Comparison of the B- and Z-form hairpin loop structures formed by d(CG)5T4(CG)5

Single C8-Arylguanine modifications render oligonucleotides in the Z-DNA conformation under physiological conditions

Z-DNA is the only DNA conformation that has a left-handed helical twist. Although Z-DNA has been implicated in both carcinogenesis and mutagenesis, its specific biological role remains uncertain. We have demonstrated that the formation of C8-arylguanine DNA adducts, derived from arylhydrazines, shifts the B/Z-DNA equilibrium toward the Z-DNA conformation in d(CG)5 sequences. However, our previous work examined the effect of two adducts in the duplex, and it was unclear whether the two base modifications were working together to cause the equilibrium shift toward the Z-DNA conformation. Here we report the synthesis and characterization of a hairpin oligonucleotide sequence (d(CG)5T4(CG)5) containing only one C8-arylguanine modified base. The unmodified hairpin and the previously studied unmodified double-stranded oligonucleotide were conformationally similar, and each required ∼3 M NaCl to yield a B-/Z-DNA ratio of 1:1. The introduction of a single C8-arylguanine modification significantly reduced the NaCl concentration needed to produce a 1:1 B-/Z-DNA ratio in the hairpin. Further, the addition of MgCl2 and spermine to the C8-arylguanine-modified hairpin shifts the B/Z-DNA equilibrium such that the Z form predominated under physiological conditions. NMR and molecular modeling indicated the conformational effects produced by the C8-arylguanine modification occurred locally at the site of modification while CD data demonstrated that the C8-arylguanine-modified base destabilized the B form. Additionally, our data show that adopting the Z-DNA conformation is preferred over denaturation to the single-stranded form. Finally, the conformational effects of the C8-arylguanine modifications were not additive and the introduction of any such modifications drive Z-DNA formation under physiological conditions, which may provide a novel carcinogenesis mechanism where DNA adducts confer their carcinogenicity through a Z-DNA-mediated mechanism.

Activity, folding and Z-DNA formation of the 8-17 DNAzyme in the presence of monovalent ions

The effect of monovalent ions on both the reactivity and global folding of the 8-17 DNAzyme is investigated, and the results are compared with those of the hammerhead ribozyme, which has similar size and secondary structure. In contrast to the hammerhead ribozyme, the 8-17 DNAzyme activity is not detectable in the presence of 4 M K(+), Rb(+), or Cs(+) or in the presence of 80 mM, [Co(NH(3))(6)](3+). Only 4 M Li(+), NH(4)(+) and, to a lesser extent, Na(+) conferred detectable activity. The observed rate constants (k(obs) approximately 10(-3) min(-1) for Li(+) and NH(4)(+)) are approximately 1000-fold lower than that in the presence of 10 mM Mg(2+), and approximately 200,000-fold slower than that in the presence of 100 microM Pb(2+). Since the hammerhead ribozyme displays monovalent ion-dependent activity that is often within approximately 10-fold of divalent metal ion-dependent activity, these results suggest that the 8-17 DNAzyme, obtained by in vitro selections, has evolved to have a more stringent divalent metal ion requirement for high activity as compared to the naturally occurring ribozymes, making the 8-17 DNAzyme an excellent choice as a Pb(2+) sensor with high selectivity. In contrast to the activity data, folding was observed in the presence of all the monovalent ions investigated, although those monovalent ions that do not support DNAzyme activity have weaker binding affinity (K(d) approximately 0.35 M for Rb(+) and Cs(+)), while those that confer DNAzyme activity possess stronger affinity (K(d) approximately 0.22 M for Li(+), Na(+) and NH(4)(+)). In addition, a correlation between metal ion charge density, binding affinity and enzyme activity was found among mono- and divalent metal ions except Pb(2+); higher charge density resulted in stronger affinity and higher activity, suggesting that the observed folding and activity is at least partially due to electrostatic interactions between ions and the DNAzyme. Finally, circular dichroism (CD) study has revealed Z-DNA formation with the monovalent metal ions, Zn(2+) and Mg(2+); the K(d) values obtained using CD were in the same range as those obtained from folding studies using FRET. However, Z-DNA formation was not observed with Pb(2+). These results indicate that Pb(2+)-dependent function follows a different mechanism from the monovalent metal ions and other divalent metal ions; in the presence of latter metal ions, metal-ion dependent folding and structural changes, including formation of Z-DNA, play an important role in the catalytic function of the 8-17 DNAzyme.

