The energetics of i‐DNA tetraplex structures formed intermolecularly by d(TC₅) and intramolecularly by d[(C₅T₃)₃C₅]

Abstract

Cytosine-rich DNA at low pH adopts an antiparallel tetraplex structure via the intercalation of two partially protonated, parallel stranded duplexes. This intriguing structural motif has been named i-DNA. We have used a combination of spectroscopic and calorimetric techniques to characterize the properties of an intermolecular i-DNA formed by d(TC(5)) and an intramolecular i-DNA formed by d[(C(5)T(3))(3)C(5)]. Our measurements reveal that both i-DNA complexes are enthalpically stabilized by 6.5-7.0 kcal/mol(base) and entropically destabilized by 20 cal/mol(base)/K. These values are about 50% larger than the corresponding enthalpy and entropy values per base for Watson and Crick duplexes and for Hoogsteen triplexes, while being similar to per base enthalpy and entropy values reported for G-quadruplexes. Our data also reveal a positive heat capacity change between 20 and 30 cal/mol(base)/K, values similar to that reported for polymeric Watson & Crick DNA duplexes. Solution-dependent studies reveal the overall thermal and thermodynamic stability of i-DNA complexes to be dictated by an interplay between pH and ionic strength. Based on the thermodynamic data measured, we discuss the feasibility of i-DNA formation in the context of conventional DNA sequences, while commenting on potential roles for this structural motif in biological regulatory mechanisms.

Formation and Dissociation of the Interstrand i-Motif by the Sequences d(XnC4Ym) Monitored with Electrospray Ionization Mass Spectrometry

“…In addition, all of oligonucleotides showed an obvious and unaltered turning point in absorbance versus temperature curve of 265nm ( Figure S2d, Supporting Information) and a solid UV melting temperature (Table1). This further supported the formation of intercalated i-motifs [45].…”

“…All measurements were performed at least three times; the T m values differed by less than 0.5°C [44]. It should be noted that the melting profiles of interstrand i-motifs mainly reflect the stability of fully intercalated i-DNA tetraplex structures, when the strands were equilibrated with sufficient time [45]. This is why the turning point of melting curves can be considered to be the T m of such structures.…”

“…Figure6 also shows that the hysteretic phenomenon of the cooling curves at 265nm is lessened with a shallower thermal gradient. It is most likely that the tetramolecular i-motif structure could not be formed completely in the given time because of the complexity of bringing together four strands and the number of nonproductive, out of register initiations that are possible [45]. There is sufficient time to form intermediates (predominantly dimers) or partially intercalated species, which are also associated with absorbance changes.…”

Ultrafast excited-state dynamics of RNA and DNA C tracts

“…More recently, structural NMR studies have shown that cytosine-rich DNAs form an unusual quadruplex structure ("i-motif DNA") consisting of two intercalated duplexes made up of hemiprotonated base pairs [27,28]. This structure, which may be biologically significant [29][30][31], is formed when two parallel-stranded duplexes associate in head-to-tail fashion, forming intercalated hemiprotonated base pairs.…”

A high-throughput fluorescent indicator displacement assay and principal component/cluster data analysis for determination of ligand-nucleic acid structural selectivity

“…In addition to the familiar duplex structure, nucleic acids can form a variety of non-canonical triplex (4,5), quadruplex (6) or i-motif (3,7,8) structures. Some of these structures have been detected in living cells (9)(10)(11) where they may play key roles in a variety of biological processes, including replication, transcription, oncogene expression, and telomere functions (11)(12)(13)(14)(15)(16)(17).…”