Modified nucleotides structure

A modified nucleotide found in RNA sequencing could either be a new nucleotide of unknown chemical structure or it could correspond to an already known modified nucleotide (up to now about 90 different modified nucleotides have been identified in RNA). Keith [124] proposed preparative purifications of major and modified ribonucleotides on cellulose plates, allowing for their further analysis by UV or mass spectrometry. Separation was realized by two-dimensional elution using the following mobile phases (1) isobutyric acid-25% ammonia-water (50 1.1 28.9,... 

FIGURE 21.5 Chemical structures of modified nucleotides used in the SELEX procedure. Aptamers containing 2 F- and 2 NH2-modified nucleotides are resistant against degradation by nucleases and therefore suitable for in vitro and in vivo applications. Aptamers containing modifications (I or Br) at the C-5 position of pyrimidine can be photo-cross-linked to their protein targets. Arrows indicate the respective chemical modifications. 

Fig. 2.7. RNA secondary structures. The nucleotide sequence oftRNAphe (shown in the upper string) is presented together with the secondary structure of minimal free energy and the symbolic notation (lower string). The sequence contains several modified nucleotides (D, M, P, T, Y) in addition to the conventional bases (A, U, C, C). Individual nucleotides in the secondary structure are shown as light gray (single bases), dark gray and black pearls (base pairs). ThetRNA structure is a clover leaf with three hairpin loops (adjacent stacks are shown in black) and a closing stack...

Two structures incorporating modified nucleotides include the co-crystal structure of pseudouridine synthase TruB with a T stem-loop of tRNA in which the modification site (U55) is modified with 5-fluorouridine, " and the crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to DNA containing an abasic site. " ... 

The determination of several modified bases has been achieved by McCloskey, using partial silylation techniques. The FD collision-induced-dissociation (CID) mass spectra of a modified nucleotide has been reported by Straub during the course of his study on the interaction of a chemical carcinogen with DNA. In that particular experiment, however, the adduct was previously separated by extraction it was not a direct application of the FD-CID technique to a structural problem. Nevertheless, the study indicated that the attachment of the carcinogenic compound takes place at the base, confirming the potential of this technique for cancer research. ... 

Transfer RNA (tRNA) has a cloverleaf structure and contains modified nucleotides. Transfer RNA molecules are relatively small, containing about 80 nucleotides. 

Radioactive or modified nucleotides can be incorporated randomly in a transcript or specifically at the 5 -position of the transcript during transcription. Thus it is feasible to incorporate cap-structures... 

In order to obtain therapeutic agents based on synthetic ribozymes, it is necessary to modify these structures chemically. Such modifications - as in the traditional antisense strategy - should confer resistance to nucleases, selectivity, and proper hybridization and uptake characteristics. In the case of ribozymes, the design of new modified nucleotides becomes more complex, since correct folding of the nucleic acid is needed in order to maintain the catalytic activity. Several studies (e.g.. X-ray structure elucidation and mapping with modified nucleotides) have shown that the presence of the 2 -hydroxyl group at specific positions in the catalytic core is essential for hydrolytic activity. Ribozymes are currently used in larger screens as a... 

The main driving force behind the chemistry of nucleotides and nucleic acids continues to be the demand for novel chemotherapeutics. Over the past few years this motivation has extended from the traditional small nucleotide drugs to the bio-polymers DNA and RNA and more importantly their modified analogues. In addition, the understanding of recognition processes involving nucleic acids, with each other, proteins and small molecules is an area of considerable interest which spans from structural studies, such as NMR and crystallography, to the synthesis of modified nucleotides and nucleic acids. Since this review did not appear last year we have endeavoured to include some material form early 1993 and therefore cover publications from January 1993 to June 1994. 

Later MD studies on DNA triplexes were often devoted to the stability and the H-bond pattern of the base triads, to the conformational properties of the sugar-phosphate backbone, to the effect of modified nucleotides and to the hydration pattern. Modified nucleotides include structures derived from 2-aminopyridine and 8-aminoguanine a triplex with the phosphodiester linkage in two strands replaced by S-methylthiourea linkers, 2 -aminoethoxy-substituted riboses and a -CH2-lengthening of the intemucleotide linkage. ... 

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