Thermodynamic characterization of binding Oxytricha nova single strand telomere DNA with the alpha protein N-terminal domain

The Oxytricha nova telemere binding protein alpha subunit binds single strand DNA and participates in a nucleoprotein complex that protects the very ends of chromosomes. To understand how the N-terminal, DNA binding domain of alpha interacts with DNA we measured the stoichiometry, enthalpy (DeltaH), entropy (DeltaS), and dissociation constant (K(D-DNA)) for binding telomere DNA fragments at different temperatures and salt concentrations using native gel electrophoresis and isothermal titration calorimetry (ITC). About 85% of the total free energy of binding corresponded with non-electrostatic interactions for all DNAs. Telomere DNA fragments d(T(2)G(4)), d(T(4)G(4)), d(G(3)T(4)G(4)), and d(G(4)T(4)G(4)) each formed monovalent protein complexes. In the case of d(T(4)G(4)T(4)G(4)), which has two tandemly repeated d(TTTTTGGGG) telomere motifs, two binding sites were observed. The high-affinity "A site" has a dissociation constant, K(D-DNA(A)) = 13(+/-4) nM, while the low-affinity "B site" is characterized by K(D-DNA(B)) = 5600(+/-600) nM at 25 degrees C. Nucleotide substitution variants verified that the A site corresponds principally with the 3'-terminal portion of d(T(4)G(4)T(4)G(4)). The relative contributions of entropy (DeltaS) and enthalpy (DeltaH) for binding reactions were DNA length-dependent as was heat capacity (DeltaCp). These trends with respect to DNA length likely reflect structural transitions in the DNA molecule that are coupled with DNA-protein association. Results presented here are important for understanding early intermediates and subsequent stages in the assembly of the full telomere nucleoprotein complex and how binding events can prepare the telomere DNA for extension by telomerase, a critical event in telomere biology.

Probing the B-to-Z-DNA duplex transition using terminally stacking ethynyl pyrene-modified adenosine and uridine bases

Pyrene-modified adenosine and uridine bases located in the dangling positions of G,C-alternating oligodeoxynucleotides undergo pi-stacking in their B-DNA duplexes, but not in their Z-DNA duplexes; fluorescence quenching in the former, through photoinduced electron transfer, but not in the latter, allows the state of the B-to-Z-DNA transition to be characterized visually.

Thermal stability, structural features, and B-to-Z transition in DNA tetraloop hairpins as determined by optical spectroscopy in d(CG)(3)T(4)(CG)(3) and d(CG)(3)A(4)(CG)(3) oligodeoxynucleotides

NMR and CD data have previously shown the formation of the T(4) tetraloop hairpin in aqueous solutions, as well as the possibility of the B-to-Z transition in its stem in high salt concentration conditions. It has been shown that the stem B-to-Z transition in T(4) hairpins leads to S (south)- to N (north)-type conformational changes in the loop sugars, as well as anti to syn orientations in the loop bases. In this article, we have compared by means of UV absorption, CD, Raman, and Fourier transform infrared (FTIR), the thermodynamic and structural properties of the T(4) and A(4) tetraloop hairpins formed in 5'-d(CGCGCG-TTTT-CGCGCG)-3' and 5'-d(CGCGCG-AAAA-CGCGCG)-3', respectively. In presence of 5M NaClO(4), a complete B-to-Z transition of the stems is first proved by CD spectra. UV melting profiles are consistent with a higher thermal stability of the T(4) hairpin compared to the A(4) hairpin. Order-to-disorder transition of both hairpins has also been analyzed by means of Raman spectra recorded as a function of temperature. A clear Z-to-B transition of the stem has been confirmed in the T(4) hairpin, and not in the A(4) hairpin. With a right-handed stem, Raman and FTIR spectra have confirmed the C2'-endo/anti conformation for all the T(4) loop nucleosides. With a left-handed stem, a part of the T(4) loop sugars adopt a N-type (C3'-endo) conformation, and the C3'-endo/syn conformation seems to be the preferred one for the dA residues involved in the A(4) tetraloop.

Fluorometric sensing of the salt-induced B–Z DNA transition by combination of two pyrene-labeled nucleobases

We have developed a new fluorescent DNA sensor containing two pyrene-labeled nucleobases, (Pet)G and (Py)C, and the fluorescence color was altered by the salt-induced B-Z DNA transition.

