Nucleic acids 3+1 coordination

One of the important questions in metal ion-nucleic acid coordination is to find out to what extent neighboring nucleotide units affect binding of a metal ion at a given site [58]. Some answers to this question can be found by studying ligands of the... 

Much effort has been placed in the synthesis of compounds possessing a chiral center at the phosphoms atom, particularly three- and four-coordinate compounds such as tertiary phosphines, phosphine oxides, phosphonates, phosphinates, and phosphate esters (11). Some enantiomers are known to exhibit a variety of biological activities and are therefore of interest Oas agricultural chemicals, pharmaceuticals (qv), etc. Homochiral bisphosphines are commonly used in catalytic asymmetric syntheses providing good enantioselectivities (see also Nucleic acids). Excellent reviews of low coordinate (coordination numbers 1 and 2) phosphoms compounds are available (12). 

Technetium-99m coordination compounds are used very widely as noniavasive imaging tools (35) (see Imaging technology Radioactive tracers). Different coordination species concentrate ia different organs. Several of the [Tc O(chelate)2] types have been used. In fact, the large majority of nuclear medicine scans ia the United States are of technetium-99m complexes. Moreover, chiral transition-metal complexes have been used to probe nucleic acid stmcture (see Nucleic acids). For example, the two chiral isomers of tris(1,10-phenanthroline)mthenium (IT) [24162-09-2] (14) iateract differentiy with DNA. These compounds are enantioselective and provide an addition tool for DNA stmctural iaterpretation (36). 

More traditional applications of internal coordinates, notably normal mode analysis and MC calculations, are considered elsewhere in this book. In the recent literature there are excellent discussions of specific applications of internal coordinates, notably in studies of protein folding [4] and energy minimization of nucleic acids [5]. 

Figure 3 The underlying tree of a furanose ring in nucleic acids. Atoms are numbered 1,. . . , 5 corresponding to the natural tree ordering. All bond lengths are fixed. Arrows illustrate five internal coordinates that determine the ring conformation.

Microarray hybridization is a process by which nucleic acids are detected by hybridizing with complementary sequences bound to wafers at specific array coordinates. Hundreds to thousands of gene products may be measured in a single experiment. 

According to Barbieri et al., it can not be excluded that some of the coordination sites are occupied by (Nj atoms of the nucleic acid constituents. The precipitate obtained from [Ph2Sn(IV)] would contain both the [R2Sn(IV)] -DNA complex and distannoxane [(Ph2SnCl)20]. The main products of the... 

There are therefore four adjustable parameters per atom in the refinement (xy, yy, Zj, By). In the computer experiments we have carried out to test the assumptions of the nucleic acid refinement model we have generated sets of observed structure factors F (Q), from the Z-DNA molecular dynamics trajectories. The thermal averaging implicit in Equation III.3 is accomplished by averaging the atomic structure factors obtained from coordinate sets sampled along the molecular dynamics trajectories at each temperature ... 

P2j Z = 2 DX = 1.43 R = 0.067 for 1269 intensities. The uracil residue is in the anti (63.4°) disposition. The conformation of the D-ribosyl group is 2T3 (176.8°, 37.5°). The orientation about the exocyclic, C-4 -C-5 bond is t (—174.2°). The phenyl and uracil ringsofthe same molecule lie in almost parallel planes, 120 pm apart. The phenyl group is disordered. The uracil ring is sandwiched by the phenyl rings, and vice versa. The 0-1 and N-a atoms of the peptide backbone are hydrogen-bonded to 0-4 and N-3 of atranslationally related uracil to form cyclic dimers. Such interactions serve as models for nucleic acid-protein interactions. [Coordinate errors H(02 ) x should be —1574, instead of —1474 H(Na)2 z should be —145 instead of— 645.]... 

Several mathematical techniques have been used to obtain atomic coordinates for nucleic acid structures. They incorporate several different approaches. (a) Systematic rotations about all backbone torsional angles are performed and those conformations which form helicies and have adjacent bases parallel or in a given orientation are selected (59 6o). (b) Least squares techniques are used to re-... 

Auld, D.S. (2001) Zinc coordination sphere in biochemical zinc sites, BioMetals, 14, 271-313. Klug, A. and Rhodes, D. (1988) Zinc fingers a novel protein motif for nucleic acid recognition, TIBS, 12, 464-469. 

It is well known that a great variety of biomolecules exist where metals and metalloids are bound to proteins and peptides, coordinated by nucleic acids or complexed by polysaccharides and small organic ligands such as organic acids.55 Most proteins contain amino acids with covalently bonded heteroelements such as sulphur, selenium, phosphorus or iodine.51 Several reviews have been published on the development of mass spectrometric techniques for bioanalysis in metal-lomics , which integrate work on metalloproteins, metalloenzymes and other metal containing biomolecules.1 51 53 54 56-59 The authors consider trace metals, metalloids, P and S (so-called... 

---