Single-stranded regions

Single-stranded regions consist of unpaired nucleotides between helices in the secondary structure and at the 5 and 3 ends. The single-stranded regions may be ordered by base stacking in a helical geometry unless they are involved in tertiary structures. 

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Double-stranded DNA has a unique property in that it is able to make identical copies of itself when supplied with precursors, relevant enzymes, and cofactors. In simplified terms, two strands begin to unwind and separate as the hydrogen bonds are broken. This produces single-stranded regions. Complementary deoxyribonu-cleotide triphosphates then pair with the exposed bases under the control of a DNA polymerase enzyme. 

DNA polymerase 1. For most applications DNA polymerase 1 from E. coli is used. The enzyme attaches to a short single-stranded region in a dsDNA molecule and then synthesizes a new strand of DNA, degrading the existing strand as it proceeds. When used in vitro this incubation is carried out at 12-15 °C to prevent more than one round of replication occurring. It is used for in vitro labelling of DNA by the nick translation method (described below). 

If one then adds DNA polymerase and sufficient amounts of all four deoxyri-bonucleotide triphosphates to a solution containing the hybridized DNA, the DNA polymerase will bind to the duplex region and start to synthesize new DNA that is complementary in sequence to the single-stranded region. The DNA polymerase synthesizes new DNA by stepwise attachment of the 5 phosphate of an incoming... 

DNA polymerase III in its holoen-zyme form is the major polymerase for DNA replication. It elongates the primer chains rapidly and pro-cessively leaving only very small gaps at the ends of single-stranded regions. The rate of elongation, which is 3 nucleotides / s for 8 kb... 

It would appear from these studies that the excision of thymine, and more generally pyrimidine dimers may be a two-step process. The initial single-stranded incision is probably dependent upon the presence of a distorted area in the DNA duplex resulting from the formation of a thymine dimer. Once the initial break has been introduced, a short single-stranded region containing the photoproduct results which is then susceptible to the action of the exonuclease. 

A detailed model for discontinuous synthesis could now be proposed (fig. 26.6). First, RNA primers are made on the single-strand region of the template then DNA is synthesized. Finally, the RNA is removed from the fragments, and the gaps are filled in and ligated. An understand-... 

At the growth fork it is necessary that the parental double helix be unwound to present further single-stranded regions to serve as templates for continued replication. The dnaB protein of E. coli is believed to be a helicase that directly catalyzes this process. 

Flenderson PT, Armitage B, Schuster GB (1998) Selective photocleavage of DNA by anthrachinone derivatives Targeting the single-strand region of hairpin structures. Biochemistry 37 2991-3000... 

Nishikawa, S., Suh, Y.A., Kumar, P.K., Kawakami, J., Nishikawa, F. and Taira, K. (1992) Identification of important bases for the self-cleavage activity at two single-stranded regions of genomic HDV ribozyme. Nucleic Acids Symp. Sen. 27,41—42. 

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