Circular Dichroism and NMR Studies of Metabolically Stableα-Methylpolyamines: Spectral Comparison with Naturally Occurring Polyamines

Three synthetic polyamine analogs, alpha-methylspermine, and alpha,alpha'-dimethylspermine, were compared with their naturally occurring counterparts, spermidine and spermine, by two different spectral techniques. The interaction of polyamines with oligodeoxynucleotides was measured by circular dichroism in order to monitor the polyamine-induced conversion of right-handed B-DNA to the left-handed Z-form. The methylated analogs were shown to be equally effective as the natural polyamines in inducing the B --> Z transition. The pH dependence of the chemical shift of all carbon atoms in each of the five polyamines was measured by (13)C-NMR spectroscopy. With the exception of expected changes in chemical shift due to the presence of the alpha-methyl substituents, the chemical shifts and pH dependence of all carbon atoms in the three alpha-methyl polyamines were similar to the corresponding naturally occurring polyamines. The combined data indicate that alpha-methyl polyamines have physical properties that are very similar to their natural counterparts. The two metabolically stable polyamine analogs, alpha-methylspermidine and alpha,alpha'-dimethylspermine, are therefore useful surrogates for spermidine and spermine in the study of numerous polyamine-mediated effects in mammalian cell cultures and can be used in such studies without the requirement for coadministration of amine oxidase inhibitors.

Similar conformations of hairpins with TTT and TTTT sequences: NMR and molecular modeling evidence for T.T base pairs in the TTTT hairpin

The conformations of the d[G(1)C(2)G(3)C(4)-T(a)T(b)T(c)T(d)-G(5)C(6)G(7)C(8)] (T4) and d[G(1)C(2)G(3)C(4)-T(a)T(b)T(c)-G(5)C(6)G(7)C(8)] (T3) DNA hairpins have been studied. The 1H and 31P signals of the two hairpins have been nearly completely assigned by means of two-dimensional NMR spectroscopy in D2O (NOESY (two-dimensional nuclear Overhauser effect and exchange spectroscopy) at mixing times of 5, 50, 100, 300 and 500 ms, double-quantum-filtered correlation spectroscopy (DQF-COSY) and 1H-31P reverse chemical shift correlation (RCSC), and one-dimensional NOE spectra in 90% H2O. Conformational analysis using distance geometry (DG), molecular mechanics (MM) and molecular dynamics (MD) gave model conformations, which were evaluated by comparison of experimental and simulated 2D NOESY spectra. For the T4 sequence in T4, both NMR data and modeling indicated a T(a).T(d) wobble base pair. Although two types of T(a).T(d) base pairs are possible, the one with T(a)NH-T(d)O4 and T(a)O2-T(d)NH H-bonds was calculated to be more stable. Because the T(a).T(d) base pair of T4 extends the stem, there are only two residues (T(b) and T(c) in the loop. Although there are three residues in the T3 loop, the T(c) base projects into the solvent. The resulting conformational models have very similar loop folding patterns (FP): the bases of the two adjacent residues that begin the loop [T(b)T(c) of T4 and T(a)T(b) or T3] have a minor groove/major groove orientation with the first residue each having a trans alpha torsion angle; and the phosphodiester group that links the residues at the 3' end of the loop and the 5' top of the stem [T(c)pT(d) of T4 and T(c)pG(5) of T3] has a gauche+, gauche+ zeta,alpha conformation with a trans gamma angle for the second residue in both. These or similar features appear to be present in most of the few other hairpins studied previously by conformational methods. Thus, we believe that the conformations of the loops in T3 and T4 hairpins have greater similarities than previously recognized.

Use of aminopropyltransferase inhibitors and of non-metabolizable analogs to study polyamine regulation and function

The polyamines spermidine and spermine are essential for the growth of mammalian cells. This review describes the properties of the two aminopropyltransferases that are responsible for their biosynthesis, the synthesis and use of specific aminopropyltransferase inhibitors, and the use of analogs of the polyamines to investigate polyamine transport and function. Highly specific and potent multisubstrate adduct inhibitors of these enzymes have been synthesized while less potent inhibitors have been obtained by the synthesis of amines that bind at the active site. Studies with these inhibitors indicate that polyamines are needed for a normal rate of growth and that, although some of the functions of polyamines may be interchangeable, other functions may have a specific requirement for spermidine or spermine. Two groups of growth-promoting polyamine analogs can be distinguished: the many that are effective in short-term experiments compared to the few that can act over a prolonged period. The more stringent structural requirements for long-term growth are probably due to a need for spermidine, or a closely related analog, as a precursor of hypusine in the protein eIF-5A. Metabolically resistant polyamine analogs can be used as model substrates for studies of the polyamine transport system, which plays a critical role in maintaining normal cellular polyamine levels. The feedback regulation by high levels of polyamines that downregulates transport is essential to prevent the accumulation of polyamines at toxic levels. Such accumulation may be associated with apoptosis and, therefore, polyamine analogs are useful tools for investigating the mechanism(s) of polyamine-mediated toxicity.

