Question

Denaturation of Nucleic Acids A duplex DNA oligonucleotide in which one of the strands has the sequence TAATACGACT CACTATAGGG has a melting temperature \(\left(t_{\mathrm{m}}\right)\) of \(59^{\circ} \mathrm{C}\). If an RNA duplex oligonucleotide of identical sequence (substituting U for T) is constructed, will its melting temperature be higher or lower?

Short answer

The RNA duplex will have a higher melting temperature than the DNA duplex.

Step-by-step solution

Understand Nucleotide Pairing

In DNA, adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G) through hydrogen bonds. In RNA, uracil (U) replaces thymine (T), so adenine (A) pairs with uracil (U). Pairing strength between nucleotides is crucial to determine the melting temperature of a nucleic acid duplex.

Analyze Bond Strength

In DNA, A-T pairing involves 2 hydrogen bonds, whereas C-G pairing involves 3 hydrogen bonds. In RNA, A-U pairing also involves 2 hydrogen bonds, similar to A-T in DNA. However, RNA typically forms more stable structures due to additional factors such as more favorable stacking interactions and additional 2'-OH group interactions that stabilize RNA duplex.

Compare Thermodynamic Stability

More hydrogen bonds and favorable interactions generally lead to higher melting temperatures ( (t_m) ). RNA duplexes are known to have more stable bonding owing to the additional interactions possible in RNA structures, making RNA duplexes typically more stable than DNA duplexes of an identical sequence.

Conclusion on Stability and Melting Temperature

Given that RNA duplexes generally experience more favorable interactions and enhanced stacking compared to DNA duplexes, an RNA duplex with a sequence identical to a DNA duplex (with U replacing T) usually has a higher melting temperature.

Key concepts

DNA melting temperature

The melting temperature \( (t_m) \) of DNA is the point at which half of the DNA strands are in the double-helix form and the other half are in the melted or single-strand form. This temperature is an important indicator of the stability of the DNA duplex.

Various factors influence DNA melting temperature, including:

• The number of G-C pairs, which contribute more to stability due to three hydrogen bonds as opposed to two in A-T pairs.
• The length of the DNA strand, as longer strands hold more hydrogen bonds, contributing to a higher melting temperature.
• The ionic strength of the solution, since positively charged ions can stabilize the negatively charged DNA backbone, raising the melting temperature.

Understanding these factors can help predict and manipulate DNA stability, which is crucial for various biological processes and applications, such as PCR and DNA sequencing.

RNA stability

RNA is generally more stable than DNA when it comes to duplex formations. This is largely due to the 2'-OH group present in RNA's ribose sugar, which allows for more extensive hydrogen bonding and creates tighter fits between the strands.

RNA stability is further enhanced by:

• Better base stacking interactions due to the geometric structure of RNA, giving it a more rigid form.
• The ability to form a greater variety of secondary structures, such as stem-loops or hairpins, which can improve overall stability.

These characteristics usually result in RNA duplexes having higher melting temperatures compared to their DNA counterparts, especially when they have identical sequences.

Nucleotide Pairing

Nucleotide pairing is fundamental to the structure of DNA and RNA, allowing these molecules to carry genetic information and perform other vital roles. In DNA, nucleotide pairing is characterized by:

• Adenine (A) pairing with Thymine (T) through two hydrogen bonds.
• Cytosine (C) pairing with Guanine (G) through three hydrogen bonds.

In RNA, the Thymine (T) is replaced by Uracil (U):

• Adenine (A) pairs with Uracil (U), similar to the A-T pairing in DNA with two hydrogen bonds.
• This substitution affects the pairing strength but allows RNA to perform unique functions that DNA cannot.

These pairing rules ensure the proper transmission of genetic information, maintaining the integrity of biological processes.

Hydrogen bonds in nucleic acids

Hydrogen bonds play a critical role in the structure and function of nucleic acids. They are non-covalent bonds that occur between a hydrogen atom and a more electronegative atom, such as nitrogen or oxygen, serving as the glue that holds the nucleotide pairs together.

Key points about hydrogen bonds in nucleic acids include:

• In DNA, A-T pairs have two hydrogen bonds, while G-C pairs have three hydrogen bonds, making G-C pairs more stable.
• Hydrogen bonds contribute not only to the mechanical stability but also to the specificity of base pair interactions, thus aiding in accurate DNA replication and RNA transcription.

The presence of more hydrogen bonds typically increases the melting temperature, as more energy is required to break them apart, which explains why G-C rich regions are harder to denature.