Conformational analysis of a hybrid DNA-RNA double helical oligonucleotide in aqueous solution: d(CG)r(CG)d(CG) studied by 1D- and 2D-1H NMR spectroscopy

Mitochondrial DNA Damage: Prevalence, Biological Consequence, and Emerging Pathways

Mitochondria have a plethora of functions within a eukaryotic cell, ranging from energy production, cell signaling, and protein cofactor synthesis to various aspects of metabolism. Mitochondrial dysfunction is known to cause over 200 named disorders and has been implicated in many human diseases and aging. Mitochondria have their own genetic material, mitochondrial DNA (mtDNA), which encodes 13 protein subunits in the oxidative phosphorylation system and a full set of transfer and rRNAs. Although more than 99% of the proteins in mitochondria are nuclear DNA (nDNA)-encoded, the integrity of mtDNA is critical for mitochondrial functions, as evidenced by mitochondrial diseases sourced from mtDNA mutations and depletions and the vital role of fragmented mtDNA molecules in cell signaling pathways. Previous research has shown that mtDNA is an important target of genotoxic assaults by a variety of chemical and physical factors. This Perspective discusses the prevalence of mtDNA damage by comparing the abundance of lesions in mDNA and nDNA and summarizes current knowledge on the biological pathways to cope with mtDNA damage, including mtDNA repair, mtDNA degradation, and mitochondrial fission and fusion. Also, emerging roles of mtDNA damage in mutagenesis and immune responses are reviewed.

Atomic resolution structure of a chimeric DNA-RNA Z-type duplex in complex with Ba(2+) ions: a case of complicated multi-domain twinning

The self-complementary dCrGdCrGdCrG hexanucleotide, in which not only the pyrimidine/purine bases but also the ribo/deoxy sugars alternate along the sequence, was crystallized in the presence of barium cations in the form of a left-handed Z-type duplex. The asymmetric unit of the P21 crystal with a pseudohexagonal lattice contains four chimeric duplexes and 16 partial Ba(2+) sites. The chimeric (DNA-RNA)2 duplexes have novel patterns of hydration and exhibit a high degree of discrete conformational disorder of their sugar-phosphate backbones, which can at least partly be correlated with the fractional occupancies of the barium ions. The crystals of the DNA-RNA chimeric duplex in complex with Ba(2+) ions and also with Sr(2+) ions exhibit complicated twinning, which in combination with structural pseudosymmetry made structure determination difficult. The structure could be successfully solved by molecular replacement in space groups P1 and P21 but not in orthorhombic or higher symmetry and, after scrupulous twinning and packing analysis, was refined in space group P21 to an R and Rfree of 11.36 and 16.91%, respectively, using data extending to 1.09 Å resolution. With the crystal structure having monoclinic symmetry, the sixfold crystal twinning is a combination of threefold and twofold rotations. The paper describes the practical aspects of dealing with cases of complicated twinning and pseudosymmetry, and compares the available software tools for the refinement and analysis of such cases.

Measuring the elasticity of ribonucleotide(s)-containing DNA molecules using AFM

Ribonucleotides, ribonucleoside monophosphates (rNMPs), have been revealed as possibly the most noncanonical nucleotides in genomic DNA. rNMPs, either not removed from Okazaki fragments during DNA replication or incorporated and scattered throughout the genome, pose a perturbation to the structure and a threat to the stability of DNA. The instability of DNA is mainly due to the extra 2'-hydroxyl (OH) group of rNMPs which give rise to local structural effects, which may disturb various molecular interactions in cells. As a result of these structural perturbations by rNMPs, the elastic properties of DNA are also affected. Here, we show the approach to test whether the presence of rNMPs in DNA duplexes could alter the elasticity of DNA by implementing atomic force microscopy (AFM)-based single molecule force-measurements of short rNMP(s)-containing oligonucleotides (oligos).

The solution structure of [d(CGC)r(aaa)d(TTTGCG)](2): hybrid junctions flanked by DNA duplexes

The solution structure and hydration of the chimeric duplex [d(CGC)r(aaa)d(TTTGCG)](2), in which the central hybrid segment is flanked by DNA duplexes at both ends, was determined using two-dimensional NMR, simulated annealing and restrained molecular dynamics. The solution structure of this chimeric duplex differs from the previously determined X-ray structure of the analogous B-DNA duplex [d(CGCAAATTTGCG)](2)as well as NMR structure of the analogous A-RNA duplex [r(cgcaaauuugcg)](2). Long-lived water molecules with correlation time tau(c)longer than 0.3 ns were found close to the RNA adenine H2 and H1' protons in the hybrid segment. A possible long-lived water molecule was also detected close to the methyl group of 7T in the RNA-DNA junction but not with the other two thymines (8T and 9T). This result correlates with the structural studies that only DNA residue 7T in the RNA-DNA junction adopts an O4'-endo sugar conformation, while the other DNA residues including 3C in the DNA-RNA junction, adopt C1'-exo or C2'-endo conformations. The exchange rates for RNA C2'-OH were found to be approximately 5-20 s(-1). This slow exchange rate may be due to the narrow minor groove width of [d(CGC)r(aaa)d(TTTGCG)](2), which may trap the water molecules and restrict the dynamic motion of hydroxyl protons. The minor groove width of [d(CGC)r(aaa)d(TTTGCG)](2)is wider than its B-DNA analog but narrower than that of the A-RNA analog. It was further confirmed by its titration with the minor groove binding drug distamycin. A possible 2:1 binding mode was found by the titration experiments, suggesting that this chimeric duplex contains a wider minor groove than its B-DNA analog but still narrow enough to hold two distamycin molecules. These distinct structural features and hydration patterns of this chimeric duplex provide a molecular basis for further understanding the structure and recognition of DNA. RNA hybrid and chimeric duplexes.