Thermodynamics of DNA hairpins: contribution of loop size to hairpin stability and ethidium binding

A combination of calorimetric and spectroscopic techniques was used to evaluate the thermodynamic behavior of a set of DNA hairpins with the sequence d(GCGCTnGCGC), where n = 3, 5 and 7, and the interaction of each hairpin with ethidium. All three hairpins melt in two-state monomolecular transitions, with tm's ranging from 79.1 degrees C (T3) to 57.5 degrees C (T7), and transition enthalpies of approximately 38.5 kcal mol-1. Standard thermodynamic profiles at 20 degrees C reveal that the lower stability of the T5 and T7 hairpins corresponds to a delta G degree term of +0.5 kcal mol-1 per thymine residue, due to the entropic ordering of the thymine loops and uptake of counterions. Deconvolution of the ethidium-hairpin calorimetric titration curves indicate two sets of binding sites that correspond to one ligand in the stem with binding affinity, Kb, of approximately 1.8 x 10(6) M-1, and two ligands in the loops with Kb of approximately 4.3 x 10(4) M-1. However, the binding enthalpy, delta Hb, ranges from -8.6 (T3) to -11.6 kcal mol-1 (T7) for the stem site, and -6.6 (T3) to -12.7 kcal mol-1 (T7) for the loop site. Relative to the T3 hairpin, we obtained an overall thermodynamic contribution (per dT residue) of delta delta Hb = delta(T delta Sb) = -0.7(5) kcal mol-1 for the stem sites and delta delta Hb = delta(T delta Sb) = -1.5 kcal mol-1 for the loop sites. Therefore, the induced structural perturbations of ethidium binding results in a differential compensation of favorable stacking interactions with the unfavorable ordering of the ligands.

Theoretical predictions of DNA hairpin loop conformations: correlations with thermodynamic and spectroscopic data

A computational procedure for generating conformations of DNA hairpin loop structures from a broad range of low-energy starting states is described. The starting point of the modeling is the distribution of oligonucleotide chain conformations obtained from Monte Carlo simulations of feasible dinucleotide steps. Structures which meet the spatial criteria for hairpin loop formation are selected from the distributions and subsequently minimized using all-atom molecular mechanics. Both d(CTnG) and d(CAnG) oligomers, where n = 3, 4, or 5, are modeled. These sequences are chosen because of the large number of published NMR and thermodynamic studies on DNA hairpins containing thymine or adenine residues. The minimized three-dimensional hairpin loop structures are compared with one another as well as analyzed in terms of available experimental data. The computational approach provides the first detailed analysis of DNA hairpin loop structure in terms of a multistate conformational model. Investigation of the minimized conformations reveals several interesting structural features. First, hairpin loops of the same sequence adopt several distinctly different conformations, as opposed to minor variants of the same equilibrium structure, that could potentially interconvert in solution. Second, in contrast to double-helical nucleic acids, the hairpin loop models exhibit hydrophobic and hydrophilic surfaces. The different disposition of hydrophobic groups in loops versus duplexes could modulate both protein-nucleic acid interactions and nucleic acid self-associations. Third, perpendicular aromatic interactions of loop residues are observed in many of the computed hairpins. This sort of interaction might be important in the stabilization of non-hydrogen-bonded nucleic acid secondary and tertiary structures. The predicted structural features in the models help, in addition, to account for the unusual thermodynamic properties of DNA hairpin loops. Comparison of the theoretically-generated NOEs in different structures further reveals that very different molecular structures and interactions can, in principle, produce the same NOEs. The multistate description suggested by this observation differs from the conventional interpretation of DNA solution structure in terms of the fluctuations about a single preferred chain conformation. There is not necessarily only one set of closely related structures consistent with the observed data.

Two-dimensional NMR and restrained molecular dynamics studies of the hairpin d(T8C4A8): detection of an extraloop cytosine

The 1H and 31P NMR resonances of the partly self-complementary 20-mer DNA d(T8C4A8) were assigned by two-dimensional HOHAHA, NOESY, and heteronuclear COSY NMR spectroscopy. The chemical shifts, NOEs, and H-H coupling patterns are indicative of the formation of a hairpin structure with the four C residues forming a loop and the T8.A8 portion of a double-stranded stem. The observation of unusual across-strand NOEs between the A H2 and the T H1' of the corresponding 3'-end neighboring base pairs of the stem residues suggests that the structure of the hairpin stem deviates from regular B-DNA. A total number of 296 interproton NOEs were used as approximate proton-proton distance constraints in restrained molecular dynamics calculations. Several different starting models, all generated manually from standard B-DNA coordinates, gave rise to virtually the same refined hairpin structure. In the final structure, the interior A-T base pairs of the hairpin stem show a high degree of propeller twist as well as base pair buckle, while the minor groove is slightly narrower compared with a normal B-DNA structure; these features are all common to bent DNA. The first three A-T pairs from the end of the hairpin have a propeller twist and base pair buckle which more closely resemble those of regular B-DNA. The four-residue loop was formed mainly by variations in the phosphate backbone torsion angle epsilon at the loop-stem junctions (residues 8 and 13) and at the first C residue (C 9). The base of the first C residue is positioned outside of the loop.(ABSTRACT TRUNCATED AT 250 WORDS)

