DNA clamp protein

Figure 2.39 A DNA clamp protein - a trimer of the protein Proliferating Cell Nuclear Antigen (PCNA). The three different trimer units are shown in different colours (image courtesy of www. wikipedia.org). 

Two other protein complexes also function in eukaryotic DNA replication. RPA (replication protein A) is a eukaryotic single-stranded DNA-binding protein, equivalent in function to the E. coli SSB protein. RFC (replication/actor (J) is a clamp loader for PCNA and facilitates the assembly of active replication complexes. The subunits of the RFC complex have significant sequence similarity to the subunits of the bacterial clamploading (y) complex. 

Actual reproduction steps involving DNA and RNA often occur in concert with protein where the protein can act as a clamp or vice holding the various important members involved with the particular reproduction step in place. Thus, the protein complex acts as an assembly line tunnel or doughnut with the reactants present within the interior. 

Not only does DNA form itself into catenated and knotted structures, it also rotaxanates itself with macrocyclic enzymes. A,-Exonuclease [30, 37] is an enzyme that participates in DNA replication and repair by fully encircling DNA as it sequentially hydrolyzes nucleotides - a biomolecular rotaxane The structure of the enzyme is shown in Fig. 3d. T4 DNA polymerase holoenzyme [38] is an analogous example its protein subunits clamp around a DNA strand to form a toroid in what chemists of the mechanical bond would call a clipping process. It should be noted that chemists have been able to mimic this concept of a topologically linked catalyst on a polymer [39] using traditional organic catalytic reactions. 

Figure 5 Starting from natural mRNA, a cDNA library (A blue) is produced and like ribosomal display, the cDNA is transcribed into mRNA (B) with no stop codons. The 3 -end of each mRNA molecule is ligated to a short synthetic DNA linker (C) and sometimes a polyethyleneglycol spacer, which terminates with a puramycin molecule (small red sphere). The ligation is stabilized by the addition of psoralen (green clamp), which is photoactivated to covalently join both strands. Addition of crude polysomes or purified ribosomes (D) results in translation of the mRNA into protein, but the ribosome stalls at the mRNA-DNA junction. Since there are no stop codons, release factors cannot function and instead the puromycin enters the A-site of the ribosome (A). Because puramycin is an analog of tyrosyl-tRNA, the peptidyl transferase subunit catalyzes amide bond formation between the puromycin amine and the peptide carboxyl terminus, but is unable to hydrolyze the amide link (which should be an ester in tyrosyl-tRNA) to release the dimethyladenosine. The ribosome is dissociated to release the mRNA-protein fusion (E), which is protected with complementary cDNA using RT-PCR (F). The mRNA library can then be selected against an immobilized natural product probe (G), nonbinding library members washed away and the bound mRNA (H) released with SDS. PCR amplification of the cDNA provides a sublibrary (A) for another round of selection or for analysis/ sequencing.

Figure 2.1 Structure dictates function. A protein component of the DNA replication machinery surrounds a section of DNA double helix depicted as a cylinder The protein, which consists of two identical subunits (shown in red and yellow), acts as a clamp that allows large segments of DNA to be copied without the replication machinery dissociating from the DNA. [Drawn from 2POL.pdb.]...

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