DNA poly

The solute solvent contribution to the free energy stabilizing the DNA poly ion can be calculated within the polymer RISM theory by a charging up process " ... 

This type of DNA condensation can be classified only formally as a product of DNA/poly-mer interactions, since no binding between these two components has been observed. Polymers that cause DNA condensation serve in this case as phase separation agents and concentrate DNA in the aqueous phase in high concentration. The presence of a certain amount of salt is required to overcome phosphate repulsion. 

All earlier studies [155-158] reported the complexation of berberine with calf thymus DNA and suggested by a mechanism of intercalation. Maiti and coworkers [159-162] demonstrated first the base- and sequence-specificity of berberine from studies with several naturally occurring DNAs (Clostridium perfringenes, cholera bacteriophage 02, calf thymus, Escherichia coli, Micrococcus lysodeikticus) and synthetic DNAs ((poly(dG-dC) poly(dG-dC), poly(dG)-poly(dC), poly(dA-dT) poly(dA-dT), poly(dA)-poly(dT)) using various physicochemical techniques. Several aspects of the interaction were reported ... 

Under certain circumstances DNA has both primer and template activities. For example, the addition of mononucleotides is to the 3 end of the growing DNA primer. This presents a problem with regard to how the other strand is synthesized. Biochemists have looked hard but unsuccessfully for an enzyme that can add deoxyribonucleotides onto the 5 end of DNA primers. Such a primer should contain a triphosphate on the hydroxyl group of the 5 end. Although a very active 5 -exonuclease, actually part of DNA polymerase I, has made the search for such an activated 5 end extremely difficult, investigators conclude that a polymerase able to use such a primer probably does not exist. On the contrary, good evidence suggests that the synthesis of both strands is by the known DNA poly-merases. 

All this leads to the question of how DNA affects nucleosomal stability at the molecular level. DNA bendability has been repeatedly put forward as a candidate to play an important role [280-282]. This property is related to the persistence length of DNA [283]. A study on the characterization of nucleosomes reconstituted onto methylated DNA [poly(dG-m dC) poly (dG-m dC)] [284] provides support to this hypothesis. Poly(dG-m dC) poly (dG-m dQ DNA can be induced to change from its B to its Z conformation in the presence of millimolar amounts of divalent ions [285] such as MgCl2. The persistence length of poly(dG-m dC) poly (dG-m dC) in the Z form in high salt was found to be 208 nm (ca. 612 bp) [286], a value much lower than that of the same polymer in the B form (93.8 nm, 276 bp) at... 

Aral, C., Akbuga, J. (2003). Preparation and in vitro transfection efficiency of chitosan microspheres, containing plasmid DNA poly (L-lysine) complexes. J. Pharm. Phantn. Sci., 6(3), 321-326. 

The structure of C-DNA has hitherto been not refined since its X-ray diffraction (25) corresponded to a screw-disordered (26) fiber. We now have C-DNA in a polycrystalline system containing 9 helices of the synthetic DNA poly d(GGT)-poly d(CCA) (Figure 7a). Detailed X-ray analysis shows that C-DNA belongs to the same ttg tg+ genus as both B(IO ) and B-DNA (8 ). Figure 7b shows the negative tilt for the bases and the backward positioning of the base-pairs relative to the helix axis. 

Increasing the asymmetric unit from a mono- to a dinucleotide obviously increases the conformational flexibility of the nucleic acid structure. When the two nucleotides are only minor variants of one another, such as the differences between them are one of degree rather than kind, the resulting structure would still be of the same kind as that of the parent polymononucleotide helix. On the other hand, if the two nucleotides appear in quite different conformational domains, this could eventually lead to unusual secondary structures. For exampls, we have recently obtained from the synthetic DNA poly d(GC) poly d(GC) diffraction patterns which can be interpreted in terms of a left-handed helix... 

At present, roughly two types of methods are available for real-time PCR (1) the methods using intercalation and (2) the methods using the 5 3 exonuclease activity of DNA poly-... 

