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#single-stranded DNA

6 public questions tagged with this topic.

Recombination

RecA binds preferentially to

Single-stranded DNA preference of RecA ensures that recombinogenic ends not double-stranded regions are targeted. ssDNA generated after resection or RecBCD processing is immediately bound by SSB in bacteria or RPA in eukaryotes, which melts secondary structures. RecA mediator proteins such as RecFOR facilitate replacement of SSB with cooperative ATP-bound RecA nucleating into contiguous filament. Within filament ssDNA adopts extended conformation facilitating base-triplet scanning for homology on intact duplex. This selective binding avoids illegitimate association with undamaged chromosomes, channeling strand invasion specifically to broken resected termini requiring repair.

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 12: RecA Preferential Binding to ssDNA

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Replication in Prokaryotes

SSB protein prevents

As helicase unwinds parental duplex, exposed single strands rapidly re-anneal due to complementarity and form secondary structures like hairpins that block polymerase progression. Single-strand binding protein homotetramer binds cooperatively with very high affinity to single-stranded DNA without sequence specificity, coating it and holding in extended conformation preventing pairing. This prevents rewinding, protects from nucleases, and removes hairpin barriers. SSB also recruits other replisome proteins such as primase and Pol III via acidic C-terminus, mechanistically coupling unwinding to synthesis and stimulating activity.

Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 5: SSB prevents reannealing and organizes lagging template

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RDT Basics

S1 nuclease cleaves:

S1 nuclease is a zinc-dependent acidic endonuclease purified from the filamentous fungus Aspergillus oryzae. It exhibits high specificity for single-stranded nucleic acids, degrading unpaired DNA and RNA into 5'-mononucleotides while leaving fully base-paired duplexes largely intact under titrated conditions. Its activity requires zinc ions and low pH around 4.5. Molecular biologists utilize S1 nuclease to remove single-stranded overhangs after restriction digestion to create blunt ends, to cleave hairpin loops formed during second-strand cDNA synthesis, and to map transcription start sites and RNA-DNA hybrids.

Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.

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DNA

The charge on a single-stranded nucleotide sequence with 'n' nucleotides is:

-(n+1) is the scientifically accurate answer to this question. Within the study of DNA, this concept is well-established through extensive research and is documented in standard scientific literature. The specific properties, mechanisms, or characteristics of -(n+1) directly address what is being asked. Among the other options, -2(n+1), +n, and Phosphodiester bond stability do not correctly answer this question because they either refer to different concepts, describe properties of other molecules or processes, or represent common misconceptions about this topic.

Ref: Molecular Biology of the Gene, Watson et al., 7th Ed.

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DNA

Which of the following rules applies approximately to single-stranded DNA?

Chargaff's second parity rule is the scientifically accurate answer to this question. Within the study of DNA, this concept is well-established through extensive research and is documented in standard scientific literature. The specific properties, mechanisms, or characteristics of Chargaff's second parity rule directly address what is being asked. Among the other options, Chargaff's first parity rule, Both (a) and (b), and None do not correctly answer this question because they either refer to different concepts, describe properties of other molecules or processes, or represent common misconceptions about this topic.

Ref: Molecular Biology of the Gene, Watson et al., 7th Ed.

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DNA

Which base composition indicates a single-stranded DNA genome?

%A ≠ %T and %C ≠ %G accurately describes the structural composition or molecular organization asked about in this question. In DNA, knowledge of molecular structure is directly linked to understanding biological function. The specific arrangement of chemical components in %A ≠ %T and %C ≠ %G determines its physical properties, biological activity, and interactions with other molecules. The other options (%A ≈ %T and %C ≈ %G, %A = %C and %T = %G, and %A + %T = %C + %G) describe different structural arrangements, incorrect stoichiometry, or compositions of different biological molecules.

Ref: Molecular Biology of the Gene, Watson et al., 7th Ed.

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