51. During replication, RNaseH removes all of the RNA primer except the ribonucleotide directly linked to the DNA end. This is because

(1) it can degrade RNA and DNA end. From their 5′ end.

(2) it can only cleave bonds between two

ribonucleotides.

(3) it can degrade RNA and DNA from their 3′ end.

(4) activity of RNaseHis inhibited by the presence of duplex containing both strands as DNA.

Introduction

During DNA replication, the lagging strand is synthesized discontinuously in short fragments called Okazaki fragments. Each fragment begins with a short RNA primer that must be removed and replaced with DNA to create a continuous strand. A critical enzyme in this process is RNase H, which degrades the RNA portion of RNA-DNA hybrids. However, RNase H does not remove the final ribonucleotide directly linked to the DNA end. This article explains why RNase H leaves this last ribonucleotide intact and how the remaining RNA primer is fully removed.

Role of RNase H in Primer Removal

• RNase H specifically recognizes RNA-DNA hybrids and cleaves the RNA strand.

• It degrades the RNA primer by cleaving between two ribonucleotides within the RNA segment.

• This cleavage leaves behind the last ribonucleotide attached to the DNA strand because the bond between the final ribonucleotide and the adjacent deoxyribonucleotide is a ribonucleotide–deoxyribonucleotide linkage, not a ribonucleotide–ribonucleotide bond.

Why RNase H Leaves the Last Ribonucleotide

• RNase H cannot cleave the bond between a ribonucleotide and a deoxyribonucleotide.

• It requires at least two consecutive ribonucleotides to recognize and cleave the RNA strand.

• The RNA-DNA junction presents a chemical structure that RNase H does not target, causing it to stop degradation one nucleotide short of the DNA end.

How the Last Ribonucleotide Is Removed

• The remaining ribonucleotide attached to the DNA is removed by other enzymes, primarily 5′→3′ exonucleases such as DNA polymerase I in prokaryotes.

• DNA polymerase I uses its 5′→3′ exonuclease activity to remove this final ribonucleotide and simultaneously fill in the gap with DNA nucleotides, completing Okazaki fragment maturation.

Additional Factors Affecting RNase H Activity

• RNase H activity is influenced by the presence of RNA-DNA duplexes, showing preference for RNA segments hybridized to DNA.

• It does not degrade DNA strands or RNA strands not in an RNA-DNA hybrid.

• RNase H cannot degrade RNA primers completely alone; it works in coordination with other enzymes to ensure complete primer removal and DNA synthesis.

Summary Table

Conclusion

RNase H plays a vital role in removing RNA primers during DNA replication by cleaving RNA segments within RNA-DNA hybrids. However, its inability to cleave the bond between the last ribonucleotide and the DNA strand leaves this ribonucleotide attached. This final ribonucleotide is subsequently removed by 5′→3′ exonuclease enzymes, completing the primer removal process and allowing DNA polymerase to fill in the gap with DNA. This coordinated mechanism ensures accurate and efficient replication of the lagging strand.

Correct Answer to the Query

(2) it can only cleave bonds between two ribonucleotides.

Keywords

RNase H, RNA primer removal, RNA-DNA hybrid, ribonucleotide cleavage, 5′ exonuclease, DNA replication, Okazaki fragments, DNA polymerase I, lagging strand synthesis, primer processing

This detailed explanation clarifies why RNase H leaves the last ribonucleotide attached to DNA during replication and highlights the enzymatic coordination required for complete RNA primer removal.