Stabilities of double- and triple-strand helical nucleic acids

Abstract

In this selected literature survey, we have seen that the stabilities of duplexes and triplexes are governed by the vertical base stacking, the horizontal specific base-paired H-bonding and the environmental parameters. The entropic contribution in the solvation/desolvation process is important in driving the aggregation of NA strands and duplex formation, but base stacking and specific H-bonding maintain the helical order. Triplex formation shares most of the physical environmental prerequisites with those of duplex NAs. However, some additional environmental conditions are often needed. Only in low pH solution is the polycytidylic strand protonated and, thus, it is possible for the strand to bind to a G.C duplex sequence to give the C+(G.C) triplex. High ionic strength is often necessary for the screening of inter-phosphate repulsion due to the high linear charge density in triplexes. The presence of specific counterions is important for complexation. In the absence of negative supercoiling, existence of an intramolecular triplex is rare except under very acidic conditions for the formation of C+(G.C)-type intramolecular triplex. As expected, the stabilities of both inter- and intramolecular triplexes increase with sequence length. The thermodynamic principles of helix-coil transition of oligo-duplex may be described by the van't Hoff relationship, which assumes a two-state cooperative melting profile. Thus, the enthalpy, entropy and free energy of transition can be evaluated from the experimental melting curves (e.g. OD, DSC). For polynucleotides, because of the non-two-state nature of transition, the simple van't Hoff relationship is no longer valid, and direct calorimetry is needed to obtain reliable thermodynamic parameters. The pH and salt concentration dependence of duplex stability can be formulated and derived from a van't Hoff equation. Base-stacking patterns are simple in duplexes but not so in triplexes due to the diversity in triplet schemes. The sequence dependence of base stacking for duplexes has been characterized and employed to predict the stability of an arbitrary sequence. In conclusion, the stability of duplex is relatively well-characterized by thermodynamic data in terms of both base stacking and specific H-bonding. Thermodynamic studies of triplexes have been far fewer in number. Oligonucleotides have found application in the detection and localization of a mRNA or its gene, the detection of bacterial or viral sequences, and the inhibition of the translation of mRNA and the transcription and replication of DNA (Englisch and Gauss, 1991). In a different approach, oligonucleotides have been targeted directly to a DNA duplex motif of a gene in order to inhibit the expression at the beginning of the transcriptional process.(ABSTRACT TRUNCATED AT 400 WORDS)

DNA triple helices: Biological consequences and therapeutic potential

“…Antiparallel GA and GT TFOs form stable triplexes at neutral pH, while parallel CT TFOs bind well only at acidic pH so that N3 on cytosine in the TFO is protonated [12], substitution of C with 5-methyl-C permits binding of CT TFOs at physiological pH [13,14] as 5-methyl-C has a higher pK than does cytosine. For both motifs, contiguous homopurine-homopyrimidine runs of at least 10 base pairs are required for TFO binding, since shorter triplexes are not substantially stable under physiological conditions, and interruptions in optimum sequence can greatly destabilize the triplex structure [15][16][17][18][19][20]. If purine bases are randomly distributed between two duplex strands, the consecutive third-strand bases should switch from one strand of the duplex to the other, resulting in a structural distortion of the sugar-phosphate backbone and lack of stacking interactions.…”

Prediction of the stability of DNA triplexes.

“…3 imply. This crossover in stability, combined with the repulsion from adjacent cytosines, produces the result that a CT repeat will be the most stable triplex below pH 7 stable. AG°for nucleation of the triplex (6.0 kcal) is about the same as that found for duplex DNA (2) and almost twice as large as that of duplex RNA (1).…”

“…Triple-helix formation can be used to recognize DNA duplexes highly specifically (for reviews, see refs. [7][8][9][10] and has potential for antisense and therapeutic applications. In this paper, we present a model for predicting DNA triplex stability using only the sequence.…”

Chemical Modification of Oligonucleotides: A Novel Approach Towards Gene Targeting

“…The magnitudes of the negative ∆H and ∆S for the 2',4'-BNA NCmodified TFOs at pH 6.8 were smaller than those observed for Pyr15TM at pH 6.1 ( Table 4). The observed negative ∆H upon the triplex formation reflects major contributions from the hydrogen bonding and the base stacking involved in the triplex formation, the protonation of the cytosine bases upon the hydrogen bonding, and the accompanying deprotonation of the cacodylate buffer releasing the protons to bind with the cytosine bases [33][34][35]. The immobilization of electrostricted water molecules around polar atoms upon the triplex formation is also considered to be the major sources of the observed negative ∆H upon the triplex formation [33][34][35].…”

“…The observed negative ∆H upon the triplex formation reflects major contributions from the hydrogen bonding and the base stacking involved in the triplex formation, the protonation of the cytosine bases upon the hydrogen bonding, and the accompanying deprotonation of the cacodylate buffer releasing the protons to bind with the cytosine bases [33][34][35]. The immobilization of electrostricted water molecules around polar atoms upon the triplex formation is also considered to be the major sources of the observed negative ∆H upon the triplex formation [33][34][35]. Because the degree of the protonation may be similar between the 2',4'-BNA NC -modified TFOs at pH 6.8 and Pyr15TM at pH 6.1 due to the similar stoichiometry discussed above and the protons to bind with the cytosine bases are released from the same cacodylate buffer in both cases, the ∆H derived from the protonation of the cytosine bases and the accompanying deprotonation of the cacodylate buffer should be similar between the two cases.…”