RNA ligation — Which enzyme can ligate a nicked RNA molecule under standard biochemical conditions?

Introduction:
Joining breaks in nucleic acids is central to cloning and RNA repair workflows. This question asks which enzyme is specifically used to ligate RNA ends or seal nicks in RNA substrates.

Given Data / Assumptions:

• Enzymes considered are standard molecular biology tools.
• Substrate is RNA with a nick or suitable termini.
• Reaction requires appropriate cofactors (often ATP) and termini (e.g., 5′ phosphate, 3′ hydroxyl).

Concept / Approach:
T4 RNA ligase catalyzes the formation of a phosphodiester bond between RNA 5′ phosphate and 3′ hydroxyl termini. Variants (e.g., Rnl1, Rnl2) are widely used for adapter ligation in small RNA library prep. T4 DNA ligase primarily ligates DNA nicks or cohesive ends; DNA polymerase fills gaps but does not ligate nicks; RNase H cleaves RNA in RNA–DNA hybrids rather than joining it.

Step-by-Step Solution:

Verification / Alternative check:
Small RNA sequencing protocols universally employ T4 RNA ligases to attach 3′ and 5′ adapters to microRNAs and other small RNAs, confirming enzyme specificity and utility.

Why Other Options Are Wrong:

• DNA polymerase: lacks ligase activity.
• T4 DNA ligase: efficient for DNA; limited utility on pure RNA ends under standard conditions.
• All of these: overinclusive; only T4 RNA ligase is appropriate.
• RNase H: endonuclease that degrades RNA in RNA–DNA hybrids.

Common Pitfalls:
Assuming DNA ligases will work equivalently on RNA. Substrate specificity and reaction conditions differ markedly between DNA and RNA ligases.

Final Answer:
T4 RNA ligase.