Structural characterization of d(CAACCCGTTG) and d(CAACGGGTTG) mini-hairpin loops by heteronuclear NMR: the effects of purines versus pyrimidines in DNA hairpins

The DNA decamers, d(CAACCCGTTG) and d(CAACGGGTTG) were studied in solution by proton and heteronuclear NMR. Under appropriate conditions of pH, temperature, salt concentration and DNA concentration, both decamers form hairpin conformations with similar stabilities [Avizonis and Kearns (1995) Biopolymers, 35, 187-200]. Both decamers adopt mini-hairpin loops, where the first and last four nucleotides are involved in Watson-Crick hydrogen bonding and the central two nucleotides, CC or GG respectively, form the loop. Through the use of proton-proton, proton-phosphorus and natural abundance proton-carbon NMR experiments, backbone torsion angles (beta, gamma and epsilon), sugar puckers and interproton distances were measured. The nucleotides forming the loops of these decamers were found to stack upon one another in an L1 type of loop conformation. Both show gamma tr and unusual beta torsion angles in the loop-closing nucleotide G7, as expected for mini-hairpin loop formation. Our results indicate that the beta and epsilon torsion angles of the fifth and sixth nucleotides that form the loop and the loop-closing nucleotide G7 are not in the standard trans conformation as found in B-DNA. Although the loop structures calculated from NMR-derived constraints are not well defined, the stacking of the bases in the two different hairpins is different. This difference in the base stacking of the loop may provide an explanation as to why the cytosine-containing hairpin is thermodynamically more stable than the guanine-containing hairpin.

An approach to the structure determination of nucleic acid analogues hybridized to RNA. NMR studies of a duplex between 2'-OMe RNA and an oligonucleotide containing a single amide backbone modification

The backbone modification amide-3, in which -CH2-NH-CO-CH2- replaces -C5'H2-O5'-PO2-O3'-, is studied in the duplex d(G1-C2-G3-T4.T5-G6-C7-G8)*mr(C9-G10-C11-A12-A13-C14-G15+ ++-C16) where . indicates the backbone modification and mr indicates the 2'-OMe RNA strand. The majority of the exchangeable and non-exchangeable resonances have been assigned. The assignment procedure differs from standard methods. The methyl substituent of the 2'-OMe position of the RNA strand can be used as a tool in the interpretation. The duplex structure is a right-handed double helix. The sugar conformations of the 2'-OMe RNA strand are predominantly N-type and the 2'-OMe is positioned at the surface of the minor groove. In the complementary strand, only the sugar of residue T4 is found exclusively in N-type conformation. The incorporation of the amide modification does not effect very strongly the duplex structure. All bases are involved in Watson-Crick base pairs.

Sequence specific thermodynamic and structural properties for DNA.RNA duplexes

DNA.RNA hybrid duplexes are found in many important biological processes and are involved in developing modes of disease treatment, such as antisense therapy, yet little is known about the sequence dependence of their structure and stability. The structure and thermodynamic stability of DNA.RNA hybrid model systems corresponding in composition and length and containing (1) all purine or all pyrimidine bases on each strand or (2) mixed purine and pyrimidine bases on each strand have been evaluated relative to pure RNA and DNA duplexes by thermal melting, CD, and electrophoresis analyses. The spread in free energies of denaturation of the homopurine.homopyrimidine systems covers over 14 kcal/mol of single strands, while the mixed sequence free energies vary by less than 4 kcal/mol. The RNA-homopurine.DNA-homopyrimidine hybrid resembles a corresponding pure RNA duplex in both structure and stability, whereas the DNA-homopurine.RNA-homopyrimidine hybrid resembles a corresponding pure DNA duplex. The mixed sequence hybrids show intermediate structure between the corresponding pure RNA and pure DNA duplexes and a stability closer to that of the pure DNA duplex. From these results and the evaluation of published hybrid data [Hall, K. B., & McLaughlin, L. W. (1991) Biochemistry 30, 10606-10613; Roberts, W. R., & Crothers, D. M. (1992) Science 258, 1463-1466], it can be predicted that a hybrid duplex containing more RNA purine bases will have a CD spectrum, and probably conformation, resembling that of A-form duplexes and will be more stable than a corresponding hybrid duplex with fewer RNA purine bases.

Structural influence of RNA incorporation in DNA: quantitative nuclear magnetic resonance refinement of d(CG)r(CG)d(CG) and d(CG)r(C)d(TAGCG)

RNA and DNA adopt different types of conformations, i.e., A-type with C3'-endo sugar pucker for RNA and B-type with C2'-endo sugar pucker for DNA, respectively. The structural influence of the incorporation of RNA nucleotides into DNA is less understood. In this paper, we present the three-dimensional structures of two RNA-containing oligonucleotides, d(CG)r(CG)d(CG) and d(CG)r(C)d-(TAGCG), as determined by the NMR refinement procedure, and assess the possible structural perturbation of DNA induced by RNA. With a single RNA insertion into an octamer DNA, its overall conformation remains as the canonical B-DNA, except that the sugar pucker of the rC3 residue is C3'-endo (pseudorotation angle P = 3.6 degrees). In contrast, the hybrid hexamer is neither the pure B-DNA nor the pure A-DNA conformation. Instead, we propose a model in which the DNA parts adopt B conformation, whereas the RNA part adopts A conformation, with the overall conformation closer to A-DNA. To ensure an exhaustive search of the conformational space, the model was subjected to 100-ps simulated annealing with slow cooling or 100-ps molecular dynamics with subsequent quenching. Models obtained at different time points of the trajectories were further subjected to the SPEDREF NOE refinement [Robinson & Wang (1992) Biochemistry 31, 3524] and they appeared to arrive at a convergent model (< 0.5 A RMSD for the central four base pairs). The consensus hexamer structure contains a significant discontinuity at the (rG4)p(dC5) step with a base pair tilt angle of 6.7 degrees and roll angle of 11.5 degrees.(ABSTRACT TRUNCATED AT 250 WORDS)

Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition

Studies of a series of short oligonucleotide double and triple helices containing either all RNA, all DNA, or a mixture of the two show strand-dependent variation in their stability and structure. The variation in stability for both groups falls over a range of greater than 10 kilocalories per mole. In forming the triple helix, RNA is favored on both pyrimidine strands, whereas DNA is favored on the purine strand. In general, relatively unstable duplexes form particularly stable triplexes and vice versa. Structural data indicate that the strands in hybrid helices adopt a conformation that is intermediate between molecules containing all DNA and all RNA. Thus, RNA-DNA hybrids were not forced into the conformation of the RNA (A-form). The provocative stability of the triplex with an RNA third strand+DNA duplex points to novel antisense strategies and opens the possibility of an in vivo role of these structures. Overall, the data emphasize the fundamental role of sugars in determining the properties of nucleic acid complexes.