A Monte Carlo method for generating structures of short single-stranded DNA sequences

A Monte Carlo method has been developed for generating the conformations of short single-stranded DNAs from arbitrary starting states. The chain conformers are constructed from energetically favorable arrangements of the constituent mononucleotides. Minimum energy states of individual dinucleotide monophosphate molecules are identified using a torsion angle minimizer. The glycosyl and acyclic backbone torsions of the dimers are allowed to vary, while the sugar rings are held fixed in one of the two preferred puckered forms. A total of 108 conformationally distinct states per dimer are considered in this first stage of minimization. The torsion angles within 5 kcal/mole of the global minimum in the resulting optimized states are then allowed to vary by +/- 10 degrees in an effort to estimate the breadth of the different local minima. The energies of a total of 2187 (3(7)) angle combinations are examined per local conformational minimum. Finally, the energies of all dinucleotide conformers are scaled so that the populations of differently puckered sugar rings in the theoretical sample match those found in nmr solution studies. This last step is necessitated by limitations in the theoretical methods to predict DNA sugar puckering accurately. The conformer populations of the individual acyclic torsion angles in the composite dimer ensembles are found to be in good agreement with the distributions of backbone conformations deduced from nmr coupling constants and the frequencies of glycosyl conformations in x-ray crystal structures, suggesting that the low energy states are reasonable. The low energy dimer forms (consisting of 150-325 conformational states per dimer step) are next used as variables in a Monte Carlo algorithm, which generates the conformations of single-stranded d(CXnG) chains, where X = A, T and n = 3, 4, 5. The oligonucleotides are built sequentially from the 5' end of the chain using random numbers to select the conformations of overlapping dimer units. The simulations are very fast, involving a total of 10(6) conformations per chain sequence. The potential errors in the buildup procedure are minimized by taking advantage of known rotational interdependences in the sugar-phosphate backbone. The distributions of oligonucleotide conformations are examined in terms of the magnitudes, positions, and orientations of the end-to-end vectors of the chains. The differences in overall flexibility and extension of the oligomers are discussed in terms of the conformations of the constituent dinucleotide steps, while the general methodology is discussed and compared with other nucleic acid model building techniques.

The lac repressor and its N-terminal headpiece can bind a mini-operator containing a hairpin loop made of a hexaethylene glycol chain

The binding of the lac repressor and the lac repressor N-terminal headpiece to a mini-operator with a hairpin loop made of a hexaethylene glycol chain was investigated using circular dichroism spectroscopy. The lac repressor's headpiece binds to the modified mini-operator with the same affinity as to a mini-operator of the same sequence without the hexaethylene glycol loop. The conformational effect due to the binding is not affected by the presence of the hexaethylene loop. It is also shown that the entire lac repressor binds to this modified mini-operator inducing a conformational change.

Coupling of sequential transitions in a DNA double hairpin: energetics, ion binding, and hydration

In an effort to evaluate the relative contributions of sequence, ion binding, and hydration to the thermodynamic stability of nucleic acids, we have investigated the melting behavior of a double hairpin and that of its component single hairpins. Temperature-dependent UV absorption and differential scanning calorimetry techniques have been used to characterize the helix-coil transitions of three deoxyoligonucleotides: d(GTACT5GTAC), d(GCGCT5GCGC), and d(GCGCT5GCGCGTACT5GTAC). The first two oligomers melt with transition temperatures equal to 28 and 69 degrees C, respectively, in 10 mM dibasic sodium phosphate at pH 7.0. The Tm's are independent of strand concentration, strongly indicating the presence of single-stranded hairpin structures at low temperatures. The third oligomer, with a sequence corresponding to the joined sequences of the first two oligomers, melts with two apparently independent monomolecular transitions with Tm's of 41 and 69 degrees C. These transitions correspond to the melting of a double hairpin. In the salt range of 10-100 mM in NaCl, we obtain average enthalpies of 24 and 38 kcal/mol for the transitions in the single-hairpin molecules. Each transition in the double hairpin has an enthalpy of 32 kcal/mol. In addition, dtm/d log [Na+] for the transitions are 4.1 and 4.7 degrees C for the single hairpins and 12.6 and 11.2 degrees C for each transition in the double hairpin. The differential ion binding parameter between the double hairpin and that of the sum of single hairpins is roughly equal to 1.1 mol of Na+ ions/mol of double hairpin and is consistent with an increase in the electrostatic behavior of the stem phosphates of this molecule.

