DNA fragment conformations IV - Helix-coil transition and conformation of d-CCATGG in aqueous solution by 1H-NMR spectroscopy

Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity

Because oligonucleotides are short sequences of nucleic acid bases, their association in solution with complementary strands (hybridization) is often seen to conform to a simple two-state model. However, experimental evidence suggests that, despite their short length, oligonucleotides may hybridize through multiple states involving intermediates. We investigate whether these apparently contradictory scenarios are possible by imposing different levels of sequence specificity on a lattice model of oligonucleotides in solution, which we introduced in Part I [J. C. Araque et al., J. Chem. Phys. 134, 165103 (2011)]. We find that both multiple-intermediate (weakly cooperative) and two-state (strongly cooperative) transitions are possible and that these are directly linked to the level of sequence specificity. Sequences with low specificity hybridize (base-by-base) by way of multiple stable intermediates with increasing number of paired bases. Such intermediate states are weakly cooperative because the energetic gain from adding an additional base pair is outweighed by the conformational entropy loss. Instead, sequences with high specificity hybridize through multiple metastable intermediates which easily bridge the configurational and energetic gaps between single- and double-stranded states. These metastable intermediates interconvert with minimal loss of conformational entropy leading to a strongly cooperative hybridization. The possibility of both scenarios, multiple- and two-states, is therefore encoded in the specificity of the sequence which in turn defines the level of cooperativity.

Structure and energy of a DNA dodecamer under tensile load

In the last decade, methods to study single DNA molecules under tensile load have been developed. These experiments measure the force required to stretch and melt the double helix and provide insights into the structural stability of DNA. However, it is not easy to directly relate the shape of the force curve to the structural changes that occur in the double helix under tensile load. Here, state-of-the-art computer simulations of short DNA sequences are preformed to provide an atomistic description of the stretching of the DNA double helix. These calculations show that for extensions larger that ∼25% the DNA undergoes a structural transformation and a few base pairs are lost from both the terminal and central part of the helix. This locally melted DNA duplex is stable and can be extended up to ∼50–60% of the equilibrium length at a constant force. It is concluded that melting under tension cannot be modeled as a simple two-state process. Finally, the important role of the cantilever stiffness in determining the shape of the force–extension curve and the most probable rupture force is discussed.

Study by (23)Na-NMR, (1)H-NMR, and ultraviolet spectroscopy of the thermal stability of an 11-basepair oligonucleotide

23Na-NMR, (1)H-NMR, and ultraviolet (UV) spectroscopy have been used to study the thermal stability of the double helix structure of an 11-basepair oligonucleotide. The denaturation curves obtained by (23)Na-NMR and UV are analyzed using a two-state model. The melting temperature and DeltaH(0) obtained are identical within experimental error, suggesting that modifications in the ionic atmosphere, probed by (23)Na-NMR, and the modifications in the basepair stacking, probed by UV, occur at the same temperature. Additional dynamical information on the denaturation process has been obtained by (1)H-NMR: slow exchange is observed between the thymine methyl resonances, and the disappearance of imino protons shows that a single basepair opening does not contribute significantly to proton exchange.

Tertiary base pair interactions in slipped loop-DNA: an NMR and model building study

Short direct repeat sequences are often found in regulatory regions of various genes; in some cases they display hypersensitivity to S1 nuclease cleavage in supercoiled plasmids. A non-standard DNA structure (Slipped Loop Structure, or SLS) has been proposed for these regions in order to explain the S1 cleavage data; the formation of this structure may be involved in the regulation of transcription. The structure can be generally classified as a particular type of pseudoknot. To date, no detailed stereochemical model has been developed. We have applied one-dimensional 1H NMR spectroscopy to study a synthetic DNA, 55 nucleotides in length, which cannot fold as a standard hairpin but which may favor the SLS formation. AT base pairs were identified, consistent only with the formation of an additional, tertiary miniduplex in the SLS. An all-atom stereochemically sound model has been developed for the SLS with the use of conformational calculations. The model building studies have demonstrated that the tertiary miniduplex can be formed for one of the plausible SLS isomers, but not for the other.

Resonance assignments of non-exchangeable protons in B type DNA oligomers, an overview

The chemical shifts of 1H resonances of non exchangeable protons (except H5', H5" and adenine H2) of over six hundred nucleotides have been collected. The influence which the base of the nucleotide itself as well as the bases on its 5' and 3' side exert on the chemical shifts of the various resonances has been investigated. Most of the resonances appear to be predominantly influenced by only one base. For H2', H2", H3', H4' and H6/H8 this is the base of the central nucleotide, for H5(C) and CH3(T) it is the one on the 5' side and for H1' it is the one on the 3' side. Chemical shift distribution profiles are presented which allow an estimation of the probability of finding a particular resonance at a particular position in the spectrum.

Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton

Using nuclear magnetic resonance line broadening, longitudinal relaxation and magnetization transfer from water, we have measured the imino proton exchange times in the duplex form of the 10-mer d-CGCGATCGCG and in seven other deoxy-duplexes, as a function of the concentration of exchange catalysts, principally ammonia. All exchange times are catalyst dependent. Base-pair lifetimes are obtained by extrapolation to infinite concentration of ammonia. Lifetimes of internal base-pairs are in the range of milliseconds at 35 degrees C and ten times more at 0 degrees C. Lifetimes of neighboring pairs are different, hence base-pairs open one at a time. Lifetimes of d(G.C) are about three times longer than those of d(A.T). The nature of neighbors usually has little effect, but lifetime anomalies that may be related to sequence and/or structure have been observed. In contrast, there is no anomaly in the A.T base-pair lifetimes of d-CGCGA[TA]5TCGCG, a model duplex of poly[d(A-T)].poly[d(A-T)]. The d(A.T) lifetimes are comparable to those of r(A.U) that we reported previously. End effects on base-pair lifetimes are limited to two base-pairs. The low efficiency of exchange catalysts is ascribed to the small dissociation constant of the deoxy base-pairs, and helps to explain why exchange catalysis had been overlooked in the past. This resulted in a hundredfold overestimation of base-pair lifetimes. Cytosine amino proteins have been studied in the duplex of d-CGm5CGCG. Exchange from the closed base-pair is indicated. Hence, the use of an amino exchange rate to evaluate the base-pair dissociation constant would result in erroneous, overestimated values. Catalyzed imino proton exchange is at this time the safest and most powerful, if not the only probe of base-pair kinetics. We propose that the single base-pair opening event characterized here may be the only mode of base-pair disruption, at temperatures well below the melting transition.

Z helix-coil transition of d(C-Br8G-C-G-C-Br8G) studied by CD, 1H-NMR and IR spectroscopies

The conformation of d(C-Br8G-C-G-C-Br8G) in aqueous solution was studied by CD and 1H-NMR spectroscopy and in condensed phase by IR spectroscopy. Whether in 0.1 M or 3 M NaCl solution or in film the only double helical structure adopted by brominated d(C-G)3 oligomer is the Z form. The IR spectrum of the film presents all the characteristic absorptions of the Z conformation and in particular is indicative of a syn conformation for the central guanosine as well as for the brominated one. Imino proton resonances of d(C-Br8G-C-G-C-Br8G) demonstrating the duplex formation were observed up to 60 degrees C. It is interesting to note that the significant highfield shifts of the dC H5" exocyclic sugar protons characteristic of the non exchangeable proton spectra of d(C-G)3 containing 5-methyl dC residues in the Z form were also detected in the proton spectrum of brominated oligomer. Whereas formation of the Z helix of methylated d(C-G)3 oligomers dependent on the salt concentration was found to occur via the preliminary formation of a B helix even in 4 M NaCl solution, the Z helix of d(C-Br8G-C-G-C-Br8G) is obtained directly from the coil form. However, IR data suggest that in the Z form of d(C-Br8G-C-G-C-Br8G), the overlapping of the base planes should be slightly different in comparison with the stacking observed in d(C-G)3 crystals. The kinetic data (activation energy and lifetime) of the Z helix-coil transition of brominated d(C-G)3 are compared to those of the B helix-coil transition observed for methylated d(C-G)3 in 0.1 M NaCl solution while the thermodynamic data of these two reactions (enthalpy and midpoint temperature) are slightly different.

Influence of uracil defect on DNA structure: 1H NMR investigation at 500 MHz

The local structure of two self complementary oligonucleotides d(GTAC-GTAC) and d(GTACGUAC) which differ only by the presence of uracil, not a normal component of DNA, have been investigated by 1H NMR at 500 MHz. The two octamers exhibit the same thermodynamical constants (t 1/2, delta H), their exchangeable protons broaden and disappear at the same temperature. The T-U substitution did not induce any significant changes on non exchangeable protons resonances from 2-D COSY and 2-D NOESY experiments. So the two octamers exhibit the same global structure. The only variation was detected by 1D NOE measurements: the base orientations around the N glycosidic bonds (chi angles) are different.

