Generation of DNA fragments

Barnett, R. W. and Erfle, H. (1990) Rapid generation of DNA fragments by PCR amplification of crude, synthetic oligonucleotides. Nucl Acids Res 18,3094... 

V. Generation of DNA fragments for dideoxy sequencing. DNase I digestion in the presence of Mn produces double-strand breaks in DNA. The average... 

Genomic library A collection of clones made from a set of randomly generated overlapping DNA fragments representing the entire genome of an organism. 

To a first approximation, the matrix element Hda is proportional to the overlap Sda for d-a distances of interest in DNA. Therefore, the couphng Vda, as given by Eq. 5, is approximately proportional to the overlap Sda- Troisi and Orlandi found an almost hnear relationship between the electronic couphng of nucleobases and the overlap of the pertinent donor and acceptor orbitals. At the level HF/3-21G, the matrix element Vda (in oV) can be estimated as —0.716 Sjj, where Sg is the overlap integral calculated between the HOMOs of the donor and acceptor sites. This approximation obviously can be very useful when combined with MD simulations of DNA fragments. However, two remarks are in order (i) the reference values of Vda should be generated with a more accurate method, e.g., based on Eq. 5 instead of Eq. 6 [32] and (ii) the very small basis set 3-2IG is insufficient for achieving satisfactory reference matrix elements (Table 1). 

An important extension of this method is the procedure of blunt-end ligation high concentrations of the T4 ligase will catalyze the ligation of DNA fragments containing flush ends (equation 14.4). Flush ends may be generated by a number... 

Fig. 11.14. Flow cytometric signatures distinguishing three different strains of bacteria according to the size distributions of DNA fragments generated by restriction enzyme digestion. From Kim et al. (1999).

Fig. 4. Details of DNA replication, (a) Primase binds to the DNA template strand (thin line) and (b) synthesizes a short RNA primer (dotted line) (c) DNA polymerase III now extends the RNA primer by synthesizing new DNA (thick line) (d) during synthesis of the lagging stand, adjacent Okazaki fragments are separated by the RNA primers (e) the RNA primers are now removed and the gaps filled with DNA by DNA polymerase I (f) generating adjacent DNA fragments that are then (g) joined by DNA ligase.

These enzymes are used to digest large DNA molecules into smaller fragments of specific size. Because a restriction enzyme always cuts at the same site, DNA from a particular individual generates a reproducible set of DNA fragments. This is convenient for the study or cloning of DNA from any source. 

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