User:Arivero01/sandbox

User:Sawagsta/sandbox

Experimental Methods

Watson-Crick canonical base pairing is not the only edge-to-edge conformation possible for the nucleotide since non-canonical pairing can take place as well. Sugar-phosphate backbone has an ionic character, which makes the bases sensitive to their environment, leading to conformational changes, such as non-canonical pairing. There are various methods of prediction for these conformations, such as NMR structure determination and X-ray crystallography. Most recently, however, a new algorithm has been created in order to analyze, reconstruct, and visualize three-dimensional nucleic acid structures, called 3DNA software. 3DNA uses the data collected from the DNA sequence of interest, and using its algorithm, can detect that two bases will pair if one or more hydrogen bonds are identified between them. The program models the exact position of the hydrogen atoms in the structure, in a three-dimensional representation. Other software has been developed, such as CURVES+, which allows researchers to submit a nucleic acid structure and alienate the individual nucleotide of interest. This allows for a more detailed study of the backbone, the grooves parameters of the nucleic acid, and the base pair bonding and geometry. There is also NUPARM-Plus, which is a free-access program that also allows the researcher to upload their nucleic acid structure and alienate the base pair of interest. However, NUPARM-Plus focuses on indicating the planarity of the axis between the bases and the quality of the hydrogen bond as well. In general, these different methods help identify and/or predeict the non-canonical base pairing that leads to different structural conformations.