DNA Sequence Dependence

The minor groove was implicated further by studies using short DNA duplexes. Molecular modeling indicated that a single DiSC2(5) H-dimer should span 

FIGURE 7.4 Comparison of functional groups in DNA major and minor grooves for A-T, G-C, and I-C base pairs. 

FIGURE 7.5 Dimerization and aggregation of a cyanine dye on DNA templates. AT-5 and AT-10 promote assembly of one and two dimers, respectively. 

FIGURE 7.6 InducedCDspectraforDiSCjlS) recorded in the presence of AT-5, AT-10, and [Poly(dA-dT)]2. The splitting observed for the latter two cases indicates assembly of multiple adjacent dimers on the DNA template. 

The origin of this cooperativity might be the impact of the bound dimer on the DNA structure in order to accommodate two ligands bound as a dimer, some studies have shown that the minor groove has to approximately double its width [30,31]. 

---

The effect of the DNA sequence dependence on the binding dynamics of 5 and 6 with ct-DNA (42% GC content) and ml-DNA (72% GC content) was investigated using laser temperature jump experiments.118 Only one relaxation process was observed for both guests, but the presence of the leveling off effect at high DNA concentration was dependent on the guest and the type of DNA. No values for the rate constants were reported in this study. 

DNA sequence-dependent nucleosome structural and dynamic polymorphism. A role for H2B N-terminal tail proximal domain... 

Widlund, H.R., Vitolo, J.M., Thiriet, C., and Hayes, J.J. (2000) DNA sequence-dependent contributions of core histone tails to nucleosome stability Differential effects of acetylation and proteolytic tail removal. Biochemistry 39, 3835-3841. 

The analysis of single DNA molecules or small self-assemblies is equally important for medical research, e.g., for the understanding of the DNA sequence-dependent and structure-dependent diseases (recently reviewed [48]), as well as for nanoengineering-oriented research, e.g., understanding of the mechanical properties of DNA [49] that are useful for the construction of future nanodevices. In the following section we will refer to the AFM studies concerning DNA molecules and small self-assembhes as single molecule studies . 

Deb, S., Bandyopadhyay, S., Roy, S. (2000). DNA sequence dependent and independent conformational changes in multipartite operator recognition by lambda-repressor. Biochemistry, 39(12), 3377-3383. 

Sanii L, Schuster GB (2000) Long-distance charge transport in DNA sequence-dependent radical cation injection efficiency. J Am Chem Soc 122 11545-11546 Saran M, Bertram H, Bors W, Czapski G (1993) On the cytotoxcity of irradiated media. To what extent are stable products of radical chain reactions in physiological saline responsible for cell death Int J Radiat Biol 64 311-318... 

The Maxam-Gilbert method for DNA sequencing depends upon (one of the following) ... 

RE "A" Cuts once within the probed sequence, and at variable sites within the host DNA sequence, depending on the bitegration site, therefore generating two bands of variable sizes per each integration site, either in the same cell, or in different cells. 

AUawi HT, SantaLucia J Jr. Nearest-neighbor thermodynamics of internal A.C mismatches in DNA sequence dependence and pH effects. Biochemistry 1998 37 9435-44. 

Tanious, F.A., Hamelbeg, D., Bailly, C., Czarny, A., Boykin, D.W. and Wilson, W.D. (2004) DNA sequence dependent monomer-dimer binding modulation of asymmetric benzimidazole derivatives. J. Am. Chem. Soc. 126, 143-153... 

Hock, L.M., and Zhurkin, V.B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. USA, 95,11163-11168. 

Figure21.1. Schematic of a dideoi ucleotidetripho ihste (ddNTP). Fluorescent and nonfluorescent dtOTITla are naed for DNA sequencing depending on the metiiod. Hie 2 groiqi ia bydrogoi in and is a hydnucyl group in RNA...

Those spikes are produced every time a DNA molecule reaches the carbon nanotube surface, and a different change in current level, positive or negative spikes, is observed for different DNA molecules. A DNA sequence dependence is further suggested by the known correlation between nucleobases polarizability and... 

---