Question

In the field of nanotechnology, DNA is used like Velcro to assemble tiny particles into structures that are \(<0.0001 \mathrm{mm}\) in size. Draw a model to illustrate how two particles (a circle and a square) could be brought together by linking them to short single-stranded DNA molecules. If the DNA sequence linked to the circle is GGATC, then provide the sequence linked to the square and identify the 5' and 3' ends of each strand.

Short answer

The complementary DNA sequence for the square particle is CCTAG with the 5' end starting at C and the 3' end at G. When illustrating the model, draw the single-stranded DNA sequence (GGATC) linked to the circle particle, starting with 5'-G and ending with 3'-C. Draw the complementary single-stranded DNA sequence (CCTAG) linked to the square particle, starting with 5'-C and ending with 3'-G. Show the DNA strands pairing through dashed lines between complementary base pairs, bringing the particles together like Velcro.

Step-by-step solution

Understand DNA sequence complementarity

In DNA, the bases adenine (A) pairs with thymine (T) and guanine (G) pairs with cytosine (C). This means that the complementary sequence for a given DNA strand will have T in place of A, A in place of T, C in place of G, and G in place of C.

Find the complementary sequence

Given the DNA sequence linked to the circle as GGATC, we can now find the complementary sequence for the square: G -> C G -> C A -> T T -> A C -> G Hence, the DNA sequence linked to the square is CCTAG.

Determine the 5' and 3' ends of each strand

In a DNA strand, the 5' end refers to the end with a free phosphate group, while the 3' end refers to the end with a free hydroxyl group. Generally, sequence notation lists the nucleotides in the 5' to 3' direction, so we can assume that the given sequences are written in this format. For the circle, the sequence GGATC has the 5' end starting at G and the 3' end at C. For the square, the sequence CCTAG has the 5' end starting at C and the 3' end at G.

Illustrate the model

Now we can draw a model to illustrate the linking process: 1. Draw a circle and a square representing the two nanoparticles. 2. Draw the single-stranded DNA molecule (GGATC) attached to the circle, starting with 5'-G and ending with 3'-C. 3. Draw the complementary single-stranded DNA molecule (CCTAG) attached to the square, starting with 5'-C and ending with 3'-G. 4. Show the DNA strands pairing through dashed lines between complementary base pairs: G-C, G-C, A-T, T-A, and C-G. Remember that the 5' end of each strand is connected with the nanoparticles, while the free 3' end is available for base pairing with the complementary strand, bringing the particles together like Velcro.

Key concepts

DNA Sequence Complementarity

Understanding DNA sequence complementarity is crucial in many biotechnological applications, including the burgeoning field of DNA nanotechnology. Essentially, DNA sequence complementarity refers to the specific pairing of nucleotides across two DNA strands that enable them to bind together, forming the familiar double helix structure.

In the exercise, we explored how this property is used to bring together two nanoparticles - a circle and a square - by attaching complementary single-stranded DNA sequences to each. When the sequence linked to the circle is GGATC, the principle of complementarity dictates that each nucleotide must pair with its complement: G (guanine) pairs with C (cytosine) and A (adenine) with T (thymine). Therefore, the sequence linked to the square needs to be CCTAG to ensure proper binding through complementary base pairing.

Such precision in sequence recognition is the basis for the 'Velcro-like' capability of DNA. When the complementary strands find each other, they can hold together with remarkable strength, allowing for the construction of complex nanostructures.

Nucleotide Base Pairing

The heart of DNA sequence complementarity lies in the fundamental mechanism of nucleotide base pairing, which can be likened to the rules of engagement for the molecular dance of DNA strands. Nucleotide base pairing follows a strict set of rules: adenine (A) pairs with thymine (T), while guanine (G) pairs with cytosine (C).

In the context of the exercise we discussed, the base pairing is illustrated by matching each nucleotide of the circle's DNA sequence (GGATC) with its appropriate partner on the square's sequence (CCTAG). This specific pairing is mediated by hydrogen bonds - A with T forms two hydrogen bonds, and G with C forms three - providing the chemical attraction needed to zip the strands together.

Key to Stability

The paired bases create steps like a staircase that stabilizes the DNA structure. This stability makes DNA an excellent material for constructing nanoscale objects, as we saw with the docking of a circle to a square nanoparticle.

5' and 3' Ends of DNA

In addition to knowing which nucleotides pair up, recognizing the orientation of DNA strands is important. DNA has directionality, defined by its 5' and 3' ends, which is fundamental when it comes to reading and synthesizing DNA. The 5' end contains a phosphate group, while the 3' end contains a hydroxyl group. DNA is always synthesized and read in the 5' to 3' direction.

In the exercise solution, we identified that the 5' end for the circle's sequence (GGATC) begins with G, and for the square's sequence (CCTAG), it begins with C. The opposite end of each sequence is the 3' end. During the creation of DNA nanostructures, maintaining the correct orientation for the complementary DNA strands is vital for successful assembly. If the strands are oriented incorrectly, they will not properly attach to each other, and the desired nanostructures will not form.

This 5' to 3' rule is not only important in nanotechnology but also in cellular processes such as DNA replication and transcription, reinforcing the inherent directional nature of DNA.