Jesse Stombaugh
= Jesse Stombaugh
{c}
\b[Jesse Stombaugh] has contributed to the geometric analysis of <RNA> structures. His 2002 paper with <Neocles B. Leontis> and <Eric Westhof> classifies <noncanonical base pairs> and organizes their geometric compatibility in <RNA isostericity matrices>. The paper's byline associates Stombaugh with Bowling Green State University's chemistry and biomolecular-sciences research.<The non-Watson-Crick base pairs and their associated isostericity matrices by Neocles B. Leontis and others>[Title-page byline and affiliation; isostericity matrices, Tables 3–5]{ref}
The underlying problem is that <nucleotide sequence> alone does not specify which edges of two <nucleobases> contact or how their attached backbones are arranged. A replacement can preserve a contact's geometry while changing its chemical composition. Stombaugh's coauthored classification provides a framework for testing such replacements, rather than treating every <base pair> with the same two letters as the same structure.
Stombaugh is first author of the 2009 study <Frequency and isostericity of RNA base pairs by Jesse Stombaugh and others>, with <Craig L. Zirbel>, <Eric Westhof> and <Neocles B. Leontis>. It introduces the <RNA IsoDiscrepancy Index> and compares geometrically aligned <ribosomal RNA> structures with sequence variation.<Frequency and isostericity of RNA base pairs by Jesse Stombaugh and others>[Abstract and Results, definition and application of the index]{ref}
An original comparison illustrates the question. The standard cis Watson–Crick A–U and G–C contacts are geometrically compatible, even though they have two and three <hydrogen bonds>, respectively. Replacing A–U by G–C can therefore preserve the approximate backbone scaffold without preserving every contribution to <free energy> or recognition by a <protein>. Conversely, simply reversing the order of a wobble pair need not preserve its geometry. Geometry, contact chemistry and local sequence context must be assessed separately.
These studies combine structural coordinates with comparative analysis; they do not infer a unique three-dimensional fold from a short sequence alone. A correlated substitution can support a structural hypothesis, but actual contacts and model errors still need checking against experimental structures.