A temperature-dependent Z to B to single-strand transition in d(CGCG)

A thermally induced left- to right-handed helical interconversion for the self-complementary tetradeoxynucleotide d(CGCG) has been observed in the presence of NaCl at concentrations from 1.5 to 2.25M. Analysis of the Raman spectrum of d(CGCG) in aqueous solution as a function of temperature indicates that at low temperature a left-handed Z-helical form is the predominant species. An increase in temperature results in a decrease in the population of the left-handed form and an increase in the population of the right-handed form. Further elevation in temperature results in extensive disruption of base stacking and a loss of secondary structure. This unstacking presumably represents dissociation to a single-stranded structure. The data suggest that a temperature-dependent Z to B to single-strand transition occurs under the conditions employed. A direct Z to single-strand conversion was not identified. In contrast to previous examples, the thermally induced left- to right-handed helical conversion for d(CGCG) can occur in the absence of chemically modified nucleic acid bases, alcohol solutions, or divalent ions.

Thermodynamics of the various forms of the dodecamer d(ATTACCGGTAAT) and of its constituent hexamers from proton nmr chemical shifts and UV melting curves: three-state and four-state thermodynamic models

Chemical shifts of base and H1' protons of the single-stranded hexamers d(ATTACC) and d(GGTAAT), of the 1:1 mixtures of these complementary hexamers, and of the self-complementary dodecamer d(ATTACCGGTAAT) were measured at various temperatures in aqueous solution. Four different sample concentrations were used in the case of the dodecamer and of the mixture of the complementary hexamers; the individual hexamers were measured at two different DNA concentrations. Absorbance temperature profiles at five different NaCl concentrations were measured for the dodecamer in order to quantify the effect of the ionic strength on the duplex formation. Under suitable conditions of nucleotide concentration, temperature, and ionic strength, the dodecamer adopts either a B-DNA duplex or a hairpin-loop structure. Chemical shift vs temperature profiles, constructed for all samples, were used to obtain thermodynamic parameters either for the various stacking interactions in the single strands or for the duplex or the hairpin-loop formation. In the analysis of the duplex formation of the hexamers, a two-state approach appeared too simple, because systematic deviations were revealed. Therefore, a new three-state model (DUPSTAK) was developed. In order to investigate the magnitude of error arising from the use of the two-state approach in cases where the DUPSTAK model appears more appropriate, a series of test calculations was made. The magnitude of error in the enthalpy and in the entropy of duplex melting is found to depend linearly upon the actual melting temperature and not upon the individual delta Hd degrees and delta Sd degrees values. Thermodynamic analysis of the chemical shift vs temperature profiles in D2O solution (no added salt) yields an average Tmd value of 341 K (1M DNA) and delta Hd degrees of - 121 kJ.mol-1 for the dimer/random-coil transition of the hexamer duplex d(ATTACC).d(GGTAAT). For the duplex in equilibrium random-coil transition of the 12-mer d(ATTACCGGTAAT) an average Tmd value of 336 K (1M DNA) and delta Hd degrees of -372 kJ.mol-1 are found. The hairpin/random-coil transition of d(ATTACCGGTAAT) is characterized by a rather large delta Hh degrees value, -130 kJ.mol-1, and an average Tmh value of 304 K.

Bulge-out structures in the single-stranded trimer AUA and in the duplex (CUGGUGCGG).(CCGCCCAG). A model-building and NMR study

Model-building studies were carried out on the trimer AUA. Bulge-out structures which allow incorporation into a continuous RNA helix were generated and energy-minimized. All geometrical features obtained by previous NMR studies on purine-pyrimidine-purine sequences are accounted for in these models. One of the models was used to fit into a double helical fragment. Only minor changes were necessary to construct a central bulge-out in an otherwise intact duplex. NMR and model-building studies were performed on the duplex (CUGGUGCGG).(CCGCCCAG) which contains an unpaired uridine residue. NOE data, chemical-shift profiles and imino-proton resonances provided evidence that the extra U is bulged out of the duplex. The relatively small dispersion in 31P chemical shifts (approximately equal to 0.7 ppm) indicate the absence of t/g or g/t combinations for the phosphodiester angles zeta/alpha. An energy-minimized model of the duplex, which fits the present collection of data, is presented.

Influence of uracil on the conformational behaviour of RNA oligonucleotides in solution

NMR studies were carried out on some alternating pyrimidine-purine sequences: the single-stranded tetramers CACA and UGUG and the self-complementary octamer CACAUGUG. Assignments, based upon COSY, homonuclear Hartmann-Hahn, and NOESY experiments, are given for the resonances of all base protons and of several sugar protons. Chemical shift vs temperature profiles were used to obtain thermodynamic parameters for the single-stranded stack in equilibrium with random coil and the duplex in equilibrium with random coil equilibria. The populations of N-type conformer of the ribose rings were estimated from the observed J1'2'. Comparisons with another alternating pyrimidine-purine sequence Um2(6)AUm2(6)A and with the deoxyribose counterparts d(CACA), d(TGTG) and d(CACATGTG) are given. Previous 1H-NMR investigations of Um2(6)AUm2(6)A revealed that the population of bulge-out structure diminishes compared to m2(6)AUm2(6)A due to the U(1)-m2(6)A(2) stacking interaction. In CACA a strong stacking proclivity (Tm = 310 K) together with a clear preference for N-type ribose is observed. However, the stacking interactions in UGUG are relatively less stable (Tm = 288 K) and a bias towards S-type sugar is present. Besides a small amount of stack, a significant contribution of bulge out structure is proposed for UGUG. We conclude that the nature of the pyrimidine base mainly determines the formation of bulge-out structures. The poor stacking properties of uracil now appear to be mainly responsible for this phenomenon. Comparison with the deoxyribose counterparts shows a reasonable agreement between the Tm values of CACA and d(CACA), whereas the Tm of UGUG (288 K) is much lower than the Tm of d(TGTG) (315 K). It is suggested that the absence of bulge-out structures in DNA purine-pyrimidine-purine sequences is related to the relatively strong stacking proclivity of dT residues compared to that of U residues. The Tm values (average 341 K) for the duplex in equilibrium with random coil transition obtained for each residue of CACAUGUG appear very similar. All ribose rings, except the G(8), adopt a pure N conformer in the duplex. This is taken to mean that the differences in conformational behaviour of the constituent tetramers disappear upon duplex formation.

