Molecular dynamics simulation of a DNA duplex labeled with triarylmethyl spin radicals

19F electron nuclear double resonance (ENDOR) spectroscopy for distance measurements using trityl spin labels in DNA duplexes

“…31 The interaction of TAM and a terminal base pair generally could affect the real distance distribution in DNA and has been a subject of debate. [29][30][31][32] In the range of shorter distances, it is not possible to utilize PELDOR and DQC owing to the above-mentioned limitations. It is also difficult to attach bulky TAM radicals to adjacent nucleotides so that this modification does not lead to their combined hydrophobic adhesion.…”

Determination of Base-Flipping Free-Energy Landscapes from Nonequilibrium Stratification

“…Duplex, triplex and various other conformations are observed in DNA systems. [1][2][3][4][5] The information carried by DNA systems is mostly buried in the hydrophobic core of the helix and the phenomenon called base flipping enables the interaction between external agents and the bases. Base flipping is widely observed in DNA methylation, [6][7][8][9] melting, [10][11][12][13][14][15][16] bubbling, [17][18] breathing, [19][20][21] and protein-DNA interaction.…”

“…Understanding the fundamental driving force of conformational changes in DNA systems are of great importance because of the unique functionality of DNA molecules. Duplex, triplex and various other conformations are observed in DNA systems. − The information carried by DNA systems is mostly buried in the hydrophobic core of the helix and the phenomenon called base flipping enables the interaction between external agents and the bases. Base flipping is widely observed in DNA methylation, − melting, − bubbling, , breathing, − and protein–DNA interaction .…”

“…Wang 1,2 and Zhaoxi Sun 1,3* 1 State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China…”