DNA breathes Hoogsteen

Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

“…To gain insight of transition pathways from WC to HG base pairing in duplex DNAs, a reasonably converged free energy profile of the A-tract was obtained from the PMF simulation of 20 ns as a function of the 2D reaction coordinates. Considering that the flexibility of duplex DNA causes spontaneous structural fluctuations through base flipping ( 11 ), the inclusions of CPDb angle for base flipping and χ-angle for anti–syn rotation were necessary to obtain realistic descriptions of free energy profiles. Our simulated 2D-PMF profile at ambient temperature showed that in addition to the free energy minimum basins of WC and HG bp states, a relatively stable intermediate state is located in the minor groove pathway.…”

“…Until now, HG base pairing has been observed primarily in damaged DNAs and duplex DNAs complexed with enzymes and small ligands ( 4 – 10 ). However, for many reasons, experimental observation of HG bps in free duplex DNA has been a difficult and elusive task ( 11 ). Recently, a major breakthrough was made regarding the identification of such HG bps in naked B-DNA using a nuclear magnetic resonance (NMR) relaxation method.…”

Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs

“…Exactly this model could quantitatively explain in details the melting of DNA processing in the multistate way due the different length and heterogeneous sequence (Vologodskii et al, 1984 ; Wartell and Benight, 1985 ; Wada and Suyama, 1986 ; SantaLucia, 1998 ). At this, predicted lifetimes of the open state of the base pairs lie in the sub microsecond range (~10 −7 s) (Craig et al, 1971 ; Porschke and Eigen, 1971 ; Frank-Kamenetskii, 2011 ). However, according to the literature data it remains unknown, what the nature of the open state of the DNA base pairs is and whether there is a barrier on the potential energy surface for providing its existence (Lavery, 1994 ; Stofer et al, 1999 ; Yang et al, 2015 ).…”

“…Since the model of two states—H-bonded base pair and opened base pair—is not able to describe in details the dynamical behavior of DNA, which experimentally manifests itself in a number of its physico-chemical properties (Lazurkin et al, 1970 ; Craig et al, 1971 ; Porschke and Eigen, 1971 ; Frank-Kamenetskii and Lazurkin, 1974 ; Lukashin et al, 1976 ; Chay, 1979 ; Frank-Kamenetskii, 1981 , 1983 , 1985 , 2011 ; Vologodskii et al, 1984 ; Wartell and Benight, 1985 ; Wada and Suyama, 1986 ; Guéron et al, 1987 ; Lavery, 1994 ; Guéron and Leroy, 1995 ; SantaLucia, 1998 ; Stofer et al, 1999 ; Giudice et al, 2001 ; Ababneh et al, 2003 ; Coman and Russu, 2005 ; Nikolova et al, 2011 , 2013 ; Bohnuud et al, 2012 ; von Hippel et al, 2013 ; Frank-Kamenetskii and Prakash, 2014 ; Yang et al, 2015 ; Singh and Singh, 2017 ), the searching of new conformational states of the DNA base pairs near their Watson-Crick global minima has been intensified (Keepers et al, 1982 ; Pechenaya and Volkov, 1984 ; Volkov, 1995 ; Giudice et al, 2003 ; Pérez et al, 2007 ; Lindahl et al, 2017 ).…”

Structural and energetic properties of the four configurations of the А•Т and G•C DNA base pairs

“…Інтерес до цієї те-матики «підігрітий» роботою [7], результати якої справили ефект «бомби, що вибухнула» [8], бо переконливо як експериментально, так і теоретично було продемонстровано, що комплементарні пари основ ДНК у водному розчині «дихають за Гугстином» [8]. Її авто-ри дійшли висновку, що пари А⋅Т і G⋅C «ди-хають» по-різному -перша за молекулярним механізмом, а друга -за іонізаційним, який передбачає захоплення цитозином протону із середовища у положення N3.…”