Extra thymidine stacks into the d(CTGGTGCGG).d(CCGCCCAG) duplex. An NMR and model-building study

NMR and model-building studies were carried out on the duplex d(CTGGTGCGG).d(CCGCCCAG), referred to as (9+8)-mer, which contains an unpaired thymidine residue. Resonances of the base and of several sugar protons of the (9+8)-mer were assigned by means of a NOESY experiment. Interresidue NOEs between dG(4) and dT(5) as well as between dT(5) and dG(6) provided evidence that the extra dT is stacked into the duplex. Thermodynamic analysis of the chemical shift vs temperature profiles yielded an average TmD value of 334 K and delta HD of -289 kJmol-1 for the duplex in equilibrium random-coil transition. The shapes of the shift profiles as well as the thermodynamic parameters obtained for the extra dT residue and its neighbours again indicate that the unpaired dT base is incorporated inside an otherwise intact duplex. This conclusion is further supported by (a) the observation of an imino-proton resonance of the unpaired dT; (b) the relatively small dispersion in 31P chemical shifts (approximately 0.5 ppm) for the (9+8)-mer, which indicates the absence of t/g or g/t combinations for the phosphate diester torsion angles alpha/zeta. An energy-minimized model of the (9+8)-mer, which fits the present collection of experimental data, is presented.

Preparation of covalently linked DNA-RNA hybrids and arabinocytidine containing DNA fragments

It will be demonstrated that 5'-O-DMT-N-acyl-deoxyribonucleosides, 5'-O-Lev-2'-O-MTHP-N-acyl-ribonucleosides and, also, 2'-O-MTHP-N-acyl-ara-cytidine can be coupled, via the hydroxybenzotriazole phosphotriester approach, to afford two types of DNA-RNA hybrids as well as ara-C containing DNA-fragments. The final removal of acid-labile DMT and MTHP groups could be effected by 1 h treatment with 80% acetic acid of the otherwise unprotected DNA-RNA hybrids. The same acidic hydrolysis did not result in complete removal of the 2'-O-MTHP group from the ara-C unit. Complete deblocking was accomplished after an additional 2 h aqueous HC1 (0.01 M; pH 2.00) treatment.

An NMR study of polymorphous behaviour of the mismatched DNA octamer d(m5C-G-m5C-G-A-G-m5C-G) in solution. The B-duplex and hairpin forms

By means of one- and two-dimensional NMR spectroscopy the solution structures of the partly self-complementary octamer d(m5C-G-m5C-G-A-G-m5C-G) were investigated. It is shown that this DNA fragment, under conditions of high DNA concentration (8 mM DNA) and/or high ionic strength prefers to adopt a duplex structure. At low DNA concentration (0.4 mM DNA), the duplex exists in a 1:1 slow equilibrium with a monomeric hairpin form. Addition of salt destabilizes the hairpin structure in favour of the dimer. At high temperatures the hairpin form, as well as the dimer structure, exist in a fast equilibrium with the random-coil form. For the hairpin/random-coil equilibrium a Tm of 329 K and a delta H degree of -121 kJ.mol-1 were deduced. These thermodynamic parameters are independent of the DNA concentration, as is expected for a monomeric structure. For the dimer to coil transition a Tm of 359 K (1 M DNA) and a delta H degree of -285 kJ.mol duplex-1 were derived. The thermodynamic data of the hairpin-coil transition mutually agree with those recently reported for the hairpin to random coil equilibrium of the DNA octamer d(m5C-G-m5C-G-T-G-m5C-G) [Orbons, L. P. M., van der Marel, G. A., van Boom, J. H. & Altona, C. (1987) J. Biomol. Struct. Dyns. 4, 939-963]. It is demonstrated that the dimer structure exhibits B-DNA characteristics, as is witnessed by the NOESY experiments and the analysis of the proton-proton coupling data. It is shown that the base-pair formation of the G x A mismatches is anti-anti. A comparison of 1H and 31P chemical-shift data of the title compound with those of a well-characterized B-DNA structure reveals large differences in the dm5C(3)-dG(4)-dA(5) part of the mismatched dimer structure. These differences apparently indicate some major local structural changes due to the incorporation of the G x A mismatches. Under the most extreme conditions used (i.e. up to 3 M NaCl or 75% CH3OH in the presence of 10 mM MgCl2) no Z-DNA structure was observed. It is shown that the structural features of the hairpin form of the title compound mimic those of the hairpin structure of d(m5C-G-m5C-G-T-G-m5C-G). An energy-minimized model of the hairpin form is given.

Synthesis and proton-NMR studies of oligonucleotides containing an apurinic (AP) site

In order to elucidate the conformational properties of base-deleted oligodeoxyribonucleotides, the molecules d-CpS(pCpG)n (n = 1,2; S = sugar) were synthesized by the phosphotriester method and characterized by 1H-NMR spectroscopy. Complete assignment of all non-exchangeable proton resonances of both compounds was obtained by 1D- and 2D-NMR techniques. In combination with computer simulation, these spectra yielded proton-proton and proton-phosphorus coupling constants of high accuracy. These data provide valuable information about the sugar and the backbone conformation. It appears that d-Cp1Sp2Cp3G4 does not form a duplex under any of the conditions studied. On the contrary, the base-deleted hexamer d-Cp1Sp2Cp3Gp4Cp5G6 occurs as a right-handed' staggered' DNA duplex at 280 K: the core of this duplex is formed by the residues C(3)-G(6); two 'dangling' residues C(1) and S(2) are located at the two 5'-ends of the duplex. The assignment of the corresponding imino proton resonances for [d-CpS(pCpG)2]2 was based on their thermal behavior: the line broadening of these resonances was studied as a function of temperature. The chemical shift and the number of imino proton resonances accord well with the number and type of Watson-Crick base pairs which can be formed in the staggered duplex described above. Thermodynamic parameters of duplex formation were obtained from an analysis of the chemical shift versus temperature profiles of aromatic base and H-1' protons. It is suggested that the cytosine ring of C(1) stacks, at least part of the time, with the guanine ring on the nucleotide residue, G(6), situated in the complementary strand. The binding of Lys-Trp-Lys to [d-CpS(pCpG)2]2 as well as to [d-CpGpCpG]1 was investigated. It is concluded that the indole ring of the tryptophan residue probably stacks on top of the 3'-terminal guanine base of both duplexes, but not on the nucleic acid bases next to the apurinic (AP) site.

