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Single-Strand DNA Binding Proteins

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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
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DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
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Nanosecond chain dynamics of single-stranded nucleic acids.

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Single-stranded nucleic acids exhibit rapid chain dynamics, reconfiguring in the 10-nanosecond range. These dynamics are primarily governed by solvent friction, not internal friction, offering new insights into nucleic acid behavior.

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Area of Science:

  • Biophysics
  • Molecular Biology
  • Polymer Physics

Background:

  • Conformational dynamics of single-stranded nucleic acids are crucial for their folding and function.
  • Experimental resolution of elementary chain dynamics in these molecules remains challenging.

Purpose of the Study:

  • To determine the conformational ensembles and rapid chain dynamics of short single-stranded nucleic acids in solution.
  • To elucidate the factors governing the speed and nature of single-stranded nucleic acid reconfigurations.

Main Methods:

  • Employed single-molecule Förster resonance energy transfer (smFRET).
  • Utilized nanosecond fluorescence correlation spectroscopy (nfCS) with nanophotonic enhancement.
  • Applied hierarchical chain growth, polymer models, and Bayesian inference for data interpretation.

Main Results:

  • Resolved exceedingly rapid chain reconfiguration times for single-stranded nucleic acids, on the order of 10 nanoseconds.
  • Demonstrated that these dynamics are dominated by solvent friction, with negligible internal friction.
  • Generated structural ensembles that closely align with experimental data, detailing conformational distributions.

Conclusions:

  • Single-stranded nucleic acids possess remarkably fast conformational dynamics.
  • Solvent interactions play a dominant role in governing the dynamics of single-stranded nucleic acids.
  • Provides a detailed experimental and computational view of single-stranded nucleic acid conformational ensembles and dynamics.