DNA hairpin loops in solution. Correlation between primary structure, thermostability and reactivity with single-strand-specific nuclease from mung bean

Hairpin structures formed by seven DNA inverted repeats have been studied by PAGE, UV(CD)-spectroscopy and nuclease cleavage. The hairpins consisted of (CG)3 stems and loops of 2, 3 and 4 residues. Thermal stabilities (Tm) have been determined in low and high ionic strength buffers, where the hairpins were structured in the B- and Z-DNA form respectively. The thermodynamic parameters of hairpin formation have been obtained by a two-state analysis of the hairpin-coil transitions. It is found that, on increasing the number of bases in the loop from 2 to 3 and 4, the Tms of the B-hairpins decrease, whereas the Tms of the same hairpins in the Z-form increase. This confirms previous evidence (1,2) that in a hairpin molecule the size and structure of the loop are modulated by the conformation of the helical stem. Moreover, B-hairpins with loops comprising 2, 3 and 4 bases have been digested with the single-strand-specific nuclease from mung bean. In our experimental conditions (0 degrees C) the nuclease preferentially cleaves the unbonded nucleotides of the loops. However, the rates of loop hydrolysis, which roughly follow a first-order kinetics, markedly depend on the size of the loop. At a ratio of 3 enzyme units/micrograms DNA, the half-lives of hairpins which are expected to form loops of 4, 3 and 2 residues are 90, 145 and 440 minutes respectively. Thermostability and enzymatic digestion data suggest that two-membered loops can be formed in B-hairpins but not in Z-hairpins.

Analysis of melting transitions of the DNA hairpins formed from the oligomer sequences d[GGATAC(X)4GTATCC] (X = A, T, G, C)

Optical melting transitions of the short DNA hairpins formed from the self-complementary DNA oligomers d[GGATACX4GTATCC] where X = A, T, G, or C measured in 100 mM NaCl are presented. A significant dependence of the melting transitions on loop sequence is observed and transition temperatures, tm, of the hairpins vary from 58.3 degrees C for the T4 loop hairpin to 55.3 degrees C for the A4 loop. A nearest-neighbor sequence-dependent theoretical algorithm for calculating melting curves of DNA hairpins is presented and employed to analyze the experimental melting transitions. Experimental melting curves were fit by adjustment of a single theoretical parameter, Fend(n), the weighting function for a hairpin loop comprised of n single-strand bases. Empirically determined values of Fend(n) provide an evaluation of the free-energy of hairpin loop formation and stability. Effects of heterogeneous nearest-neighbor sequence interactions in the duplex stem on hairpin loop formation were investigated by evaluating Fend(n) in individual fitting procedures using two of the published sets of nearest-neighbor stacking interactions in DNA evaluated in 100 mM NaCl and given by Wartell and Benight, 1985. In all cases, evaluated values of Fend(n) were obtained that provided exact theoretical predictions of the experimental transitions. Results of the evaluations indicate: (1) Evaluated free-energies of hairpin loop formation are only slightly dependent on loop sequences examined. At the transition temperature, Tm, the free-energy of forming a loop of four bases is approximately equal for T4, G4, or C4 loops and varies from 3.9 to 4.8 kcal/mole depending on the set of nearest-neighbor interactions employed in the evaluations. This result suggests, in light of the observed differences in stability between the T4, G4, and C4 loop hairpins, that sequence-dependent interactions between base residues of the loop are most likely not the source of the enhanced stability of a T4 loop.(ABSTRACT TRUNCATED AT 400 WORDS)

Circular dichroism studies of an oligodeoxyribonucleotide containing a hairpin loop made of a hexaethylene glycol chain: conformation and stability

An oligodeoxyribonucleotide, d(GCTCACAAT-X-ATTGTGAGC), where X represents a hexaethylene glycol chain, was studied using circular dichroism spectroscopy. Its conformation and conformational stability were compared to those of compounds where X was replaced by four thymines and to the duplex of same sequence without loop. The compound with the hexaethylene glycol chain can form a hairpin looped structure as well as a bulged duplex structure. In both cases the duplex region of the oligodeoxyribonucleotide exhibits the same conformation. In similar conditions the oligodeoxyribonucleotide with a four thymines loop forms exclusively a hairpin structure. Comparison between the thermodynamic parameters (delta H, delta S, delta G) associated with the formation of the structure of the three compounds are presented. In the case of the compound with the hexaethylene glycol chain it is shown that the large increase in its melting temperature (by about 35 degrees C in our experimental conditions) when compared to the non looped structure is mainly due to the fact that its melting process is intramolecular (monomolecular) whereas the other one is bimolecular.

