_acid_double_helix#Helix_geometries" rel="nofollow noreferrer">Nucleic acid double helix</a> to be quite informative for <a href="https://www.printables.com/model/79337-dna-model" rel="nofollow noreferrer">modeling DNA</a> for 3D printing and as flavour graphics. Here's the table of structural features (averaged, because they differ from base to base), which gives a value for the diameter of B-DNA of 20 Å (2.0 nm). That means that if you were to treat it as a full circle in cross section (not quite accurate), then the cross-sectional area would be (on average) π nm<sup>2</sup> (or 100 Å<sup>2</sup>) :</p>
  <div class="s-table-container"><table class="s-table">
  <thead>
  <tr>
  <th style="text-align: left;">Geometry attribute</th>
  <th style="text-align: center;">A-DNA</th>
  <th style="text-align: center;">B-DNA</th>
  <th style="text-align: center;">Z-DNA</th>
  </tr>
  </thead>
  <tbody>
  <tr>
  <td style="text-align: left;">Helix sense</td>
  <td style="text-align: center;">right-handed</td>
  <td style="text-align: center;">right-handed</td>
  <td style="text-align: center;">left-handed</td>
  </tr>
  <tr>
  <td style="text-align: left;">Repeating unit</td>
  <td style="text-align: center;">1 bp</td>
  <td style="text-align: center;">1 bp</td>
  <td style="text-align: center;">2 bp</td>
  </tr>
  <tr>
  <td style="text-align: left;">Rotation/bp</td>
  <td style="text-align: center;">32.7°</td>
  <td style="text-align: center;">34.3°</td>
  <td style="text-align: center;">60°/2</td>
  </tr>
  <tr>
  <td style="text-align: left;">bp/turn</td>
  <td style="text-align: center;">11</td>
  <td style="text-align: center;">10.5</td>
  <td style="text-align: center;">12</td>
  </tr>
  <tr>
  <td style="text-align: left;">Inclination of bp to axis</td>
  <td style="text-align: center;">+19°</td>
  <td style="text-align: center;">−1.2°</td>
  <td style="text-align: center;">−9°</td>
  </tr>
  <tr>
  <td style="text-align: left;">Rise/bp along axis</td>
  <td style="text-align: center;">2.3 Å (0.23 nm)</td>
  <td style="text-align: center;">3.32 Å (0.332 nm)</td>
  <td style="text-align: center;">3.8 Å (0.38 nm)</td>
  </tr>
  <tr>
  <td style="text-align: left;">Pitch/turn of helix</td>
  <td style="text-align: center;">28.2 Å (2.82 nm)</td>
  <td style="text-align: center;">33.2 Å (3.32 nm)</td>
  <td style="text-align: center;">45.6 Å (4.56 nm)</td>
  </tr>
  <tr>
  <td style="text-align: left;">Mean propeller twist</td>
  <td style="text-align: center;">+18°</td>
  <td style="text-align: center;">+16°</td>
  <td style="text-align: center;">0°</td>
  </tr>
  <tr>
  <td style="text-align: left;">Glycosyl angle</td>
  <td style="text-align: center;">anti</td>
  <td style="text-align: center;">anti</td>
  <td style="text-align: center;">C: anti,<br> G: syn</td>
  </tr>
  <tr>
  <td style="text-align: left;">Sugar pucker</td>
  <td style="text-align: center;">C3'-endo</td>
  <td style="text-align: center;">C2'-endo</td>
  <td style="text-align: center;">C: C2'-endo,<br>G: C2'-exo</td>
  </tr>
  <tr>
  <td style="text-align: left;">Diameter</td>
  <td style="text-align: center;">23 Å (2.3 nm)</td>
  <td style="text-align: center;">20 Å (2.0 nm)</td>
  <td style="text-align: center;">18 Å (1.8 nm)</td>
  </tr>
  </tbody>
  </table></div>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-07-29T07:39:02.670Z
Answers.Text: Thanks for your answer though! You suggest taking cross sectional area of a circle for DNA?
Answers.UserDisplayName: Katie Smith
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-07-29T19:58:22.157Z
Answers.Text: As I said, I'm not sure what you're asking, so I don't know if cross-sectional area would be appropriate. I don't know if (for example) electron density matters.
Answers.UserDisplayName: gringer
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-07-26T22:28:09.547Z
Answers.LastActivityDate: 2024-07-26T22:33:12.370Z
Answers.LastEditDate: 2024-07-26T22:33:12.370Z
Answers.UserDisplayName: gringer
Body: <p>i wish to determine the persistence length of double strand DNA with different bases (10 to 150). i found an equation: P= B_s/ K T where B_s is the bending stiffness and B_s= E * I where I is the cross sectional area</p>
  <p>The persistence length qualifies the bending stiffness of a polymer. If the pieces of the polymer is less than persistence length, then the molecule behaves like a rigid rod. however, if it's longer, the polymer can bend. Such is the case of double strand DNA.</p>
  <p>So, I just need to determine cross section of double strand DNA.</p>
  <p>Also, has anyone ever used oxDNA on Python before? i want to determine the persistence length on oxDNA as well to be able to compare the values</p>
  <p>Well, i am currently exploring oxDNA. And for the cross section, i wonder if i should take that of a cylinder or circle..</p>
  
