Question

The Structure of DNA Elucidation of the threedimensional structure of DNA helped researchers understand how this molecule conveys information that can be faithfully replicated from one generation to the next. To see the secondary structure of double-stranded DNA, go to the Protein Data Bank website (www.rcsb.org). Use the PDB identifiers provided in parts (a) and (b) below to retrieve the structure summary for a double-stranded DNA segment. View the 3D structure using JSmol. The viewer select menu is below the right corner of the image box. Once in JSmol, you will need to use both the display menus on the screen and the scripting controls in the JSmol menu. Access the JSmol menu by clicking on the JSmol logo in the lower right corner of the image screen. Refer to the JSmol help links as needed. a. Access PDB ID 141D, a highly conserved, repeated DNA sequence from the end of the genome of HIV-1 (the virus that causes AIDS). Set the Style to Ball and Stick. Then use the scripting controls to color by element (Color > Atoms > By Scheme > Element

Short answer

Use PDB ID 141D to view the 3D DNA structure in Ball and Stick style and color it by element using JSmol.

Step-by-step solution

Access the Protein Data Bank

Go to the Protein Data Bank website at www.rcsb.org. Once there, locate the search bar to find the DNA segment you want to view.

Search for PDB ID 141D

In the search bar, input the PDB ID '141D' to locate the specific DNA structure of interest, which is a sequence from the genome of HIV-1.

Open the Structure Summary

After searching for PDB ID 141D, navigate to the structure summary page by clicking on the relevant result link to gather information about the DNA segment.

Launch the JSmol Viewer

On the structure summary page, look for the 3D structure visualization box. Click on it to launch the JSmol viewer, which will allow you to manipulate and view the DNA structure in three dimensions.

Set Viewing Style to Ball and Stick

Within the JSmol viewer, use the display menu to change the visualization style. Select 'Style' and choose 'Ball and Stick' to better observe the details of the DNA structure.

Color the Structure by Element

Open the JSmol menu by clicking on the logo in the lower right corner. Navigate to 'Color', select 'Atoms', then choose 'By Scheme', and finally select 'Element' to color the atoms according to their elemental type for clear differentiation.

Key concepts

3D molecular visualization

Visualizing the 3D structure of molecules like DNA helps researchers understand their complex form and function. By using specialized software, scientists can explore the intricate details of molecular configurations. It allows for an interactive look at atoms and their spatial arrangements.
This type of visualization is crucial in bioinformatics and molecular biology because:

• It reveals the spatial arrangements of molecules.
• It aids in understanding the chemical properties emerging from the 3D structure.
• It is essential for the study of interactions within biological systems.

Using tools like the JSmol viewer, mentioned later, provides a more hands-on approach to learning about the structure of molecules like double-stranded DNA.
Through visualization, we can better appreciate how specific configurations affect biological processes.

Protein Data Bank

The Protein Data Bank (PDB) is a vast repository for 3D structural data of biological molecules. This was established to provide researchers around the world with a centralized resource of molecular data.
PDB offers access to:

• Structures of proteins and nucleic acids, including DNA.
• Information contributed by scientists globally.
• Various formats and tools for data analysis, such as molecular viewers and scripts.

Searching the PDB is made straightforward with unique identifiers known as PDB IDs. For example, the PDB ID '141D' specifically references a piece of HIV-1 genomic DNA. Using PDB IDs, researchers can quickly locate and examine detailed molecular structures.

JSmol viewer

The JSmol viewer is an interactive tool used to visualize and manipulate 3D models of biological structures, directly online. Unlike static images, JSmol allows users to explore and rotate molecular structures, changing the way we engage with molecular data.
Key features of JSmol include:

• The ability to change visualization styles, such as 'Ball and Stick'.
• Scripting controls to modify elements like color and representation.
• Built-in help links to assist new users.

Working with JSmol enhances understanding by allowing students and researchers to experiment with different views and settings, such as coloring atoms by their elements for a clearer comprehension of molecular arrangements.

HIV-1 genome

The HIV-1 genome consists of the genetic material of HIV, the virus that causes AIDS. This genome is made up of RNA in the virus, which, upon infecting a host cell, is converted into DNA for incorporation into the host genome.
The importance of studying the HIV-1 genome includes:

• Understanding the mechanisms of viral replication.
• Identifying key targets for antiviral drugs.
• Gaining insights into mutations that lead to drug resistance.

The PDB ID '141D' refers to a part of this genome known as a conserved sequence, making it a crucial area of study for researchers combating HIV/AIDS.

double-stranded DNA

Double-stranded DNA is the standard form of DNA in biological organisms, featuring two complementary strands that form a double helix. This structure is fundamental for DNA's role in storing genetic information.
Features of double-stranded DNA include:

• Its antiparallel strands held together by hydrogen bonds between complementary bases.
• A helical shape that allows tight packing of long DNA molecules.
• Base pairing, where adenine pairs with thymine and guanine pairs with cytosine.

The discovery and visualization of this structure enabled significant advances in genetics and molecular biology, laying the foundation for understanding how genetic information is inherited and expressed.