Sequence-specific assignments and their use in NMR studies of DNA structure

There has been a surge of recent interest, reflected by a sharp increase in the number of publications, in the area of high-resolution nuclear magnetic resonance (NMR) studies of DNA. The goal of many of these studies is to monitor the structure of biologically important DNA sequences directly in solution; the impetus for such studies was the realization, from early single-crystal X-ray structures, that nearest-neighbor context effects are a major determinant of local structure in short double-helical DNAs (Dickerson & Drew, 1981; Dickerson, 1983). Thus, instead of the previously assumed regular averaged structure of the double helix derived from fibre diffraction analysis, the more interesting concept emerged that specific sequence-dependent distortions from ‘classical’ DNA structure might be responsible for the recognition of such sequences by a variety of ligands such as repressors, polymerases, drugs, etc.

DNA and RNA: NMR studies of conformations and dynamics in solution

The early NMR research on nucleic acids was of a qualitative nature and was restricted to partial characterization of short oligonucleotides in aqueous solution. Major advances in magnet design, spectrometer electronics, pulse techniques, data analysis and computational capabilities coupled with the availability of pure and abundant supply of long oligonucleotides have extended these studies towards the determination of the 3-D structure of nucleic acids in solution.

Conformational and model-building studies of the hairpin form of the mismatched DNA octamer d(m5C-G-m5C-G-T-G-m5C-G)

The hairpin form of the mismatched octamer d(m5C-G-m5C-G-T-G-m5C-G) was studied by means of NMR spectroscopy. In a companion study it is shown that the hairpin form of this DNA fragment consists of a structure with a stem of three Watson-Crick-type base pairs and a loop consisting of only two nucleotides. The non-exchangeable proton resonances were assigned by means of two-dimensional correlation spectroscopy and two-dimensional nuclear Overhauser effect spectroscopy. Proton-proton coupling constants were used for the conformational analysis of the deoxyribose ring and for some of the backbone torsion angles. From the two-dimensional NMR spectra and the coupling-constant analysis it is concluded that: (i) the stem of the hairpin exhibits B-DNA characteristics; (ii) the sugar rings are not conformationally pure, but display a certain amount of conformational flexibility; (iii) the stacking interaction in the stem of the hairpin is elongated from the 3'-side in a more or less regular fashion with the two loop nucleotides; (iv) at the 5'-side of the stem a stacking discontinuity occurs between the stem and the loop; (v) at the 5'-side of the stem the loop is closed by means of a sharp backbone turn which involves unusual gamma' and beta+ torsion angles in residue dG(6). The NMR results led to the construction of a hairpin-loop model which was energy-minimized by means of a molecular-mechanics program. The results clearly show that a DNA hairpin-loop structure in which the loop consists of only two nucleotides bridging the minor groove in a straightforward fashion, (i) causes no undue steric strain, and (ii) involves well-known conformational principles throughout the course of the backbone. The hairpin form of the title compound is compared with the hairpin form of d(A-T-C-C-T-A-T4-T-A-G-G-A-T), in which the central -T4- part forms a loop of four nucleotides. Both models display similarities as far as stacking interactions are concerned.

Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: a graphical method

A graphical method is presented for the conformational analysis of the sugar ring in DNA fragments by means of proton-proton couplings. The coupling data required for this analysis consist of sums of couplings, which are referred to as sigma 1' (= J1'2' + J1'2''), sigma 2' (= J1'2' + J2'3' + J2'2''), sigma 2'' (= J1'2'' + J2''3' + J2'2'') and sigma 3' (= J2'3' + J2''3' + J3'4'). These sums of couplings correspond to the distance between the outer peaks of the H1', H2', H2'' and H3' [31P] resonances, respectively, (except for sigma 2' and sigma 2'' in the case of a small chemical shift difference between the H2' and H2'' resonances) and can often be obtained from 1H-NMR spectra via first-order measurement, obviating the necessity of a computer-assisted simulation of the fine structure of these resonances. Two different types of graphs for the interpretation of the coupling data are discussed: the first type of graph serves to probe as to whether or not the sugar ring occurs as a single conformer, and if so to analyze the coupling data in terms of the geometry of this sugar ring. In cases where the sugar ring does not occur as a single conformer, but as a blend of N- and S-type sugar puckers, the second type of graph is used to analyze the coupling data in terms of the geometry and population of the most abundant form. It is shown that the latter type of analysis can be carried out on the basis of experimental values for merely sigma 1',sigma 2' and sigma 2'', without any assumptions or restrictions concerning a relation between the geometry of the N- and S-type conformer. In addition, the question is discussed as to how insight can be gained into the conformational purity of the sugar ring from the observed fine structure of the H1' resonance. Finally, a comparison is made between experimental coupling data reported for single-stranded and duplex DNA fragments and covalent RNA-DNA hybrids on the one hand and the predicted couplings and sums of couplings presented in this paper on the other hand.

Residue-specific assignments of resonances in the 1H nuclear magnetic resonance spectrum of ribosomal protein E-L30 by systematic application of two-dimensional Fourier transform nuclear magnetic resonance methods

A two-dimensional Fourier transform nuclear magnetic resonance study of the ribosomal protein E-L30 is reported. Five two-dimensional techniques, namely: nuclear magnetic resonance J-resolved spectroscopy, correlated spectroscopy, double quantum spectroscopy, relayed coherence transfer and nuclear Overhauser enhancement spectroscopy were used. Qualitative inspection of the spectra obtained by these techniques provided evidence that the E-L30 molecule has a well-defined structure in solution. This analysis indicated that, despite the fact that the protein is stable only at moderate temperatures and neutral pH, a structural analysis of the molecule would be feasible. A detailed analysis of the spectra permitted unambiguous discrimination between the spin systems of different amino acids, resulting in residue-specific resonance assignments. We were able to assign all resonances of all six threonine, four valine, five alanine, two histidine, two serine, one phenylalanine, one asparagine and one aspartic acid residue of E-L30. Complete resonance assignment was obtained for two glycine residues. Partial assignments became available for all six isoleucine, three glycine and one glutamine residue. These results form a sound basis for the structure determination of the protein described in the accompanying paper.

