caa a22 4500 467939039 CHVBK 20180406153006.0 cr unu---uuuuu 170328e20061001xx s 000 0 eng 10.1007/s10822-006-9083-x doi (NATIONALLICENCE)springer-10.1007/s10822-006-9083-x Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis [Elektronische Daten] [Shayantani Mukherjee, Manju Bansal, Dhananjay Bhattacharyya] Non-canonical base pairs contribute immensely to the structural and functional variability of RNA, which calls for a detailed characterization of their spatial conformation. Intra-base pair parameters, namely propeller, buckle, open-angle, stagger, shear and stretch describe structure of base pairs indicating planarity and proximity of association between the two bases. In order to study the conformational specificities of non-canonical base pairs occurring in RNA crystal structures, we have upgraded NUPARM software to calculate these intra-base pair parameters using a new base pairing edge specific axis system. Analysis of base pairs and base triples with the new edge specific axis system indicate the presence of specific structural signatures for different classes of non-canonical pairs and triples. Differentiating features could be identified for pairs in cis or trans orientation, as well as those involving sugar edges or C-H-mediated hydrogen bonds. It was seen that propeller for all types of base pairs in cis orientation are generally negative, while those for trans base pairs do not have any preference. Formation of a base triple is seen to reduce propeller of the associated base pair along with reduction of overall flexibility of the pairs. We noticed that base pairs involving sugar edge are generally more non-planar, with large propeller or buckle values, presumably to avoid steric clash between the bulky sugar moieties. These specific conformational signatures often provide an insight into their role in the structural and functional context of RNA. Springer Science+Business Media, LLC, 2006 Base pair conformation nationallicence RNA structure nationallicence Non-Watson-Crick nationallicence Intra-base pair parameters nationallicence Propeller twist nationallicence Mukherjee Shayantani Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, 700064, Kolkata, India aut Bansal Manju Molecular Biophysics Unit, Indian Institute of Science, 560012, Bangalore, India aut Bhattacharyya Dhananjay Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, 700064, Kolkata, India aut Journal of Computer-Aided Molecular Design Kluwer Academic Publishers 20/10-11(2006-10-01), 629-645 0920-654X 20:10-11<629 2006 20 10822 https://doi.org/10.1007/s10822-006-9083-x text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s10822-006-9083-x text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Mukherjee Shayantani Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, 700064, Kolkata, India aut NATIONALLICENCE 700 1- Bansal Manju Molecular Biophysics Unit, Indian Institute of Science, 560012, Bangalore, India aut NATIONALLICENCE 700 1- Bhattacharyya Dhananjay Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, 700064, Kolkata, India aut NATIONALLICENCE 773 0- Journal of Computer-Aided Molecular Design Kluwer Academic Publishers 20/10-11(2006-10-01), 629-645 0920-654X 20:10-11<629 2006 20 10822 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer