Double-strand, defined

Figure 40-7. The polymerase chain reaction is used to amplify specific gene sequences. Double-stranded DNA is heated to separate it into individual strands. These bind two distinct primers that are directed at specific sequences on opposite strands and that define the segment to be amplified. DNA polymerase extends the primers in each direction and synthesizes two strands complementary to the original two. This cycle is repeated several times, giving an amplified product of defined length and sequence. Note that the two primers are present in excess.

Incorporation of an artificial flavin nucleobase and of a cyclobutane pyrimidine dimer building block into DNA DNA double strands, DNArPNA hybrid duplexes, and DNA-hairpins, provided compelling evidence that an excess electron can hop through DNA to initiate dimer repair even at a remote site. The maximum excess electron transfer distance realised so far in these defined Donor-DNA-Acceptor systems is 24 A. New experiments are now in progress to clarify whether even larger transfer distances can be achieved. 

Structure-based and source-based nomenclature rules have been extended to regular double-strand (ladder and spiro) organic polymers [7]. A double-strand polymer is defined as a polymer the molecules of which are formed by an uninterrupted sequence of rings with adjacent rings having one atom in common (spiro polymer) or two or more atoms in common (ladder polymer). 

Major emphasis has been on the isolation and identification of the main decomposition products arising from one electron oxidation reactions with the pyrimidine and purine bases of isolated DNA and related model compounds13,14D. In recent years, major interest has been devoted on the delineation of the mechanistic features of charge transfer within double stranded DNA. This is mostly achieved using defined-sequence oligonucleotides in which radical cations are generated in most cases by photo-ionization of selected nucleobases and 2-deoxyribose. For more information on these systems, the reader is encouraged to read the recent review article by Cadet et al.134 and other references mentioned there in. 

FIGURE 24-15 Linking number, Lk. Here, as usual, each blue ribbon represents one strand of a double-stranded DNA molecule. For the molecule in (a), Lk = 1. For the molecule in (b), Lk = 6. One of the strands in (b) is kept untwisted for illustrative purposes, to define the border of an imaginary surface (shaded blue). The number of times the twisting strand penetrates this surface provides a rigorous definition of linking number. 

As indicated in the introduction, we have also extended our studies to oligomeric single and double strands of well-defined length [13]. An example is shown in Fig. 3, where... 

One of the major obstacles to molecular analysis of genomic DNA is the immense size of the molecules involved. The discovery of a special group of bacterial enzymes, called restriction endonucleases (restriction enzymes), which cleave double-stranded DNA into smaller, more manageable fragments, has opened the way for DNA analysis. Because each enzyme cleaves DNA at a specific nucleotide sequence, restriction enzymes are used experimentally to obtain precisely defined DNA segments called restriction fragments. 

The most striking specificity in DNA hydrolysis is displayed by the restriction endonucleases which are discussed further in Chapter 26. These fussy catalysts cleave only at points within or close to a defined sequence of several nucleotides in double-stranded DNA. For example, the enzyme EcoR I cuts only at the following palindromic sequence ... 

Synthetic oligonucleotides are being developed to target defined sites on DNA sequences or genes (double-strand DNA triplex approach) or messenger RNA (antisense approach) so that the production of disease-related proteins is blocked. These oligonucleotides offer prospects of treatment for cancers and viruses without harming healthy tissues.8,9... 

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