NMR studies of the complex between the decadeoxynucleotide d-(GCATTAATGC)2 and a minor-groove-binding drug

Nearly all 1H NMR lines of the complex formed between the bis(quaternary ammonium) heterocycle 4-[p-[p-(4-quinolylamino)benzamido]anilino]pyridine (1, also known as SN 6999) and the decadeoxyribonucleoside nonaphosphate d-(GCATTAATGC)2 were sequentially assigned by using one- and two-dimensional NMR techniques. Intermolecular nuclear Overhauser effects between the ligand and the DNA show that the drug binds in the minor groove of the DNA, interacting with the central A-T base pairs. Over the temperature range from 277 to 313 K, the lifetime of the drug in the DNA binding sites is short relative to the NMR time scale, since fast exchange is observed for all but a few protons. A model for the binding of 1 to d-(GCATTAATGC)2 is proposed, where the drug binds to two equivalent sites covering approximately five A-T base pairs, which assumes exchange of 1 between these two binding sites.

The B and Z forms of the d(m5C-G)3 and d(br5C-G)3 hexamers in solution. A 300-MHz and 500-MHz two-dimensional NMR study

The non-exchangeable proton resonances of the hexadeoxynucleoside pentakisphosphates d(m5C-G)3 and d(br5C-G)3 in the B form as well as in the Z form were assigned by means of two-dimensional correlated spectroscopy and two-dimensional nuclear Overhauser enhancement spectroscopy. The complete proton NMR spectrum of the B form of the methylated compound was assigned in a pure 2H2O solution as well as in a 2H2O/C2H3O2H mixed solvent, containing 5 mM MgCl2. In the latter solvent the B form occurs in slow equilibrium (on the NMR time scale) with the Z form, the resonances of which also were fully assigned. The proton resonances of the B and Z forms of the brominated fragment were assigned in a 2H2O/C2H3O2H solution containing 5 mM MgCl2. A new and general method is described for the sequential assignment of the non-exchangeable proton resonances of oligonucleotides in the Z form.

Conformational analysis of the octamer d(G-G-C-C-G-G-C-C) in aqueous solution. A one-dimensional and two-dimensional proton NMR study at 300 MHz and 500 MHz

Proton NMR studies in H2O and 2H2O were carried out on the self-complementary DNA octamer d(G-G-C-C-G-G-C-C) and compared with similar studies on the dimethylated analogue d(G-G-m5C-m5C-G-G-C-C) [Sanderson, M. R., Mellema, J.-R., van der Marel, G. A., Wille, G., van Boom, J. H. & Altona, C. (1983) Nucleic Acids Res. 11, 3333-3346]. Base, H1', H2' and H2" resonances were assigned by means of two-dimensional nuclear Overhauser spectroscopy (NOESY) and correlated spectroscopy (COSY) experiments. Chemical shift vs temperature profiles were used to analyze the temperature-dependent conformational behaviour and to extract thermodynamic parameters for the duplex-to-coil transition. Analysis of proton-proton couplings were used to discriminate between J1'2' and J1'2" and between the H2' and H2" resonances as well as to obtain conformational parameters of the sugar rings. From the NOESY and COSY experiments, the temperature profiles and the analysis of the coupling data it is concluded that: (a) the compound adopts a B-DNA-type helix in solution; (b) the sugar rings in the intact duplex display limited conformational freedom; (c) methylation of the cytosine bases at the C5 position has no measurable effect on the conformational behaviour of the octamer, nor on the conformation of the sugar rings; however, methylation does increase the stability of the duplex in aqueous solution under conditions of low salt concentration.

1H nuclear magnetic resonance assignments for d-(GCATTAATGC)2 using experimental refinements of established procedures

Sequence-specific 1H nuclear magnetic resonance assignments are presented for d-(GCATTAATGC)2. Using omega 1-scaled double quantum-filtered correlated spectroscopy, two-quantum spectroscopy, relayed coherence transfer spectroscopy and detailed analysis of the fine structure in these phase-sensitive spectra, the spin system of the bases and deoxyribose rings were identified entirely via scalar proton-proton couplings. The sequential connectivities were established with two-dimensional nuclear Overhauser enhancement spectra recorded with a short mixing time of 60 milliseconds. These spectra contain only a small number of cross-peaks, corresponding to the shortest proton-proton distances prevailing in the DNA. They are thus easy to interpret, and therefore the presently proposed modifications of the established assignment procedures should enable studies of larger DNA duplexes with intrinsically more complex nuclear magnetic resonance spectra, and they also provided an improved basis for conformational studies of DNA fragments.

DNA modified by platinum derivatives cannot adopt the A-form

DNA fragments from chicken erythrocytes were modified by cis-diamminedichloroplatinum(II), its trans-isomer and chlorodiethylenetriaminoplatinum(II) chloride. The conformation of the modified DNA fragments in ethanolic solutions was studied by circular dichroism spectroscopy. Non-modified DNA adopted the A-form in 81% ethanol. The modification of DNA by the three platinum compounds inhibited the B to A transition of DNA induced by high concentrations of ethanol roughly to the same extent. The results support the view that the binding of the platinum complexes to B-DNA lowers the conformational freedom of DNA so that it cannot acquire the A-conformation.

