Nucleic acid interaction

Chemotherapeutic agents, useful in me treatment of neoplastic diseases, exert their therapeutic effects by modifying me synthesis or functions of nucleic acids (see Chapter 51 and Chapter 58). For example, 6-mercaptopurine inhibits purine-ring biosynthesis, cytarabine inhibits DNA polymerase, alkylating agents crosslink DNA, and hydroxyurea inhibits the conversion of ribonucleotides into deoxyribonucleotides. However, other pharmacologic agents such as chlorpromazine, a 

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Steitz, T.A. Stmctural studies of protein-nucleic acid interaction the sources of sequence-specific binding. 

Harrison, S.C., Sauer, R.T. (eds.) Protein-nucleic acid interactions. Curr. Opin. Strue. Biol. 4 1-35, 1994. 

Chen, Z., et al. Protein-nucleic acid interactions in a spherical virus the structure of beanpod mottle virus at 3.0 A resolution. Science 245 154-159, 1989. 

CD spectroscopy has been used extensively to study peptide-nucleic acid interactions. Conformation changes induced by either the peptide or nucleic acid can be detected readily using this spectroscopic technique. Although the CD spectra of... 

Physical Techniques for Alkaloid-Nucleic Acid Interaction. 167... 

Protoberberine Alkaloid-Triplex Nucleic Acid Interaction. 194... 

Keywords Berberine Palmatine Coralyne Polymorphic nucleic acid structures Alkaloid-nucleic acid interactions... 

Appropriately designed biophysical studies can elucidate the mode(s), the binding affinities and the nature of the ligand-nucleic acid interaction that give rise to the observed selectivity and specificities. Thus, it is worthwhile to describe briefly the various physical techniques used to study alkaloid-DNA/RNA interactions. 

M. T. Record, Jr., E. S. Courtenay, S. Caley, and H. J. Guttman, Biophysical compensation mechanisms buffering E. coli protein—nucleic acid interactions against changing environments,... 

Arya DP (2005) Aminoglycoside-Nucleic Acid Interactions The Case for Neomycin. 253 ... 

Chaires JB (2005) Structural Selectivity of Drug-Nucleic Acid Interactions Probed by Competition Dialysis. 253 33-53 Cherkinsky M, see Braverman S (2007) 275 67-101... 

The reaction of metabolically generated polycyclic aromatic diol epoxides with DNA Ua vivo is believed to be an important and critical event in chemical carcinogenesis Cl,2). In recent years, much attention has been devoted to studies of diol epoxide-nucleic acid interactions in aqueous model systems. The most widely studied reactive intermediate is benzo(a)pyrene-7,8-diol-9,10-epoxide (BaPDE), which is the ultimate biologically active metabolite of the well known and ubiquitous environmental pollutant benzo(a)pyrene. There are four different stereoisomers of BaPDE (Figure 1) which are characterized by differences in biological activities, and reactivities with DNA (2-4). In this review, emphasis is placed on studies of reaction mechanisms of BPDE and related compounds with DNA, and the structures of the adducts formed. 

Considerable progress has been made in understanding the chemical principles in Pt-nucleic acid interactions since the discovery of Pt antitumor drugs. At the same time, however, new questions have been raised upon development of novel drugs that violate the early structure-activity relationships. A common feature for various Pt drugs is that their initial binding to nucleic acid fragments seems to be controlled by the... 

Equation 4.9 has been extensively applied to study the mechanisms of electrophilic (e.g., protonation) reactions, drug-nucleic acid interactions, receptor-site selectivities of pain blockers as well as various other kinds of biological activities of molecules in relation to their structure. Indeed, the ESP has been hailed as the most significant discovery in quantum biochemistry in the last three decades. The ESP also occurs in density-based theories of electronic structure and dynamics of atoms, molecules, and solids. Note, however, that Equation 4.9 appears to imply that p(r) of the system remains unchanged due to the approach of a unit positive charge in this sense, the interaction energy calculated from V(r) is correct only to first order in perturbation theory. However, this is not a serious limitation since using the correct p(r) in Equation 4.9 will improve the results. 

Structure and Conformation of Nucleic Acids and Protein-Nucleic Acid Interactions , ed. M. Sundaralingam and S. T. Rao, University Park Press, Baltimore, 1975. 

Hanson, C. L., Robinson, C. V. Protein-nucleic acid interactions and the expanding role of mass spectrometry. J Biol Chem 2004, 279, 24907-24910. 

The results of these three dynamic systems highlight the ability of DCC to identify the sites and appendages that most efficiently stabilize nucleic acid interactions. 

To advantageously use these unique properties of aminoglycoside-nucleic acid interaction, aminoglycoside-nucleic acid conjugates have been developed. 

Any technique designed to characterize binding interactions by determining the accessibility of the backbone of macromolecules to cleavage or modification reactions. For nucleic acid interactions, footprinting was originally accomplished by changes in phosphodiester accessibility to DNase 1, but numerous chemical and enzymatic methods continue to be elaborated. 

To characterize interactions between biologically relevant molecules, e.g., protein-protein and protein-nucleic acid interactions, as well as immunoreactions... 

Huang, W. M. and. Tso, P O. P. (1966). Physicochemical basis of recognition process in nucleic acid interactions. I. Interactions of polyuridylic acid and nucleosides. J. Mol. Biol, 16, 523. 

A similar situation is found in the structure of putrescine diphosphate " (a model system for amine-nucleic acid interactions) which divides into layers of HjPOJ anions bridged by protonated putrescine (1,4-diamino-n-butane) cations. In a real biological system (yeast phenylalanine transfer RNA) phosphate residues are found to be enveloped by the polyamine spermine [NH2(CH2)jNH(CH2)4NH(CH2)jNH2] which again adopts a linear, nonchelating conformation. ... 

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