Q.Dinucleotide is obtained by joining two nucleotides together by phosphodiester linkage. Between which carbon atoms of pentose sugars of nucleotides are these linkages present?

The key idea is that a phosphodiester bond links the sugar-phosphate backbone of nucleic acids.

Reasoning:

1. Each nucleotide has a pentose sugar with carbon atoms numbered $1'$ to $5'$.
2. The phosphate group is attached to the $5'$ carbon of one nucleotide.
3. This phosphate forms a bond with the $3'$ carbon of the next nucleotide's sugar. …

Why this question is about backbone direction

A dinucleotide is simply two nucleotides covalently joined. The bond that holds them together is the phosphodiester linkage — a phosphate group that bridges two sugar molecules. To understand which carbons are involved, you need to recall the structure of a nucleotide and how they polymerise.

Each nucleotide has a pentose sugar (ribose in RNA, deoxyribose in DNA). The sugar has five carbon atoms, numbered 1' through 5'. The nitrogenous base is attached at the 1' carbon. The phosphate group(s) attach at the 5' carbon (the one outside the ring). The 3' carbon has a free hydroxyl group ($-OH$) that can react with the phosphate of another nucleotide.

When two nucleotides join, the phosphate on the 5' carbon of one nucleotide forms an ester bond with the 3' hydroxyl of the next nucleotide. This creates a 5'–3' phosphodiester bond.

Step-by-step reasoning

1. Identify the reactive groups on a single nucleotide

   • The phosphate group is attached to the 5' carbon of the sugar.
   • The hydroxyl group ($-OH$) is attached to the 3' carbon of the sugar.
   • The base is at the 1' carbon — this is not involved in backbone formation.

2. Understand the condensation reaction …

Concept: Structure of a Dinucleotide & Phosphodiester Linkage

A phosphodiester linkage is the bond that connects two nucleotides in a nucleic acid chain. It forms between the sugar of one nucleotide and the sugar of the next.

Method: Carbon Numbering & Bond Tracing

Step 1 — Recall the numbering of carbons in the pentose sugar

In a nucleotide, the pentose sugar (ribose or deoxyribose) has carbons numbered $1'$ to $5'$ (prime denotes sugar carbons, to distinguish from base carbons).

• The nitrogenous base is attached at the $1'$ carbon.
• The phosphate group is attached at the $5'$ carbon.

Step 2 — Trace the linkage between two nucleotides

When two nucleotides join: …

Common Mistakes & How to Avoid Them

Mistake 1: Confusing the Carbon Numbering in the Sugar Ring

Many students pick (B) 1' and 5' because they remember that the phosphate is attached to the 5' carbon and the nitrogenous base is attached to the 1' carbon. They incorrectly assume the linkage involves the base-attachment carbon.

Why it's wrong:

The phosphodiester linkage connects two different nucleotides — it does not involve the base. The 1' carbon is always bonded to the nitrogenous base, not to another nucleotide.

How to avoid:

• Memorise the roles of each carbon:
  • 1' → base attachment
  • 3' → OH group (free in a single nucleotide)
  • 5' → phosphate group
• The phosphodiester bond is between the 5' phosphate of one nucleotide and the 3' OH of the next.

Mistake 2: Thinking the Linkage is Between Two 5' Carbons or Two 3' Carbons

Some students pick (C) 5' and 5' or (D) 3' and 3', imagining that both ends of the bond are the same carbon.

Why it's wrong:

A phosphodiester bond is asymmetric — it always connects a 5' carbon (via its phosphate) to a 3' carbon (via its OH group). Two identical carbons would not allow the chain to grow in a directional manner.

How to avoid:

• Visualise the dinucleotide structure:
  • First nucleotide: 5' phosphate is free (or attached to something else)
  • The 3' OH of the first nucleotide forms a bond with the phosphate on the 5' carbon of the second nucleotide
• So the linkage is always 5' → 3'.

Mistake 3: Forgetting the Directionality of Nucleic Acid Chains …