1H-NMR study of the interaction of daunomycin with B-DNA helices of methylated oligodeoxynucleotides

The interaction of daunomycin with B-DNA double helices of several methylated deoxynucleotides, d(C-G-m5C-G), d(m5C-G-C-G), d(C-G-m5C-G-C-G) and d(m5C-G-C-G-m5C-G) in solution was investigated by 1H-NMR spectroscopy at 500 MHz. At low temperature (t less than 20 degrees C for the tetramer and t less than 40 degrees C for the hexamers), several daunomycin-DNA complexes were observed in slow exchange with the drug-free DNA duplexes. The presence of daunomycin in a self-complementary double helix cancels the conformational symmetry of the two strands; the proton signals can split into several others owing to the difference between free and intercalated duplexes and to the many possible intercalation sites in a duplex (three for a tetramer, five for an hexamer). A model relating the chemical shifts of splitted proton signals to the various intercalated duplex conformations was given. The results show that one daunomycin molecule is associated with one duplex and that it can enter any intercalation site with equal probability; no side-effects were observed even for very short helices (of a tetramer). In the case of d(C-G-m5C-G) the association constant and the dissociation and association rates of the intercalated complex were evaluated.

Nuclear magnetic resonance study of d-TGGCCA in solution

The 1H NMR spectrum of a self complementary deoxyhexanucleotide (d-TGGCCA) in water solution has been completely and unambiguously assigned by use of two-dimensional techniques and phosphorus off-resonance decoupling experiments. The helix-coil transition has been monitored by following most of the non-exchangeable protons against temperature and was shown to be a cooperative dissociation-association process. Sequential fraying is sizable even at low temperature. Considerations of coupling constants and of Nuclear Overhauser effects show the helix to be of the B-DNA type.

DNA fragment conformations. A 1H-NMR conformational analysis of the d(G-G)-chelated platinum-oligonucleotide d(A-T-G-G)cisPt

The conformation of d(A-T-G-G) and d(A-T-G-G)cisPt has been investigated by 1H-NMR at 500 MHz and 90 MHz under various experimental conditions of temperature and concentration. Analysis of the coupling constants between the deoxyribose protons shows that all the sugar rings of d(A-T-G-G) adopt the S(C2'-endo) conformation most of the time. By contrast, in the platinated tetramer, d(A-T-G-G)cisPt, the N(C3'-endo) conformation is highly predominant for the internal dG residue while the S(C2'-endo) conformation is largely favoured for the other residues as in the case of the unplatinated compound. The relaxation time and nuclear Overhauser effect measurements indicate that the orientation of the two guanines of d(A-T-G-G)cisPt is anti in agreement with the previous results obtained for the dimers: r(G-G)cisPt, d(G-G)cisPt. On lowering the temperature from 80 degrees C to 20 degrees C, several proton resonances of d(A-T-G-G)cisPt exhibit large chemical shift and linewidth variations. The most spectacular temperature effect was observed for the internal dG(H1') and dT(H4') protons. All the delta = f(t) curves display a sigmoid form with the same mid-point temperature of 44 +/- 2 degrees C. This mid-point temperature together with the observed chemical shift and linewidth variations were found to be independent of the d(A-T-G-G)cisPt concentration. These results suggest that d(A-T-G-G)cisPt can adopt two different conformations depending on the temperature. The enthalpy for the transition between the high and low temperature conformations is about 84 kJ/mol.

B,Z conformations and mechanism of the Z-B-coil transitions of the self-complementary deoxy-hexanucleotide d(C-G-m5C-G-C-G) by 1H-NMR and CD spectroscopy

