Base short-patch

Thus, DNA gaps produced in BER can be filled in with a small number of bases (short patch repair) by these enzymes (Figure 7.1). 

Guan L, Bebenek K, Kunkel TA, Greenberg MM. Inhibition of short patch and long patch base excision repab by an oxidized abasic site. Biochemistry. 2010 49 9904-9910. 

Fig. 1. Schematic representation of base excision repair (BER) mechanism. BER consists of two main pathways, short patch repair(left) and long patch repair (right). The first step of BER involves recognition, base removal and incision. The choice between short-patch BER or long-patch BER depends on the state of the 5 deoxyribose phosphate (5 dRP) terminus.

Timeliness and duration certain control methods are effective only in earliest stages of a bloom, and the effect is short-lived. Copper sulfate pentahydrate, has been found to be effective in killing off small patches of G. breve in early stages of a bloom, but copper sulfate cannot be used to control the organism when blooms cover many square miles of the sea. The cost estimates vary, but a value of about 1050 per square mile was reported. Using activated charcoal to absorb hormones and vitamins required by G. breve has been suggested, and cost estimates (based on 3 tons of activated charcoal) are 150-810 per square mile (34). 

The protein (26kDa) is a bundle of seven helices, A through G, with three helices normal to the membrane plane and the rest inclined at small angles to the normal. The retinal is covalently bound through a protonated Schiff base to Lys-216 at the middle of helix G, and it lies nearly parallel to the membrane in the space surrounded by the seven helices. The protein forms in vivo a homotrimer, and the trimers are assembled into an extended hexagonal lattice (P3 symmetry), the purple membrane. Protein-protein contact in these patches is through a continuous boundary layer of lipids no more than one lipid wide, at the monomer periphery. The interhelical loops as well as the N- and C-termini are short, with the exception of the connection of helices B and C through a structured fS-turn on the extracellular side, and the E-F interhelical loop with a twist, on the cytoplasmic side. 

Fortini P, DogUotti E. Base damage and single-strand break repair mechanisms and functional significance of short- and long-patch repair subpathways. DNA Repair 2007 6 398-409. 

Dianov GL, Bischoff C, Piotrowski J, Bohr VA (1998) Repair pathways for processing of 8-oxoguanine in DNA by mammalian cell extract J Biol Chem 273 33811-6 Fortini P, Pascucci B, Parlanti E, Sobol RW, Wilson SH, Dogliotti E (1998) Different DNA polymerases are involved in the short- and long-patch base excision repair in mammalian. Biochemistry 37 3575-80... 

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