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Advanced DNA Structure Generation and Manipulation with mdna¶
In this section, we'll explore more advanced functionalities of the mdna module, focusing on generating various DNA structures, modifying their topological properties, and using custom shapes. These tools allow you to create complex DNA configurations for detailed structural analysis.
1. Basic DNA Creation¶
You can create a DNA structure with no initial sequence, which will output a placeholder sequence ('DDD').
Alternatively, you can provide a specific sequence or define the number of base pairs (n_bp) to generate a random sequence.
# Or provide a sequence
dna = mdna.make(sequence='GCGCGCGCGC')
dna.describe()
# Or provide a number of basepairs, resulting in a random sequence
dna = mdna.make(n_bp=10)
dna.describe()
2. Circular DNA and Topology Manipulation¶
The mdna module allows the creation of circular DNA (minicircles) and the manipulation of their topological properties, such as the linking number (Lk).
# Or make a minicircle DNA in circular form
dna = mdna.make(n_bp=200, circular=True)
print('Lk, Wr, Tw', dna.get_linking_number())
dna.draw()
# Lets also minimize the DNA configuration
dna.minimize()
# See the final configuration
dna.draw()
# or save it to a file
dna.save('minimized_nbp_200_closed.pdb')
You can also change the linking number by under- or overwinding the DNA using the dLk parameter.
# Also change the linking number by under or overwinding the DNA using the dLk parameter
dna = mdna.make(n_bp=200, circular=True, dLk=8)
dna.describe()
dna.get_linking_number()
# Minimize the DNA configuration, note to equilibrate the writhe use equilibrate_writhe=True, otherwise the Lk will not be conserved
dna.minimize(equilibrate_writhe=True)
dna.get_linking_number()
3. Using Custom Shapes¶
You can create DNA structures that follow custom shapes using the Shape class. For instance, you can generate DNA in the shape of a helix or define a completely custom path using control points.
# We can also use custom shapes using the Shape class
control_points = mdna.Shapes.helix(height=3, pitch=5, radius=7, num_turns=4)
dna = mdna.make(n_bp=300, control_points=control_points)
dna.draw()
# Or use the control points to define a custom shape
control_points = np.array([[0,0,0],[30,10,-10],[50,10,20],[3,4,30]])
dna = mdna.make(n_bp=100, control_points=control_points, sequence=['A']*100)
dna.draw()
dna.describe()
dna.sequence
4. Extending DNA¶
The extend function allows you to add additional bases to an existing DNA structure, either in the forward or reverse direction.
# We can also extend our DNA
dna.extend(sequence=['G']*120)
# Or extend it in the opposite direction
dna.extend(sequence=['C']*120, forward=False)
dna.draw()
5. Connecting DNA Strands¶
You can generate two separate strands of DNA and connect them to form a continuous double helix. The connect function optimizes the connection to minimize the twist between the strands.
# Lets generate two strands of DNA and displace the second one away from the first one
dna0 = mdna.make(sequence='AAAAAAAAA', control_points=mdna.Shapes.line(1))
dna1 = mdna.make(sequence='GGGGGGGGG', control_points=mdna.Shapes.line(1) + np.array([4,0,-5]))
# Now we can connect the two strands, the function will find the optimal number of basepairs to connect the two strands to minimize the twist
dna2 = mdna.connect(dna0, dna1)
dna2.draw()
dna2.describe()
6. Visualization¶
For advanced visualization, you can use nglview to visualize the Monte Carlo minimized configuration of the DNA structure.
This concludes the advanced tutorial on generating, manipulating, and visualizing DNA structures with the mdna module. These examples illustrate the flexibility and power of the module in creating detailed and customized DNA configurations for a wide range of research applications.