Question 1

What are siRNAs and how long are they?

Accepted Answer

Small interfering RNAs, or siRNAs, are non-coding RNA molecules approximately 22 nucleotides long that regulate mRNA synthesis and stability. They originate from double-stranded RNA processed by the enzyme Dicer, which cleaves long RNA into multiple short siRNA fragments. siRNAs can come from endogenous DNA transcription, viral RNA, or be added experimentally by scientists.

Question 2

How does the RISC complex form and function?

Accepted Answer

Each siRNA binds to the Argonaute protein along with other proteins to form the RNA-induced silencing complex, or RISC. Within RISC, the guide strand separates from its complementary strand and directs the complex to target mRNA. Argonaute then cleaves the target mRNA using its RNase activity, and the RISC complex is recycled to target additional mRNAs.

Question 3

How do siRNAs protect cells against viral infections?

Accepted Answer

When RNA-based viruses enter host cells, they produce double-stranded RNA recognized by Dicer and processed into siRNAs. These siRNAs help fight viral infections by promoting the degradation of viral mRNA in the cytoplasm. This mechanism allows cells to rapidly eliminate viral genetic material and prevent viral replication.

Question 4

What happens when siRNA shows suboptimal base-pairing with target mRNA?

Accepted Answer

If the guide strand shows suboptimal base-pairing with target mRNA, Argonaute will not cleave the mRNA. Instead, the RISC complex obstructs ribosome binding and translocation, causing translational arrest. These mRNAs are then directed to processing bodies where they are gradually degraded.

Question 5

How do nuclear siRNAs silence transposable elements?

Accepted Answer

In the nucleus, centromere-associated DNA repeats encode transcripts processed by Dicer into specific siRNAs that inhibit mRNA synthesis. These siRNAs bind to Argonaute and other proteins to form the RNA-induced transcriptional silencing, or RITS, complex. RITS directs recruitment of histone-modifying proteins that promote heterochromatin formation, making genes inaccessible and silencing transposons.

Question 6

What are the therapeutic applications of siRNA?

Accepted Answer

siRNAs are being explored as treatments for neurological disorders like Alzheimer's and cancers by targeting disease-causing genes. They enable personalized gene therapy due to their high specificity and ease of design for different target genes. Since therapeutic siRNAs target mRNA rather than DNA, they significantly reduce the risk of permanent DNA modification.

Question 7

How can siRNAs be used in molecular biology research?

Accepted Answer

Researchers use siRNAs to study specific gene functions in vivo and in vitro by silencing target genes. They can also silence genes from deadly viruses and serve as effective anti-viral agents. The ability to design siRNAs for different target genes makes them valuable tools for investigating gene function and developing therapeutic strategies.

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