The triplex-hairpin transition in cytosine-rich DNA

Biophysical Journal
Anton S PetrovGeorge R Pack

Abstract

We present a theoretical study of the self-complementary single-stranded 30-mer d(TC*TTC*C*TTTTCCTTCTC*CCGAGAAGGTTTT) (PDB ID: 1b4y) that was designed to form an intramolecular triplex by folding back twice on itself. At neutral pH the molecule exists in a duplex hairpin conformation, whereas at acidic pH the cytosines labeled by an asterisk (*) are protonated, forming Hoogsteen hydrogen bonds with guanine of a GC Watson-Crick basepair to generate a triplex. As a first step in an investigation of the energetics of the triplex-hairpin transition, we applied the Bashford-Karplus multiple site model of protonation to calculate the titration curves for the two conformations. Based on these data, a two-state model is used to study the equilibrium properties of transition. Although this model properly describes the thermodynamics of the protonation-deprotonation steps that drive the folding-unfolding of the oligomer, it cannot provide insight into the time-dependent mechanism of the process. A series of molecular dynamics simulations using the ff94 force field of the AMBER 6.0 package was therefore run to explore the dynamics of the folding/unfolding pathway. The molecular dynamics method was combined with Poisson-Boltzmann calculati...Continue Reading

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Citations

Jan 16, 2007·Journal of Molecular Biology·Christopher L TangBarry Honig
Jul 12, 2017·The Journal of Physical Chemistry Letters·Pei Guo, Sik Lok Lam
Sep 20, 2019·Physical Chemistry Chemical Physics : PCCP·Manas MondalYi Qin Gao
Jan 28, 2021·Chemistry : a European Journal·Liqi WanPei Guo
Feb 24, 2007·Biochemistry·Ana Maria SotoDavid E Draper
Dec 25, 2012·Biophysical Journal·Il-Buem LeeAlbert Johner

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