DNA formation

Section 28 14 The nucleotide sequence of DNA can be determined by a technique m which a short section of single stranded DNA is allowed to produce its complement m the presence of dideoxy analogs of ATP TTP GTP and CTP DNA formation terminates when a dideoxy analog is incorporated into the growing polynucleotide chain A mixture of polynucleotides dif fermg from one another by an incremental nucleoside is produced and analyzed by electrophoresis From the observed sequence of the comple mentary chain the sequence of the original DNA is deduced... 

Luo K, Wang T, Liu B, Tian C, XiaoZ, Kappes J, YuXF (2007) Cytidine deaminases APOBEC3G and APOBEC3F interact with human immunodeficiency virus type 1 integrase and inhibit proviral DNA formation. J Virol 81(13) 7238-7248... 

Poly(8-methyladenylic acid) can form a regular, single-strand helix, the first such structure found to exist in aqueous solution. In this polymer, the glycosidic conformation is a regularly alternating syn-anti structure. It is interesting that the alternation of syn and anti conformations may be correlated with Z-DNA formation and that the bulky 8-methyl group is expelled to the outside of the stack s array of bases 171). 

Hardenbol, P. and van Dyke, M.W. (1996) Sequence specificity of triplex DNA formation analysis by a combinatorial approach, restriction endonuclease protection selection and amplification. Proc. Natl. Acad. Sci. USA, 93, 2811-2816. 

The mechanism of biological action for camptothecin is not yet entirely known. It has been suggested that this alkaloid may inhibit DNA formation or may catalyze the formation of DNA-damaging free radicals in vivo [256]. 

Another dinuclear Mn enzyme with quite a different functionality is MnRNR. Cell replication and deoxyribonucleic acid (DNA) formation require the reduction of the 2 hydroxyl group of a ribonucleoside phosphate [13a]. 

Figure 12.5 DNA hybridization reactions performed on ZnO NR arrays. (A) Strong fluorescence emission is observed from a sample containing fully complementary ssDNA strands whereas no signal is detected from noncomplementary strands. (B and C) Concentration dependent assays displaying the detection sensitivity of ZnO NR platforms. Data shown in red and blue correspond to assays empolying a covalent and non-covalent linking scheme of DNA strands on ZnO respectively. (D) Fluorescence emission due to duplex DNA formation on open-squared ZnO NR arrays. The easy integration potentkl of ZnO NR arrays into high density platforms is...

Lee K, Lee SE. Saccharomyces cerevisiae Sae2- and Tell-dependent single-strand DNA formation at DNA break promotes microhomology-mediated end joining. Genetics 2007 176 2003-2014. 

The enzyme immunoassay technique described below is a simple and sensidve method to detect left-handed Z-DNA formation in synthedc poly-nucleoddes, recombinant plasmids, and nadve DNAs. This method udlizes the differences in the andgenic properdes of right-handed B-DNA and left-handed Z-DNA. 

An intrastrand cross-link formed by cisplatin and adjacent guanine residues causes an unusally distorted base pair (bp) step, known as the Lippard bp step. A study of the effects of neighbouring nucleotides to the cross-linked G G has shown that the 3 -nucleotide has little effect, but the 5 -nucleotide has a dramatic effect. The 5 residue always maintains an S pucker, but the canting varies, depending on the substituent. Bleomycin causes two major lesions to DNA, formation of a 4 -keto abasic site and strand cleavage to yield a 3 -phosphog-lycolate and a 5 -phosphate. As a model for the 4 -keto abasic site, an NMR structure of a 13-mer DNA duplex containing an abasic site has been reported." It was found that for both the a- and p-anomers, the abasic site was extrahelical, and that the duplex showed very little distortion to the backbone. This was discussed in terms of repair of such lesions in vivo. 

The enzyme dihydrofolic acid (DHF) S5mthase (see below) converts p-aminobenzoic acid (PABA) to DHF which is subsequently converted to tetrahydric folic acid (THF), purines and DNA. The sulphonamides are structurally similar to PABA, successfully compete with it for DHF s)mthase and thus ultimately impair DNA formation. Most bacteria do not use preformed folate, but humans derive DHF from dietary folate which protects their cells from the metabolic effect of sulphonamides. Trimethoprim acts at the subsequent step by inhibiting DHF reductase, which converts DHF to THF. The drug is relatively safe because bacterial DHF reductase is much more sensitive to trimethoprim than is the human form of the enzyme. Both sulphonamides and trimethoprim are bacteriostatic. 

Cadet J., Berger M., Douki T, Ravanat J.-L., Oxidative damage to DNA Formation, measurement and biological significance, Reviews Physiol. Biochem. Pharmacol., 1997,131,1-87. 

Verazine (309) was active against Candida albicans and Trichophyton rubrum [684], and inhibited DNA formation by hepatoma and S180 cells [691], Verazine isolated from Veratrum maackii was found by and 13c NMR studies to be a 20RI20S epimeric mixture [692]. Verazinine (310) was isolated from Zygadenus sibiricus as a new alkaloid [693]. 

Tuite E, Kelly JM. The interaction of methylene blue, azure B, and thionine with DNA Formation of complexes with polynucleotides and mononucleotides as model systems. Biopolymers 1995 35 419-33. 

If aqueous solutions of eis- or traws-DDP are allowed to equilibrate, the kinetics of the reactions of these equated species with DNA can be measured Atlow r j the reaction is pseudo-first-order with respect to platinum concentration. For eis-DDP, the half-life of the reaction of the diaquo species with 10"4 M DNA at 25 C, pH 5-6 is 0,8 min and the monoaquo species, and t2 ans-[Pt(NH3)2(H20)Cl]J have half-lives of 6 h and 2 h respectively The forms [Pt(NH3)2Cl(OH)] and [Pt(NH3)2(OH)2] do not react with DNA and ais-[Pt(NH372 (H2O) (OH) ]" reacts with the same kinetics as the diaquo form (20). However, if freshly dissolved solutions of platinum compounds are added to the DNA, formation of the monoaquo species is the rate limiting step (22). Figure 2 shows the reactions of fresh solutions of the three compounds with DNA at 37 C Under these conditions the half-lives of the reactions were 3.9, 2.5 and 0.65 h for ais-DDP, trons-DDP and [Pt(dien)Cl]Cl respectively (19). 

Fluorouracil is a pyrimidine analogue that substitutes for uracil in the synthesis pathway for thymidylate, a necessary step in the synthesis of DNA. Formation of a false nucleotide inhibits an enzyme necessary for DNA synthesis. This is similar to the mode of action of the antifungal drug, flucytosine (Chapter 9, page 167). 

---