Tags: <python><dna>
Title: What is the cross sectional area of DNA? Can we find persistence length using oxDNA?
ThreadText: # What is the cross sectional area of DNA? Can we find persistence length using oxDNA?
  
  (Asked by: username_0 on 2024-07-26)
  
  i wish to determine the persistence length of double strand DNA with different bases (10 to 150). i found an equation: P= B\_s/ K T where B\_s is the bending stiffness and B\_s= E \* I where I is the cross sectional area
  
  The persistence length qualifies the bending stiffness of a polymer. If the pieces of the polymer is less than persistence length, then the molecule behaves like a rigid rod. however, if it's longer, the polymer can bend. Such is the case of double strand DNA.
  
  So, I just need to determine cross section of double strand DNA.
  
  Also, has anyone ever used oxDNA on Python before? i want to determine the persistence length on oxDNA as well to be able to compare the values
  
  Well, i am currently exploring oxDNA. And for the cross section, i wonder if i should take that of a cylinder or circle..
  
  **Tags:** python, dna
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-07-26. Score: 0
  
  Not quite sure what you're asking, but I have found the Wikipedia page on [Nucleic acid double helix](https://en.wikipedia.org/wiki/Nucleic_acid_double_helix#Helix_geometries) to be quite informative for [modeling DNA](https://www.printables.com/model/79337-dna-model) for 3D printing and as flavour graphics. Here's the table of structural features (averaged, because they differ from base to base), which gives a value for the diameter of B-DNA of 20 Å (2.0 nm). That means that if you were to treat it as a full circle in cross section (not quite accurate), then the cross-sectional area would be (on average) π nm2 (or 100 Å2) :
  
  | Geometry attribute | A-DNA | B-DNA | Z-DNA |
  | --- | --- | --- | --- |
  | Helix sense | right-handed | right-handed | left-handed |
  | Repeating unit | 1 bp | 1 bp | 2 bp |
  | Rotation/bp | 32.7° | 34.3° | 60°/2 |
  | bp/turn | 11 | 10.5 | 12 |
  | Inclination of bp to axis | +19° | −1.2° | −9° |
  | Rise/bp along axis | 2.3 Å (0.23 nm) | 3.32 Å (0.332 nm) | 3.8 Å (0.38 nm) |
  | Pitch/turn of helix | 28.2 Å (2.82 nm) | 33.2 Å (3.32 nm) | 45.6 Å (4.56 nm) |
  | Mean propeller twist | +18° | +16° | 0° |
  | Glycosyl angle | anti | anti | C: anti,  G: syn |
  | Sugar pucker | C3'-endo | C2'-endo | C: C2'-endo, G: C2'-exo |
  | Diameter | 23 Å (2.3 nm) | 20 Å (2.0 nm) | 18 Å (1.8 nm) |
  
  > **Comments:**
  > **username_0**: Thanks for your answer though! You suggest taking cross sectional area of a circle for DNA?  
  > **username_1**: As I said, I'm not sure what you're asking, so I don't know if cross-sectional area would be appropriate. I don't know if (for example) electron density matters.  
  
  ---
  
  