Nucleic acids, reviews

The infrared investigations on nucleic acids reviewed here demonstrate that, although the method is not so widely applied, important information concerning conformations and interactions can be obtained. 

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). 

Once kiside the host ceU, the vims must repHcate its own nucleic acid. To do this, it often uses part of the normal synthesizing machinery of the host ceU. If the vims is to continue its growth cycle, vkal nucleic acid and vkal proteki must be properly transported within the ceU, assembled kito the kifective vims particle, and ultimately released from the ceU. AH of these fundamental processes kivolve an intimate utilization of both ceUular and vkal enzymes. Certain enzymes that ate kivolved ki this process ate specificaHy suppHed by the invading vims. It is this type of specificity that can provide the best basis for antivkal chemotherapy Thus an effective antivkal agent should specificaHy inhibit the vkal-encoded or vims-kiduced enzymes without inhibition of the normal enzymes involved in the biochemical process of the host ceH. Vims-associated enzymes have been reviewed (2,3) (Table 1). 

Woodward s synthesis, 4, 416-419 Chlorophyll b, 4, 382 Chlorophyll c, 4, 382 Chlorophyll d, 4, 382 Chlorophylls, 4, 378 biosynthesis reviews, 1, 99 structure, 4, 370 substituents reactions, 4, 402 Chloroporphyrin e, 4, 404 Chloroprothixene pharmacology, 3, 942 Chloropyramine as antihistamine, 1, 177 Chloropyrifos synthesis, 2, 201 Chloropyrifos-ethyl as insecticide, 2, 516 Chloropyrifos-methyl as insecticide, 2, 516 Chloroquine, 1, 145 adsorption on nucleic acids, 1, 179 as antimalarial, 1, 173, 2, 517 Chloroquine, hydroxy-as antimalarial, 2, 517 Chlorosulfonyl isocyanate cycloaddition reactions... 

This chapter lists some representative examples of biochemicals and their origins, a brief indication of key techniques used in their purification, and literature references where further details may be found. Simpler low molecular weight compounds, particularly those that may have been prepared by chemical syntheses, e.g. acetic acid, glycine, will be found in Chapter 4. Only a small number of enzymes and proteins are included because of space limitations. The purification of some of the ones that have been included has been described only briefly. The reader is referred to comprehensive texts such as the Methods Enzymol (Academic Press) series which currently runs to more than 344 volumes and The Enzymes (3rd Edn, Academic Press) which runs to 22 volumes for methods of preparation and purification of proteins and enzymes. Leading referenees on proteins will be found in Advances in Protein Chemistry (59 volumes. Academic Press) and on enzymes will be found in Advances in Enzymology (72 volumes, then became Advances in Enzymology and Related Area of Molecular Biology, J Wiley Sons). The Annual Review of Biochemistry (Annual Review Inc. Patio Alto California) also is an excellent source of key references to the up-to-date information on known and new natural compounds, from small molecules, e.g. enzyme cofactors to proteins and nucleic acids. 

This series in heterocychc chemistry is being introduced to collectively make available critically and comprehensively reviewed hterature scattered in various journals as papers and review articles. All sorts of heterocyclic compounds originating from synthesis, natural products, marine products, insects, etc. will be covered. Several heterocyclic compounds play a significant role in maintaining life. Blood constituents hemoglobin and purines, as well as pyrimidines, are constituents of nucleic acid (DNA and RNA). Several amino acids, carbohydrates, vitamins, alkaloids, antibiotics, etc. are also heterocyclic compounds that are essential for life. Heterocyclic compounds are widely used in clinical practice as drugs, but all applications of heterocyclic medicines can not be discussed in detail. In addition to such applications, heterocyclic compounds also find several applications in the plastics industry, in photography as sensitizers and developers, and the in dye industry as dyes, etc. 

The helicases are enzymes central to life itself. The nature of double-stranded DNA means that before a polymerase can begin to copy the appropriate region of the nucleic acid, the two strands have to be unwound the separation of the two strands is the function of the helicase (Fig. 2). An indication of the significance of this family of enzymes is seen in the so-called Werner syndrome, where the helicase function required in the suppression of inappropriate recombination events is defective and causes genomic instability and cancer (for a review see Cobb and Bjergbaek 2006). 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

The development of DNA sensors and high-density DNA arrays has been prompted by the tremendous demands for innovative analytical tools capable of delivering the genetic information in a faster, simpler, and cheaper manner at the sample source, compared to traditional nucleic acid assays. Nanoparticle-biopolymer conjugates offer great potential for DNA diagnostics and can have a profound impact upon bioanalytical chemistry. Nanoparticle/polynucleotide assemblies for advanced electrical detection of DNA sequences have been reviewed by Wang [145]. 

A. Mononucleotides.—A new journal has appeared in the past year consisting of abstracts of papers published in the nucleotide and nucleic acid fields. The use of nucleosides and nucleotides as potential therapeutic agents has been reviewed. Nucleotides which have been prepared recently using conventional methods of phosphorylation include those derived from 6-methylthiopurine ribonucleoside (la), 5-methylsulphonyluridine (lb), l-(jS-D-ribofuranosyl)-2-pyrimidone (Ic), 3-(jS-D-ribofuranosyl)-4-pyrimidone (Id), and various thionucleosides. - O-Phosphorylated 3 -amino-3 -deoxythymidine (2a) and 5 -amino-5 -deoxythymidine (2b)... 

Maiti and Kumar, in their contribution, review the physicochemical and nucleic acid binding properties of several isoquinoUne alkaloids (berberine, palmatine and coralyne) and their derivatives imder various environmental conditions. 

A good overview of DNA structure and function. E. Pennisi, Science 2003, 300, 282. Reviews of nucleic acid chemistry ... 

Instead, this review seeks to cover less well-known and newly emerging aspects of metal-nucleobase chemistry. In addition to biomedical relevancies, nucleic acid chemistry offers a paradigm for organizing molecules via base pairing. Combining the hydrogen bonding... 

In summary, bDNA has a number of distinct theoretical and practical advantages over target amplification systems for direct quantitation of specific nucleic acid sequences. The following sections review the specific clinical and research applications of this technology. 

These examples show that for difficult cases, and especially when a prediction is being made, a large number of simulations may be necessary. Today, the continuing increase in computer power has made such multiple simulations possible in a reasonable time frame. Several other recent studies illustrate the scope of molecular dynamics free energy for molecular recognition problems they include studies of nucleic acids [13], proteins [14-16], and methodological studies of convergence and precision [17, 18]. Several recent reviews provide additional examples [19, 20]. 

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