Occurrence and classification of T-shaped interactions between nucleobases in RNA structures

Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid–protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3261 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date dataset of <= 3.5 Å resolution crystal structures deposited in the Protein Data Bank.
Funding Information
  • Department of Science and Technology
  • University Grants Commission
  • Department of Science and Technology (DST) and University Grants Commission (UGC), New Delhi
  • DST Inspire (IFA14-CH162)
  • UGC FRP (F.4−5(176-FRP/2015)
  • Natural Sciences and Engineering Research Council of Canada
  • UGC for a Senior Research Fellowship

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