We first describe the NMR parameters for the duplex to strand transition of the synthetic DNA poly(dA-dT) (18) with occasional reference to poly(dA-dU) (24) and poly(dA- brdU) and the corresponding synthetic RNA poly(A-U) (24). This is followed by a comparison of the NMR parameters of the synthetic DNA in the presence of 1 M Na ion and 1 M tetramethylammonium ion in an attempt to investigate the effect of counterion on the conformation and stability of DNA. We next outline structural and dynamical aspects of the complexes of poly(dA-dT) with the mutagen proflavine (25) and the anti-tumor agent daunomycin (26) which intercalate between base pairs and the peptide antibiotic netropsin (27) which binds in the groove of DNA. 

Netropsin complexes with nucleic acids have been monitored by spectroscopic techniques at the oligomer duplex and DNA level (89-96). Our research focussed on the application of high resolution NMR spectroscopy to elucidate structural and dynamic aspects of netropsin complexes with the self-complementary octanucleotide dG-dG-dA-dA-dT-dT-dC-dC duplex (9 7) and the synthetic DNA poly(dA-dT) (27) in aqueous solution. 

Tab. 2.5.1. Binding constants and binding-site size of acridizinium bromides 5a and 5b as determined from spectrophotometric titrations with st DNA, (poly[dA-dT -poly[dA-dT ), and (po ly[d G-d C]-po ly[d G -d C]).

Sonawane, N. D., Szoka, F. C., and Verkman, A. S. (2003) Chloride accumulation and swelling in endosomes enhances DNA transfer by polyamine-DNA poly-plexes. J. Biol. Chem. 278,44826M48.31. 

Saponaria Saporin-L 1 Saponaria officinalis PAG (rRNA, DNA, poly A)... 

There is a growing interest in naturally occurring phenolic compounds that display biological antioxidant properties such as -hydroxycinnamic acid, ferulic zcid, caffeic acid/ and curcumin which are ubiquitous in plant food. It has been demonstrated that the interaction of the oxidizing OH adduct of DNA, poly-A and poly-G with hydrox-ycinnamic acid derivatives proceed via electron transfer. Cinnamic acid derivatives have been shown to be able to scavenge superoxide, peroxyl, and hydroxyl radicals. 

Keeping a column of wells with DNA poly ([dG-m dC]. poly [dG-m dC]) (B2 to G2) will show the extent of enzyme-substrate reaction in the absence of the andbody. 

Antibiotic (20 jUg/reaction mixture 3H-TMP incorporation1) into DNA poly (dA-dT) 3H-dGMP incorporation1) into DNA poly (dl-dC) 3H-TMP incorporation1) into DNA poly (rA) - (dT)g... 

The inhibiting activity of tilorone hydrochloride on the DNA-dependent RNA-polymerase reaction is shown in Table 20. Compared to the DNA-poly-merase reaction, the RNA-polymerase reaction requires large amounts of tilorone hydrochloride for its inhibition no significant inhibition was observed below 15 pg/re act ion mixture of tilorone hydrochloride. Whereas this amount of tilorone was able to completely inhibit the DNA polymerase reaction (see Table 19). One explanation is that in the RNA-polymerase reaction the DNA concentration is approx. 2.5 times more than that used in the DNA-polymerase reaction. However, this may not be the only reason for such differences. Our spectrophotometric data show that Mg2+ions influence the tilorone binding to DNA. Since the Mg2+ion concentrations in both systems are different, this may account for the variable sensitivity of both systems towards tilorone hydrochloride. 

For HSV at least three mechanisms have been described that generate resistance to AC V deficiency or loss of viral TK activity, alteration in substrate specificity of the virus-encoded TK, and alteration in the substrate specificity of the viral DNA polymerase (1,8). Most of the ACVr mutants that have been isolated in vitro and recovered from clinical specimens are TK-deficient (TK). However, resistant clinical mutants that have an altered TK or altered DNA polymerase activity have occasionally been described too. Although TK mutants are crossresistant with drugs that also depend on viral TK for their activation (i.e., GCV, penciclovir and brivudin (BVDU), they remain sensitive to agents, such as PFA, vidarabine (Ara-A), and the acyclic nucleoside phosphonate (ANP) analogs. PFA, a pyrophosphate analog, is a direct inhibitor of the viral DNA poly-merase in which it binds to the site involved in releasing the pyrophosphate product of DNA synthesis. Phosphorylation of Ara-A to Ara-A triphosphate is carried out by cellular enzymes phosphorylation of ANP derivatives to their mono- and diphosphoryl derivatives is also carried out by cellular enzymes. 

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