The Triplex-Hairpin Transition in Cytosine-Rich DNA

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 calculations to determine when a change in protonation state was warranted during a trajectory. This revealed a sequence of elementary protonation steps during the folding/unfolding transition and suggests a strong coupling between ionization and folding in cytosine-rich triple-helical triplexes.

Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich’s ataxia: DNA triplexes and RNA/DNA hybrids

“…Cytosines need to be protonated in order to form stable triplexes, which generally occurs under low pK a ( 28 ). However, cytosines buried in the major groove can be protonated even under p K a as high as 8 ( 101 , 102 ). Results of a smFRET study ( 36 ) show that the Y·R:Y DNA triplex is stable even under neutral pH, with pY being the most stable pyrimidine triplex, a result that confirms previous findings ( 33–35 ).…”

Calculation of pKas in RNA: On the Structural Origins and Functional Roles of Protonated Nucleotides

“…43 Here, we review the underlying theory in order to discuss its application in the context of RNA. We used a modified version of the program MCCE, 60-62 which uses a distance-dependent pairwise energy softening function 107 to help prevent large electrostatic energies from dominating the pK a calculations.…”

“…Our work builds on the extensive literature that exists for calculating pK a s in proteins, [34][35][36][37][38][39][40][41][42] and, more recently, in DNA. 43 Most of these methods rely on numerical solutions to the Poisson-Boltzmann (PB) equation to obtain electrostatic contributions to the pK a shift. The linear PB equation (LPB) has been used in most applications in proteins but, given the high charge density on RNA molecules, the nonlinear PB equation (NLPB) is more appropriate.…”

Selective Preference of Parallel DNA Triplexes Is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity between the G*GC and T*AT Triplets

“…Likewise, MD simulations [ 115 ] using AMBER force field bring out the feature intermediate to that of A and B DNA of the duplex in a triplex in accordance with geometrical stipulation [ 116 ] and NMR data [ 117 , 118 ]. Also, it has been competently used to explore conformational flexibility [ 119 ], stability [ 120 ], hydration [ 121 ], protonation and folding property [ 122 ] etc. of DNA triplexes.…”