суббота, 8 февраля 2020 г.

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A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson—Crick, Hoogsteen and the Sugar edge. Not for use in diagnostic procedures. For determining base pairs in a real structure, a least-square fit is carried out for each base. In this figure the overlap of hydrogen bonds is minimized. To determine the glycosidic bond configuration cis or trans for each basepair, we generated V 12 , the vector connecting the geometric centers of the ring systems of the interacting bases. The local strand orientation is given in column 5.

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The occurrences of each type of base pair in each of the 12 families.

If the pair has only two H-bonds and they are bifurcated with two acceptor atoms and one donor atom, the pair will be further examined. If the base pair does not belong to the canonical Watson—Crick base pair as defined above, it is examined to see whether it belongs to one of the other rnavlew non-Watson—Crick base pair families.

Most generally, the base—base rnavoew belong to one of the 12 families of the pairs discussed above.

W, Watson—Crick edge; H, Hoogsteen edge; S, Sugar edge; c, the glycosidic bond orientation is cis ; and t, the orientation is trans. Search Thermo Fisher Scientific. Structurednaview— For adenine, the amino group which is active as a donor in H bonds is on the Hoogsteen side, while for guanosine this group is on the Sugar side. A survey has been carried out for 41 unique structures selected from the NDB database. Examples of the combination rnavirw the letters HSc means that the base on the right is Hoogsteen edge and on the left is Sugar edge and the two glycosidic bond orientation are cis.

Support Center Support Center. A stacked arrangement of bases does not belong to the 12 families. Journal List Nucleic Acids Res v. USA97— The program can also be used to edit a complex secondary structure projection.

Tools for the automatic identification and classification of RNA base pairs

If the base is modified, it will be displayed as a lower case letter code i. Signal amplification is achieved through specific hybridization of adjacent oligonucleotide pairs to bDNA structures, which are formed by Pre-amplifiers, Amplifiers, and fluorochrome-conjugated Label Probes.

We wanted to produce a program able to deduce such a diagram starting from a set of 3D coordinates. They were calculated from the 41 selected structures. If the structures were from the same source and similar, only one well-refined structure or the one with the highest resolution was selected.

The first column gives the LW type of base pairs.

ViewRNA ISH Cell Assays

The trans is formed if the glycosidic bonds of the interacting nucleotides lie on opposite sides of the line. For an ideal Watson—Crick pair, the two frames overlap with opposite y and z directions.

The tertiary interactions as defined above are represented by single red dashed rnvaiew. To define the relative orientation of the two bases, a line is drawn parallel to and between the two connecting H-bonds.

Recently, Leontis and Westhof LW 3 proposed a base pair classification for nucleic acids based on the observation that the planar edge-to-edge hydrogen bonding interactions between two bases involve one of three distinct edges: The coordinate frames are chosen so that the complementary bases form an ideal, planar Watson—Crick base pair in the undistorted reference state.

Therefore, the RNAview program gives one longer pseudo-helix on the y axis. All the loops are represented by circles.