Perturbation of DNA hairpins containing the EcoRI recognition site by hairpin loops of varying size and composition: physical (NMR and UV) and enzymatic (EcoRI) studies

We have investigated loop-induced structural perturbation of the stem structure in hairpins d(GAATTCXnGAATTC) (X = A, T and n = 3, 4, 5 and 6) that contain an EcoRI restriction site in close proximity to the hairpin loop. Oligonucleotides containing either a T3 or a A3 loop were not hydrolyzed by the restriction enzyme and also showed only weak binding to EcoRI in the absence of the cofactor Mg2+. In contrast, hairpins with larger loops are hydrolyzed by the enzyme at the scission site next to the loop although the substrate with a A4 loop is significantly more resistant than the oligonucleotide containing a T4 loop. The hairpin structures with 3 loop residues were found to be thermally most stable while larger hairpin loops resulted in structures with lower melting temperatures. The T-loop hairpins are thermally more stable than the hairpins containing the same number of A residues in the loop. As judged from proton NMR spectroscopy and the thermodynamic data, the base pair closest to the hairpin loop did form in all cases studied. The hairpin loops did, however, affect the conformation of the stem structure of the hairpins. From 31P and 1H NMR spectroscopy we conclude that the perturbation of the stem structure is stronger for smaller hairpin loops and that the extent of the perturbation is limited to 2-3 base pairs for hairpins with T3 or A4 loops. Our results demonstrate that hairpin loops modulate the conformation of the stem residues close to the loop and that this in turn reduces the substrate activity for DNA sequence specific proteins.

An electron paramagnetic resonance probe to detect local Z-DNA conformations

We present spectroscopic evidence for an electron paramagnetic resonance (EPR) probe to detect local Z-DNA conformations in synthetic DNA. A spin labeled deoxycytidine-5'-triphosphate (pppDCAT) was co-polymerized with Micrococcus luteus DNA polymerase to yield the spin active alternating co-polymer (dG-dC,DCAT)n. The EPR spectrum of (dG-dC,DCAT)n in the Z-DNA conformation indicates a decrease in the local base dynamics by about a factor of two as compared to that computed for B-DNA. A control experiment conducted with (dA-dT, DUAT)n under similar salt conditions rules out the possibility of observing salt induced artifacts.

B to Z transitions of the short DNA hairpins formed from the oligomer sequences: d[(CG)3X4(CG)3] (X = A, T, G, C)

Circular Dichroism (CD) spectra were collected as a function of sodium perchlorate concentration [NaClO4] for the set of DNA hairpins formed from the oligomer sequences d[(CG)3X4(CG)3] where X = A, T, G or C. Over the range in salt concentration from 0 to 4.0 M NaClO4, the CD spectra invert in a manner characteristic of the B to Z transition. A factor analysis routine is described and employed to determine the least number of basis spectra required to fit the measured spectra of each hairpin over the entire salt range examined. In every case, linear combinations of only two sub-spectra fit the experimental spectra of the hairpins with greater than 98% accuracy, indicating the spectrally monitored structural transitions are two-state. From the relative weights of the individual sub-spectra, B-Z transition curves are constructed. The transitions are analyzed in terms of a simple two-state equilibrium model which yields an evaluation of the transition free-energy, delta GB-Z, as a function of NaClO4 concentration. At 1.0 M NaClO4 and 21 degrees C, delta GB-Z = 5.4, 4.9, 3.6 and 2.3 kcal/mole for the G4, T4, A4 and C4 loop hairpins, respectively.

Structure of a T4 hairpin loop on a Z-DNA stem and comparison with A-RNA and B-DNA loops

