On April 28, 2022, Nicy; Chakraborty, Debayan; Wales, David J. published an article.Category: pyrimidines The title of the article was Energy Landscapes for Base-Flipping in a Model DNA Duplex. And the article contained the following:
The authors explore the process of base-flipping for four central bases: adenine, guanine, cytosine, and thymine, in a DNA duplex using the energy landscape perspective. NMR imino-proton exchange and fluorescence correlation studies were 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 lifetimes obtained by the two methods implies that they are exploring different pathways, and possibly different open states. The authors’ 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. 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, the equilibrium constant for opening is large compared to flipping via the major groove. 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. Potential energy as a function of integrated path length for flipping pathways of (a) adenine, (b) guanine, (c) cytosine and (d) thymine along the major and minor groove. Pos. and neg. path lengths correspond to flipping along the minor and major groove, resp. The pathways are between closed state (as shown within Figure) and open states labeled as [A] and [B] (Figures and) for the base flipped out via major and minor groove, resp. The experimental process involved the reaction of 5-Methylpyrimidine-2,4(1H,3H)-dione(cas: 65-71-4).Category: pyrimidines
The Article related to dna duplex energy landscape base flipping model, General Biochemistry: Nucleic Acids and Their Constituents and other aspects.Category: pyrimidines
Referemce:
Pyrimidine | C4H4N2 – PubChem,
Pyrimidine – Wikipedia