Internal motions in B- and Z-form poly(dG-dC).poly(dG-dC): 1H NMR relaxation studies

Proton NMR relaxation measurements are used to compare the molecular dynamics of 60 base pair duplexes of B- and Z-form poly(dG-dC).poly(dG-dC). The relaxation rates of the exchangeable guanine imino protons (Gim) in H2O and in 90% D2O show that below 20 degrees C spin-lattice relaxation is exclusively from proton-proton magnetic dipolar interactions while proton-nitrogen interactions contribute about 30% to the spin-spin relaxation. The observation that the spin-lattice relaxation is nonexponential and that the initial spin-lattice relaxation rate of the Gim, G-H8 and C-H6 protons depends on the selectivity of the exciting pulse shows that spin-diffusion dominates the spin-lattice relaxation. The relaxation rates of the Gim, C-H5, and C-H6 in B- and Z-form poly(dG-dC).poly(dG-dC) cannot be explained by assuming the DNA behaves as a rigid rod. The data can be fit by assuming large-amplitude out of plane motions (+/- 30-40 degrees, tau = 1-100 ns) and fast, large-amplitude local torsional motions (+/- 25-90 degrees, tau = 0.1-1.5 ns) in addition to collective torsional motions. The results for the B and Z forms show that the rapid internal motions are similar and large in both conformations although backbone motions are slightly slower, or of lower amplitude, in Z DNA. At high temperatures (greater than 60 degrees C), imino proton exchange with solvent dominates the spin-lattice relaxation of B-form poly(dG-dC).poly(dG-dC), but in the Z form no exchange contribution (less than 2 s-1) is observed at temperatures as high as 85 degrees C. Conformational fluctuations that expose the imino protons to the solvent are strikingly different in the B and Z forms. The results obtained here are compared with those previously reported for poly(dA-dT).poly(dA-dT).

Investigation of the solution structure of a DNA octamer [d(GGAATTCC)]2 using two-dimensional nuclear Overhauser enhancement spectroscopy

Proton two-dimensional nuclear Overhauser enhancement (2D NOE) spectra in the pure absorption phase were obtained at 500 MHz for [d(GGAATTCC)]2 in aqueous solution at a series of mixing times. The experimental data were analyzed by comparison with theoretical spectra calculated using the complete 70 X 70 relaxation matrix including all proton dipole-dipole interactions and spin diffusion [Keepers, J. W. & James, T. L. (1984) J. Magn. Reson. 57, 404-426]. The theoretical spectra at each mixing time were calculated using two structures: a standard B-form DNA structure and an energy-minimized structure based on the similarity of the six internal residues of the title octamer with those of the dodecamer [d(CGCGAATTCGCG)]2, for which the crystal structure has been determined. Neither the standard B-form nor the energy-minimized structure will yield theoretical 2D NOE spectra which accurately reproduce all peak intensities in the experimental spectra. However, many features of the experimental spectra can be represented by both the B-form and the energy-minimized structure. Sequence-dependent structural characteristics are manifest in the 2D NOE spectra, in particular at the purine-pyrimidine junction as noted previously in the crystal structure. On the whole, the energy-minimized structure appears to yield theoretical 2D NOE spectra which mimic many, if not all, aspects of the experimental spectra. All 2D NOE data were consistent with nanosecond correction times as implied by proton spin-lattice relaxation time measurements. But better fits of some of the 2D NOE data using small variations in an effective isotropic correlation time suggest that there may be some local variations in mobility within the octamer duplex structure in solution.

Imino-proton resonances of yeast tRNAPhe studied by two-dimensional nuclear Overhauser enhancement spectroscopy

Application of two-dimensional nuclear Overhauser enhancement (NOE) spectroscopy to yeast tRNAPhe in H2O solution demonstrates that all imino-proton resonances, related to the secondary structure, and nearly all imino proton resonances, originating from the tertiary structure, can be assigned efficiently by this method. The results corroborate the assignments of the imino-proton resonances of this tRNA as established previously by one-dimensional NOE experiments (only the assignment of base pairs G1 X C72 and C2 X G71 should be reversed). The advantages of two-dimensional NOE spectroscopy over one-dimensional NOE spectroscopy for the assignments of imino-proton resonances and the structure elucidation of tRNA are illustrated and discussed. Furthermore, the use of non-exchangeable proton resonances as probes of the molecular structure is explored.

cis-diamminedichloroplatinum(II) induced distortion of a single and double stranded deoxydecanucleosidenonaphosphate studied by nuclear magnetic resonance

The structural distortion of a single- and a double-stranded decadeoxynucleotide upon binding of cis-PtCl2(NH3)2 was studied by 1H-NMR. After selective platination of d(T-C-T-C-G-G-T-C-T-C) (I) at the central d(-GpG-) site (resulting in I-Pt), several non-exchangeable base protons as well as H1', H2', H2" and H3' protons could be assigned by means of conventional NMR double-resonance techniques. Addition of the complementary decamer strand to I and I-Pt yielded the double-stranded III and III-Pt, respectively. All non-exchangeable base, H1', and most of the H2' and H2" protons in the two double stranded compounds could be assigned using 2D-chemical shift correlation (COSY) and nuclear Overhauser enhancement (NOESY) techniques. The double stranded compound III appears to adopt a B-DNA like structure. Comparison of NOEs and proton-proton coupling constants in the d(-GpG-).cisPt part in I-Pt and III-Pt reveals that their structure displays large similarity. Significant chemical shift changes (i.e. larger than 0.1 ppm) between III and III-Pt are restricted to the central four base pairs. It follows that the outer three base pairs, located on either side of the central four base pairs in III-Pt are likely to adopt a regular B-DNA type helix. The observed large upfield and downfield chemical shifts in the d(-CpGpG-) part of III with respect to III-Pt can be rationalized by describing the distortion of the double helix as a kink. A discussion of the observed physical effects upon platination of a double-stranded oligonucleotide is presented.

Conformational characteristics of the hexanucleoside pentaphosphate AUAUAU: a 2D NMR study at 500 MHz

All 36 ribose proton resonances and most of the base proton resonances of the hexanucleoside pentaphosphate AUAUAU have been assigned unequivocally using 2D J-resolved spectroscopy, spin echo correlated spectroscopy (SECSY) and 2D NOE spectroscopy (NOESY). The NMR parameters of AUAUAU are compared with those of smaller fragments that contain methylated adenine bases: m62AU, m62AUm62A, m62AUm62AU and m62AUm62AUm62A. Previous studies on this series of compounds have shown that in all these cases purine-pyrimidine-purine sequences prefer to adopt a mixture of states which have as common feature that the interior pyrimidine residues are bulged out, whereas the purine residues stack upon each other. Chemical shift data, proton-proton coupling constants, as well as the observation of imino-proton resonances for AUAUAU show unambiguously that upon lowering the temperature the high-temperature "bulged out" situation reverts to a normal A-RNA-like double helix.

