DNA conformation and

Mei and Barton [66, 67] have used photo-sensitised damage to DNA by /1-Ru(TMP)3 (induced by 02 formation) as a means of probing A-DNA conformations, and they have compared the damage so caused on a linear... 

In order to test the hypothesis that efficient promoter sequences will be more likely to acquire an A-DNA like conformation than other sequences, we carried out a collection of molecular dynamics simulations of the DNA double stranded dodecamers listed in Table 3. All these simulations were done with the CHARMM23 potential [93], in the presence of explicit solvent (-3500 TIP3 [99] water molecules) and 22 sodium ions (the simulation protocol is detailed in [89,100,101]). The DNA sequences were chosen to include known functional promoters (MLP, MLP2, AT, E4, 6T, CYCl, EFIA, and R28), nonfunctional promoters which could function with a mutant TBP (2C and 7G) [69,70], an inosine variant which can promote transcription (I) [102], and negative controls (GC, POLYA). This collection of sequences also includes two pairs of TATA boxes located in different contexts (MLP and MLP2, and AT and E4) in order to explore the sensitivity of the results to end effects. All the simulations started from a canonical B-DNA conformation and relaxed into a structure closer to A-DNA after 2 ns of simulation, not all the sequences achieved the same structure, as shown in Table 3, an indication that the simulation protocol is capable of identifying sequence dependent features. 

Summary. Physicochemical studies of the alteration of DNA conformation and stability by the fixation of ois-DDP, trans- PP and [Pt(dien)Cl]Cl at 0 005 < rb < 0 05 reveal that each compound alters the DNA in a characteristic manner. Table III represents an attempt to quantify these effects for rb 0.01. 

It is worth noting that the alterations of DNA conformation and stability for rb = 0.01 which have just been described are... 

HOW THE OBSERVED PLATINUM-DNA ADDUCTS MIGHT ALTER DNA CONFORMATION AND STABILITY IE VITRO... 

These optical transitions of metal complexes are commonly affected by their microenvironment, thereby outfitting metal complexes with sensitive spectroscopic handles on their molecular surroundings. In particular, complexes of Ru(II) and other d metal complexes have optical properties that are strongly affected by the extent and type of binding to DNA. One means for a metal complex to impart information about DNA structure is to elicit a spectroscopic change upon binding. This method is noninvasive and provides an excellent means to obtain solution-state data about DNA conformation and structure. 

Raman Spectra of Deoxyoligonucleotide Crystals Using a Raman Microscope Determination of Relation between Base Sequence and DNA Conformation and Polarization Effects... 

Svozil D, Kalina J, Omelka M, Schneider B (2008) DNA conformations and their sequence preferences. Nucleic acids res 36 3690-3706. doi 10.1093/nar/gkn260 Schneider B, Neidle S, Berman HM (1997) Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42 113-124. doi 10.1002/(SICI)1097-0282(199707)42 1<113 AID-BIP10>3.0.CO 2-0... 

It is interesting to add that simple modifications of the glycosidic angle x. which fixes the base plane with respect to the phosphodiester backbone, are also a powerful way of provoking important conformational transitions. This was demonstrated in early modeling by Olson which lead to unusual ribbon-like structures of DNA. More recently, it has been shown that such deformations are related to certain protein induced DNA deformations, leading to the so-call TA-DNA conformation and to the conformations created by extreme stretching of the double helix (see Section 3.5 and Protein-Nucleic Acid Interactions). 

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