Cyclobutane pyrimidine dimer, CPD

Scheme 2 Mechanism of repair of cyclobutane pyrimidine dimers (CPD) by a CPD photolyase. 8-HDF 8-hydroxy-5-deazaflavin, ET electron transfer. FADH reduced and de-protonated flavin-coenzyme...

There are two major types of DNA damage following UV radiation cyclobutane pyrimidine dimers (CPD) and pyrimidine-pyrimidone (6-4) photoproducts that are often simply called (6-4) photoproducts. Formation of these UV lesions may be influenced by the DNA sequence. Nevertheless, in general, CPDs are more abundant than (6-4) photoproducts in UV irradiated DNA. For example, in UVC-irradiated DNA, the overall ratio of CPDs to (6-4) photoproducts is about 3 1. 

Figure 6 Diagrammatic representation of a cyclobutane pyrimidine dimer (CPD) (top) and a (6-4)photoproduct (bottom).

Figure 7. Measured and modeled profiles of cyclobutane pyrimidine dimers (CPD) for water columns with varying intensities of vertical mixing (a) Gulf of Mexico, 8 September 1994, mixed layer 20 m, wind speed low (2 m s ) (b) Gulf of Mexico, 7 September 1994, mixed layer 20 m, wind speed high (8 m s ) (c) Gerlache Strait, Antarctica, 6 October 1996, mixed layer 25 m, wind speed high (8 m s 0- Modeled profiles are for damage (CPD formation) only, damage plus photoreactivation only, and damage and all repair mechanisms (photoreactivation and excision repair). [From Jeffrey et al. and Huot et al. 82.]...

Although much is known now about the effects of solar radiation on the DNA of aquatic organisms, there are also a few major limitations in the presently available information. First, almost all studies have described the presence of cyclobutane pyrimidine dimers (CPDs) only. The main reason for this is that this type of lesion is formed at the highest frequency. Furthermore, CPDs are formed exclusively as a result of UV-B. CPDs are therefore suitable indicators for UV-B... 

Although Pol V replicates undamaged templates with relatively low fidelity (10 3 to 10-4) [76], one striking quality is Pol V s ability to accurately bypass UV photoproducts (e.g., inserting dATP opposite thymine-thymine (TT) cyclobutane pyrimidine dimers (CPDs) [76]). Analysis of insertion tendencies opposite a variety of adducts/lesions led to the observation that Pol V seems to have two insertion modes (i) correct dNTP insertion and (ii) default dATP insertion [37]. UV light is a frequently encountered form of DNA damage for which a translesion synthesis DNA polymerase might be important and since TT CPDs are the major UV lesion... 

As expected, the Z-principal axis of g is oriented perpendicular to the 71-plane of the flavin ring. Analyses of EPR and ENDOR data revealed angles of (—29 4)° and (—14 2)° between the X axis of g and the N5-H5 (or N5-D5) bond in (6 ) photolyase [38] and cyclobutane pyrimidine dimer (CPD) photolyase [28, 30], respectively. The factors that cause the reorientation of the X and Y axes of g of a neutral flavin radical in the two highly homologous cofactor binding pockets of CPD photolyase and (6 ) photolyase remain elusive. Also, the orientations of the principal axes of g relative to the molecular frame of the isoalloxazine ring of a flavin anion radical still need to be determined experimentally. 

One of the most prevalent examples of reaction involving DNA excited states is pyrimidine-pyrimidine dimer formation. Thymine and cytosine are the two pyrimidine bases present in DNA, and pyrimidine-pyrimidine dimers can form between any combination of these two bases. The most common of these is the thymine-thymine (TT) dimer [4-7]. Two types of TT dimers are known (shown in Fig. 13.1). The first, and sole focus of this chapter due to its prevalence, is called cyclobutane pyrimidine dimer (CPD) and is formed by the [2-1-2] addition of the C5-C6 double bonds. The second is called the 6 photoadduct and is formed by the addition of the C5-C6 double bond on one thymine to the C4-04 double bond on the other. This leads to an oxetane intermediate that subsequently rearranges to form the 6-4 product. Both of these photoproducts are thought to form starting with initial excitation to a state. There is some debate in the literature... 

The first is the formation of cyclobutane pyrimidine dimers (CPDs), accounting for 75 % of direct UV-induced damage to DNA. Absorption of UV-B by thymine or cytosine causes a [2 - - 2] cycloaddition between the carbon-carbon double bonds of neighbouring bases, resulting in a four-membered ring structure, 47 or 52. 

DNA Photolyase. - Ultraviolet light (> 300 nm) damages cellular DNA by the formation of thymine dimers from adjacent pyrimidine bases on the same DNA strand. The two main photoproducts are (cis,syn)-cyclobutane pyrimidine dimers (CPDs) and the (6-4) photoproduct. Such dimers may be restored to their monomeric form through the action of two photoactive (300 < X < 500 nm) damage-specific DNA repair enzymes, named CPD photolyase (also called DNA photolyase) and (6-4) photolyase. These enzymes are found in various... 

---