The synthetic DNA oligomer C-G-C-G-C-G-T-T-T-T-C-G-C-G-C-G crystallizes as a Z-DNA hexamer, capped at one end by a T4 loop. The crystals are monoclinic, space group C2, with a = 57.18 A, b = 21.63 A, c = 36.40 A, beta = 95.22 degrees, and one hairpin molecule per asymmetric unit. The structure of the z-hexamer stem was determined by molecular replacement, and the T4 loop was positioned by difference map methods. The final R factor at 2.1 A resolution for hairpin plus 70 water molecules is 20% for 2 sigma data, with a root-mean-square error of 0.26 A. The (C-G)3 stem resembles the free Z-DNA hexamer with minor crystal packing effects. The T4 loop differs from that observed on a B-DNA stem in solution, or in longer loops in tRNA, in that it shows intraloop and intermolecular interactions rather than base stacking on the final base-pair of the stem. Bases T7, T8 and T9 stack with one another and with the sugar of T7. Two T10 bases from different molecules stack between the C1-G12 terminal base-pairs of a third and fourth molecule, to simulate a T.T "base-pair". Distances between thymine N and O atoms suggest that the two thymine bases are hydrogen bonded, and a keto-enol tautomer pair is favored over disordered keto-keto wobble pairs. The hairpin molecules pack in the crystal in herringbone columns in a manner that accounts well for the observed relative crystal growth rates in a, b and c directions. Hydration seems to be most extensive around the phosphate groups, with lesser hydration within the grooves.

Thermodynamic stability of the 5' dangling-ended DNA hairpins formed from sequences 5'-(XY)2GGATAC(T)4GTATCC-3', where X, Y = A, T, G, C

Expressions for the partition function Q (T) of DNA hairpins are presented. Calculations of Q (T), in conjunction with our previously reported numerically exact algorithm [T. M. Paner, M. Amaratunga, M. J. Doktycz, and A. S. Benight (1990) Biopolymers, 29, 1715-1734], yield a numerical method to evaluate the temperature dependence of the transition enthalpy, entropy, and free energy of a DNA hairpin directly from its optical melting curve. No prior assumptions that the short hairpins melt in a two-state manner are required. This method is then applied in a systematic manner to investigate the stability of the six basepair duplex stem 5'-GGATAC-3' having four-base dangling single-strand ends with the sequences (XY)2, where X, Y = A, T, G, C, on the 5' end and a T4 loop on the 3' end. Results show that all dangling ends of the sample set stabilize the hairpin against melting. Increases in transition temperatures as great as 4.0 degrees C above the blunt-ended control hairpin were observed. The hierarchy of the hairpin transition temperatures is dictated by the identity of the first base of the dangling end adjoining the duplex in the order: purine greater than T greater than C. Calculated melting curves of every hairpin were fit to experimental curves by adjustment of a single parameter in the numerically exact theoretical algorithm. Exact fits were obtained in all cases. Experimental melting curves were also calculated assuming a two-state melting process. Equally accurate fits of all dangling-ended hairpin melting curves were obtained with the two-state model calculation. This was not the case for the melting curve of the blunt-ended hairpin, indicating the presence of a four-base dangling-end drives hairpin melting to a two-state process. Q (T) was calculated as a function of temperature for each hairpin using the theoretical parameters that provided calculated curves in exact agreement with the experimentally obtained optical melting curves. From Q (T), the temperature dependence of the transition enthalpy delta H, entropy delta S, and free energy delta G were calculated for every hairpin providing a quantitative assessment of the effects of dangling ends on hairpin thermodynamics. Comparisons of our results are made with those of the Breslauer group [M. Senior, R. A. Jones, and K. J. Breslauer (1988) Biochemistry 27, 3879-3885] on the T2 5' dangling-ended d(GC)3 duplexes.(ABSTRACT TRUNCATED AT 400 WORDS)

Conformation and dynamics of a left-handed Z-DNA hairpin: studies of d(CGCGCGTTTTCGCGCG) in solution

The physical properties of the DNA oligomer d(CGCGCGTTTTCGCGCG) in solvents containing 4 M NaClO4 and 0.1 M NaCl were investigated by proton NMR, optical melting, and circular dichroism spectroscopy. Results of these investigations are as follows: (i) The DNA hexadecamer exists as a unimolecular hairpin in either high or low salt. (ii) In high salt the stem region of the hairpin is in the left-handed Z conformation. (iii) In either high or low salt, the duplex stem of the hairpin is stabilized against melting by approximately 40 degrees C compared to the linear core duplex. The added stability of the hairpin is entropic in origin. (iv) In high salt, as the temperature is elevated, the equilibrium structure of the duplex stem of the hairpin shifts from the Z to the B conformation before melting. (v) In low salt, when the DNA duplex exists in the B conformation, attachment of a T4 single-strand loop to one end only slightly decreases (by 14%) the correlation time of the CH5-CH6 interproton vector. In high salt, when the DNA duplex exists in the Z conformation, the correlation time of the CH5-CH6 interproton vector decreases by 51%. Since these viscosity-corrected correlation times are taken to be indicators of duplex motions on the nanosecond time scale, this result directly suggests a larger amplitude of these motions is present in the duplex stem of the hairpin when it exists in the Z conformation.