Steric hindrance nucleotides

Fig. 1. Labeling of degraded chromatin by the TUNEL assay. During apoptosis endogenous, endonucleases cleave chromatin in the hnker region between nucleosomes. The resulting nucleosome multimers are labeled by TdT and a dUTP analog with a detectable label (biotin, DIG, or FITC) shown as. The additional nucleotide in the reaction (here shown as dCTP) may be any dNTP and serves to extend the labeling reaction by preventing steric hindrance by two adjacent labeled dUTPs. (Abbreviations are as in text.)...

Other nucleotides, such as dCTP, can be substituted for dATP at equal concentrations. The addition of unlabeled dNTPs to the reaction allows for a longer tail to be added by TdT without the problem of steric hindrance caused by the modification on the nucleotide (biotin, DIG, or FITC). Fluorescein-labeled nucleotides should be protected from light at all times to avoid loss of signal. 

The structure of the isoleucyl-tRNA synthetase (IleRS) from Thermus ther-mophilus (1045 residues, Mr 120 000) has been solved, as well as its complexes with lie and Val.17 The protein contains a nucleotide binding fold (Chapter 1) that binds ATR The fold has two characteristic ATP binding motifs His-54-Val-55-Gly-56-His-57 and Lys-591-Met-592-Ser-593-Lys-594. In the L-Ile-IleRS complex, a single He is bound at the bottom of the ATP cleft, with the hydrophobic side chain in a hydrophobic pocket, surrounded by Pro-46, Trp-518, and Trp-558. L-Leucine cannot fit into this pocket because of the steric hindrance of one of its terminal methyl groups. Larger amino acids are similarly excluded from this site. In the l-Val-IleRS complex, Val is bound to the same site, but the... 

The phosphodiester bonds of xanthylic acid in deaminated RNA were scarcely split by RNase U2 (30). The susceptibility of purine nucleotide residues to RNase U2 decreases in the order of A>G>I X, indicating that the phosphodiester bonds of adenylic acid and inosinic acid without a keto group at the position of purine base are more sensitive to RNase U2 than those of guanylic acid and xanthylic acid. The resistance of TNP-RNA to RNase U2 may be also attributed to the steric hindrance by a larger substituent at 2-amino groups of guanylyl residues, as with RNase T, (SO). 

Au and Au° have been used to model interactions between gold and DNA, and a crystal structure for a metal-nucleotide interaction has been reported. In trichloro(l-methylcytosinato) gold(III), three Cl and the N3 atom of 1-methylcytosine are coordinated to the Au ion producing a nearly square-planar geometry. Due to steric hindrance, the cytosine ring is placed almost perpendicular to the AuCls plane. 

Modified dNTP approach Either capture labels or detection labels can be incorporated during amplification or primer extension. The amount of signal enhancement, however, is limited by steric hindrance. Labeled nucleotides must be stable to the conditions employed in amplification. To minimize steric... 

For nucleoside host 1, the role of the hydroxyl groups on the ribose may be understood by comparing their interactions with guests, L-Phe and L-Trp. Host 1 has one OH group per each ribose unit and therefore, at the opening of this host cavity, the hydrophobicity increases a delicate balance of hydrophobicity and hydrophilicity exists. More importantly, the steric hindrance on the sugar of the nucleotide can decrease the noninteractions with guests. For example. 

The main limitation of the method lies in the rapid decrease in yields seen in each successive coupling step. Accompanying the decreased yield is the formation of failure and truncated sequences. The decreased yields, which seem to stem from nucleotide-support incompatability and from steric hindrance of reaction sites, necessitate elaborate methods for separation of the product from unwanted material. Current methods of separation are considered to be inadequate for this purpose. Part of this problem could be overcome if fragment-type syntheses could be employed so as to maximize the difference between the starting materials and products. 

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