Phosphodiester backbone

HammerheadRtbozyme. A small RNA molecule that catalyzes cleavage of the phosphodiester backbone of RNA is known as the hammerhead ribozyme. This ribozyme occurs namrally in certain vimses where it facihtates a site-specific self-cleavage at the phosphate and generates a 2 3 -cychc phosphate and a 5 -hydroxyl terminus. The reaction requires a divalent metal ion, such as or, as a cofactor. Whereas the... 

Modification of the Phosphodiester Backbone. Oligonucleotides having modified phosphate backbones have been extensively studied (46). Because altering the backbone makes derivatives generally more resistant to degradation by cellular nucleases, these materials have the potential to be more resilient antisense dmgs. 

En me Mechanism. Staphylococcal nuclease (SNase) accelerates the hydrolysis of phosphodiester bonds in nucleic acids (qv) some 10 -fold over the uncatalyzed rate (r93 and references therein). Mutagenesis studies in which Glu43 has been replaced by Asp or Gin have shown Glu to be important for high catalytic activity. The enzyme mechanism is thought to involve base catalysis in which Glu43 acts as a general base and activates a water molecule that attacks the phosphodiester backbone of DNA. To study this mechanistic possibiUty further, Glu was replaced by two unnatural amino acids. 

FIGURE 11.29 The vicinal—OH groups of RNA are susceptible to nucleophilic attack leading to hydrolysis of the phosphodiester bond and fracture of the polynucleotide chain DNA lacks a 2 -OH vicinal to its 3 -0-phosphodiester backbone. Alkaline hydrolysis of RNA results in the formation of a mixture of 2 - and 3 -nucleoside monophosphates. 

Figure 35-1. A segment of one strand of a DNA molecule in which the purine and pyrimidine bases guanine (G), cytosine (C), thymine (T), and adenine (A) are held together by a phosphodiester backbone between 2 -de-oxyribosyl moieties attached to the nucleobases by an W-glycosidic bond. Note that the backbone has a polarity (ie,a direction). Convention dictates that a single-stranded DNA sequence is written in the 5 to 3 direction (ie, pGpCpTpA, where G, C,T, and A represent the four bases and p represents the interconnecting phosphates).

The double-stranded structure of DNA can be separated into two component strands (melted) in solution by increasing the temperature or decreasing the salt concentration. Not only do the two stacks of bases puU apart but the bases themselves unstack while still connected in the polymer by the phosphodiester backbone. Concomitant with this denaturation of the DNA molecule is an increase in the optical absorbance of the purine and pyrimidine bases—a phenomenon referred to as hyperchromicity of denaturation. Because of the... 

The depurination of DNA, which happens spontaneously owing to the thermal lability of the purine N-glycosidic bond, occurs at a rate of 5000-10,000/cell/d at 37 °C. Specific enzymes recognize a depurinated site and replace the appropriate purine directly, without interruption of the phosphodiester backbone. 

In vitro studies of DNA interactions with the reactive ben-zo[a]pyrene epoxide BPDE indicate that physical binding of BPDE occurs rapidly on a millisecond time scale forming a complex that then reacts much more slowly on a time scale of minutes (17). Several reactive events follow formation of the physical complex. The most favorable reaction is the DNA catalyzed hydrolysis of BPDE to the tetrol, BPT (3,5,6,8,17). At 25°C and pH=7.0, the hydrolysis of BPDE to BPT in DNA is as much as 80 times faster than hydrolysis without DNA (8). Other reactions which follow formation of physical complexes include those involving the nucleotide bases and possibly the phosphodiester backbone. These can lead to DNA strand scission (9 34, 54-56) and to the formation of stable BPDE-DNA adducts. Adduct formation occurs at the exocyclic amino groups on the nucleotide bases and at other sites (1,2,9,17,20, 28,33,34,57,58). The pathway which leads to hydrocarbon adducts covalently bound to the 2-amino group of guanine has been the most widely studied. 

