Energy Landscapes for Base-Flipping in a Model DNA Duplex

Abstract

We explore the process of base-flipping for four central bases, adenine, guanine, cytosine, and thymine, in a deoxyribonucleic acid (DNA) duplex using the energy landscape perspective. NMR imino-proton exchange and fluorescence correlation spectroscopy studies have been used in previous experiments to obtain lifetimes for bases in paired and extrahelical states. However, the difference of almost 4 orders of magnitude in the base-flipping rates obtained by the two methods implies that they are exploring different pathways and possibly different open states. Our results support the previous suggestion that minor groove opening may be favored by distortions in the DNA backbone and reveal links between sequence effects and the direction of opening, i.e., whether the base flips toward the major or the minor groove side. In particular, base flipping along the minor groove pathway was found to align toward the 5′ side of the backbone. We find that bases align toward the 3′ side of the backbone when flipping along the major groove pathway. However, in some cases for cytosine and thymine, the base flipping along the major groove pathway also aligns toward the 5′ side. The sequence effect may be caused by the polar interactions between the flipping-base and its neighboring bases on either of the strands. For guanine flipping toward the minor groove side, we find that the equilibrium constant for opening is large compared to flipping via the major groove. We find that the estimated rates of base opening, and hence the lifetimes of the closed state, obtained for thymine flipping through small and large angles along the major groove differ by 6 orders of magnitude, whereas for thymine flipping through small angles along the minor groove and large angles along the major groove, the rates differ by 3 orders of magnitude.

Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching

“…The parallel stacking of the indole with A and T bases suggested that the dye might be “sandwiched” and trapped into stable microstates depending on the spatial arrangement of the T and A bases, leading to the different orientations observed for bTT and bAA . As dyes occasionally changed orientation, we speculated that the transition between stable microstates would be promoted by DNA breathing [ 33 , 63 ], base flipping [ 64 ], or a mechanism in which the dye and the neighboring bases stack and unstack.…”

Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop

“…Although the base flipping process is more frequently observed to proceed through the major groove in nucleic acids, it is not uncommon to observe purine nucleotides flipping via the minor groove pathway. 93,94 Tetraloop Adopts Conformations Conducive to Binding of the Reader Protein. A crystal structure of the A*UCG tetraloop bound to the reader (YTHDC1) protein shows that the tetraloop is recognized by the reader protein in a single-stranded conformation (Figure S10).…”

“…The base flipping through the minor groove was due to a conformational change in the RNA tetraloop, which led to its opening (Figure S9). Although the base flipping process is more frequently observed to proceed through the major groove in nucleic acids, it is not uncommon to observe purine nucleotides flipping via the minor groove pathway. , …”

“…Although the base flipping process is more frequently observed to proceed through the major groove in nucleic acids, it is not uncommon to observe purine nucleotides flipping via the minor groove pathway. 93 , 94 …”

Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy

“…Lacking stabilizing RNAP interactions (and thus lacking a driving force for unstacking), t-strand bases may remain largely stacked in I1. Although the rates of interconversion between the I1 ensemble intermediates are unknown, they are likely relatively fast: in the absence of protein-DNA interactions, lifetimes of transiently open DNA bubbles (2-10 bp) 68 or extrahelical bases 69 range from 10 -2 to 10 -6 s. Because the MnO 4 - oxidation reaction rate constant is relatively slow (∼15 M - 1 s - 1 ) and decreases with decreasing temperature 70 , we suggest that the footprinting conditions (low temperature, low MnO 4 - dose) used for σP R may have prevented detection of DNA opening in I1.…”