The helical structures of d(C-G-m5C-G-C-G) were studied in aqueous solution at various salt concentrations and temperatures by CD and 1H-NMR spectroscopy. At room temperature only the B form is observed in 0.1 M NaCl whereas the B and Z forms are simultaneously present in 1.8 M NaCl. At high salt concentration (4 M NaCl) the Z form is largely predominant (greater than 95%). The Z form proton resonances were assigned by using the polarisation transfer method (between B and Z at 1.8 M NaCl) and by proton-proton decoupling (at high salt concentration). The Z-B-Coil transitions were studied as a function of temperature with the 1.8 M NaCl solution. At high temperature (95 degrees C) only the coil form (S) is present. Below 55 degrees C the coil proportion is negligible, and the B-Z exchange is slow. The disappearance of the coil gives rise at first to the B form and on lowering the temperature the Z proportion increases to the detriment of the B form. Proton linewidth, relaxation and polarisation transfer studies confirm the conclusion in the previous report on d(m5C-G-C-G-m5C-G) (Tran-Dinh et al Biochemistry 1984 in the press) that Z exchanges only with B whereas the latter also exchanges with S,Z in equilibrium B in equilibrium S. The present data show that even at high salt concentration where only the Z form of d(C-G-m5C-G-C-G) is observed the Z-S transition also passes through the B form as an intermediate stage. The B-Z transition takes place when the Watson-Crick hydrogen bonds are firmly maintained and is greatly favoured when there are three hydrogen bonds between the base-pairs.

1H NMR and circular dichroism studies of the B and Z conformations of the self-complementary deoxyhexanucleotide d(m5C-G-C-G-m5-C-G): mechanism of the Z-B-coil transitions

The double-helical conformations of d(m5-C-G-C-G-m5-C-G) in aqueous solution were studied by circular dichroism and 1H NMR spectroscopy. In 0.1 M NaCl, only the B form is detected whereas the Z form is strongly predominant in 3 M NaCl. In the presence of 2 M NaCl, two resonance signals corresponding to the B and Z duplexes were observed for each proton below 50 degrees C, indicating a slow exchange between B and Z. However, the B-Z exchange becomes intermediate or fast in the 55-80 degrees C temperature interval. By contrast the exchange between B helix and single-stranded (or coil) forms is much faster for the same temperature conditions. The Z form is only detectable when the coil form is practically absent. With decreasing temperature the B form decreases in favor of the Z form. From proton line-width measurements under various experimental conditions, it was also shown that Z exchanges only with B, while the latter also exchanges with the single-stranded form (S): Z in equilibrium B in equilibrium S. The enthalpy value is about 8 +/- 1 kcal/mol for the B-Z transition and about 40 +/- 2 kcal/mol for the B-S dissociation (2 M NaCl solution). The activation energy is about 47 +/- 2 kcal/mol for the Z----B and 39 +/- 2 kcal/mol for the B----Z reaction. Very good agreement between the experimental results and computed data (based on the above kinetic reaction model) was found for the B, Z, and coil proportions. The B-Z transition of methylated d(C-G)n oligomers is only possible when the Watson-Crick hydrogen bonds between the CG base pairs are firmly maintained; otherwise, the transformation from B to Z would not occur, and B-S dissociation would take place instead.

Theoretical study of the geometrical arrangement of GT and GA wobble pairs in two short duplexes, Proton NMR chemical shifts and interaction energy calculations

NMR shielding constants are calculated for the base protons of duplexes formed by the dodecamer d(CGTGAATTCGCG) and the decamer d(CCAAGATTGG). A good agreement with experimental data is obtained for B-DNA helices in which the wobble GT and GA pairs are in the plane of the corresponding GC pairs of the parent duplexes formed by d(CGCGAATTCGCG) and d(CCAAGCTTGG), if the glycosyl bonds of T and G or A and G are symmetrical with respect to the dyad axis of the Watson-Crick GC pair. Interaction energy calculations show that this type of geometrical arrangement, which implies a distortion of the ribonphosphate backbone of both strands of the duplexes are more stable than those in which only one strand has its conformation modified by the presence of the wobble pair. For the duplex containing the GA pair, NMR chemical shifts as well as interaction energy computations favour the Watson-Crick hydrogen bonding scheme. The variation of the different contributions (intrastrand, interstrand, pair-pair) to the interaction energy between the bases of the duplexes, with the geometrical arrangement of the wobble pairs, is reported.

Assignment of non-exchangeable base proton and H1' resonances of a deoxyoctanucleoside heptaphosphate d(G-G-C*-C*-G-G-C-C) by using the nuclear Overhauser effect

The resonances of the non-exchangeable base protons and 1' protons of the octamer d(G-G-C*-C*-G-G-C-C), C* = m5dC, have been assigned by means of NOE difference NMR spectroscopy at 500 MHz. From the measured J1'2' and J1'2" it follows that the octamer at low temperature prefers to adopt a B-DNA double-helical conformation in solution, however, some residual conformational freedom is detected at the 3' terminus. From the chemical shift versus temperature profiles it is concluded that no major conformational change occurs below 60-65 degrees C where the duplex formation for residues (2) to (6) is essentially completed under the conditions used.