Figure 2.

Structures obtained from MD simulations of a U-modified (a) RNA duplex (5′-r-CCUCAUGAGG-3′ and cRNA) and (b) DNA duplex (5′-d-CCUCATGAGG-3′ and cDNA). (c) Observed NOE contacts between nucleobase and pyrene protons in a U-modified DNA duplex (5′-C¹C²U³A⁴G⁵C⁶T⁷A⁸G⁹G¹⁰ : 3′-G¹⁰G⁹A⁸T⁷C⁶G⁵A⁴U³C²C¹). (d) Illustration of a 3′-intercalative binding mode. Panels a–c are reproduced from reference 19 with permission from Oxford University Press.