The photolytic activation of 5m was also shown to lead to DNA cleavage [33,35-38]. This reaction appeared to be faster and more efficient than the Cu+-catalyzed cleavage conditions. The mechanism(s) of DNA cleavage should be different because aryl cations (not aryl radicals) are believed to be produced under photolytic conditions (Fig. 12) [7]. Such electrophiles should target the nucleic acid bases and/or the positively charged phosphodiester backbone, and both of these could lead to DNA cleavage. 

Modified coherence length, 23 806 Modified copper-zinc, nominal composition and UNS designation, 7 722t Modified oligonucleotides, 17 626-637 applications of, 17 626-628 Modified phosphodiester backbones, 17 628-629... 

Phosphite triesters, 19 37 Phosphobetaine monomers, 20 480 Phosphobetaines, 20 482 Phosphoboranes, 4 170, 204 Phosphocreatine, 17 671 Phosphodiesterase inhibitors, 5 181t, 186 Phosphodiester backbones, modified, 17 628-629... 

J-Resolved Constant Time r Experiment for the Determination of the Phosphodiester Backbone Angles a and f 172... 

In nucleic acids, the cross-correlation studies were applied to investigation of the sugar conformation [101-103] of the phosphodiester backbone [65] as well as to some more spe-... 

As an example of the measurement of cross-correlated relaxation between CSA and dipolar couplings, we choose the J-resolved constant time experiment [30] (Fig. 7.26 a) that measures the cross-correlated relaxation of 1H,13C-dipolar coupling and 31P-chemical shift anisotropy to determine the phosphodiester backbone angles a and in RNA. Since 31P is not bound to NMR-active nuclei, NOE information for the backbone of RNA is sparse, and vicinal scalar coupling constants cannot be exploited. The cross-correlated relaxation rates can be obtained from the relative scaling (shown schematically in Fig. 7.19d) of the two submultiplet intensities derived from an H-coupled constant time spectrum of 13C,31P double- and zero-quantum coherence [DQC (double-quantum coherence) and ZQC (zero-quantum coherence), respectively]. These traces are shown in Fig. 7.26c. The desired cross-correlated relaxation rate can be extracted from the intensities of the cross peaks according to ... 

An excision endonuclease (excinudease) makes nicks in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective oligonucleotide. 

The structure showed that the three base-paired stems I, II, and III form type A-DNA helices and that the core contained the two conserved structural domains described in the previous paragraph. A single Me + ion was bound in close proximity to the pro-Rp oxygen of Ag s phosphate and the N7 position of GlO.l. The phosphodiester backbone of the DNA inhibitor strand was splayed... 

Fig. 12. Asymmetry of the DNA phosphodiester backbone trace as seen in the Oak Ridge NCP structural model (PDB access code lEQZ). No attempt has been made to regularize the geometry of the DNA positions of phosphates are based solely on the experimental electron density. Here the two DNA gyres are overlaid, with the 72 bp ventral gyre in red and the 73 bp dorsal gyre in blue. The minor groove positions facing the histone core are numbered sequentially from the dyad axis. The most pronounced asymmetry is seen in position 2 (10 o clock).

FIGURE 2.8 The general structure of transfer RNA (tRNA) showing the phosphodiester backbone as a ribbon, with bases or base pairs projecting from the backbone. (Adapted from Rich, A. [1977]. Three-dimensional structure and biological function of transfer RNA Accounts of Chem. Res., 10, 388-396, copyright 1977, American Chemical Society, with permission from Accounts of Chemical Research.)... 

DNA in cells exists mainly as double-stranded helices. The two strands in each helix wind about each other with the strands oriented in opposite directions (antiparallel strands). The bases of the nucleotides are directed toward the interior of the helix, with the negatively charged phosphodiester backbone of each strand on the outside of the helix. This is the famous B-DNA double helix discovered by Watson and Crick (Figure 3.3). 

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