A two-dimensional NMR study of the solution structure of a DNA dodecamer comprising the concensus sequence for the specific DNA-binding sites of the glucocorticoid receptor protein

A two-dimensional 500-MHz 1H-NMR study on the non-self-complementary double-stranded DNA dodecamer 5'd(C-C-A-G-A-A-C-A-G-T-G-G)5'd(C-C-A-C-T-G-T-T-C-T-G-G), is presented. This oligonucleotide contains the consensus octanucleotide sequence 5'd(A-G-A-A-C-A-G-T) for the specific DNA-binding sites of the glucocorticoid receptor protein [Payvar, F. et al. (1984) Cell 35, 381-392]. Using a combination of two-dimensional pure phase absorption nuclear Overhauser enhancement (NOESY) and homonuclear J-correlated (COSY) spectroscopy all non-exchangeable base (with the exception fo the adenine H2 protons), methyl and deoxyribose H1', H2', H2", H3' and H4' resonances are assigned unambiguously using a sequential resonance assignment strategy. From the relative intensities of the cross peaks in the pure phase absorption NOESY spectra at two mixing times it is shown that the dodecamer adopts a B-type conformation in solution.

Comparison of the conformation of poly(dI-dC) with poly(dI-dbr5C) and the B and Z forms of poly(dG-dC). One- and two-dimensional NMR studies

One- and two-dimensional nuclear Overhauser effects (2D NOE) have been used to compare the conformational properties of 60-80 base pair long duplexes of the synthetic DNA polymer poly(dI-dC) with those of poly(dI-dbr5C) and poly(dG-dC) in the B and Z conformations. Cross peaks in the 2D NOE spectra arising from proton-proton dipolar interactions which are more or less independent of the DNA conformation are used to assign the spectra of these molecules. Other cross peaks are sensitive to the conformational details, and these are used to make deductions about the average conformation in solution. The proton-proton interactions that give rise to the cross peaks in the 2D NOE spectrum of poly(dI-dC) are indicative of a B family conformation and rule out the possibility of some alternative conformations, including A, Z, alternating B, and left-handed B-DNA. The spectra are similar to those obtained from B-form poly(dI-dbr5C) and poly(dG-dC) but different from Z-form poly(dG-dC). Taken together, these results indicate that the solution conformation of poly(dI-dC) is not unusual but more closely resembles that of other B-form DNAs.

Sequence-dependent structural variation in single-helical DNA. Proton NMR studies of d(T-A-T-A) and d(A-T-A-T) in aqueous solution

The two deoxyribotetranucleoside triphosphates d(T-A-T-A) and d(A-T-A-T) were investigated in aqueous solution by one- and two-dimensional proton NMR at 300 and 500 MHz. It is demonstrated that both compounds occur predominantly in the single-helical form. Accurate coupling constants are obtained by computer simulation of several 500-MHz spectra. The data are interpreted in terms of N and S pseudorotational ranges. The geometry of the major S-type conformers displays a clear sequence dependence, as expressed by variation of the endocyclic backbone angle delta (C5'-C4'-C3'-O3'). A simple sum rule is proposed to predict delta variation in single-helical DNA fragments. Comparisons are made with other sequence-dependent geometries as observed in a double-helical B-DNA fragment in the crystalline state. Furthermore, one- and two-dimensional nuclear Overhauser effect (NOE) spectroscopy was carried out on d(T-A-T-A). An inventory is made of the observed intra- and inter-residue NOEs. The NOE data confirm the presence of a highly stacked single-helical conformation of d(T-A-T-A) in solution. No indications are found for the formation of a bulge-out structure as observed for analogous alternating purine-pyrimidine oligoribonucleotides.

Discrimination between A-type and B-type conformations of double helical nucleic acid fragments in solution by means of two-dimensional nuclear Overhauser experiments

The solution structure of two double helical nucleic acid fragments, viz, r(CGCGCG) and d(CGCGCG), was probed by means of two-dimensional nuclear Overhauser effect spectroscopy. The two compounds were selected as models for the A-type and B-type double helical conformations, respectively, and it is shown that for each of the two model compounds the intensities of the NOE cross peaks between base- and H2' (deoxy)ribose proteins are qualitatively in correspondence with the relative NOE intensities expected on basis of the supposed duplex conformations. Thus our results indicate that NOE-data can be used to differentiate between A-and B-type double helical conformations in solution. Coupling constant data show that, except for G(6), all ribose rings in r(CGCGCG) adopt pure N (C3'-endo) conformations thereby manifesting that this molecule takes up a regular A-type double helical conformation in solution. In contrast, the deoxyribose rings in d(CGCGCG) retain conformational freedom in the duplex state, albeit that the N/S-equilibrium is biased towards the S (C2'-endo) sugar conformation. This finding indicates that in solution the B-DNA backbone is highly dynamic.

Conformational analysis of r(CGCGCG) in aqueous solution: an A-type double helical conformation studied by two-dimensional nuclear Overhauser effect spectroscopy

The conformation of the hexanucleoside pentaphosphate r( CGCGCG ) in aqueous solution was studied by circular dichroism, 1H- and 31P-NMR spectroscopy. The base-, H1'- and H2'-proton resonances were assigned by means of 2D-NOE spectroscopy. The base- and H1'-proton chemical shifts were studied as a function of temperature. Proton-proton distances are computed in A- and A'-RNA as well as in A-, B- and Z-DNA. A qualitative interpretation of the observed 2D-NOE intensities shows that r( CGCGCG ) adopts a regular A-type double helical conformation under our experimental conditions. The CD- and 31P-NMR experiments described in this paper are in agreement with this structure both under low- and high-salt conditions.

Complete assignment of the non-exchangeable proton nmr resonances of [d-(GGAATTCC)]2 using two-dimensional nuclear overhauser effect spectra

Proton two-dimensional nuclear Overhauser effect (2D NOE) spectra have been obtained for [d-(GGAATTCC)]2 at a series of mixing times. By performing the experiment at 500 MHz and obtaining pure absorption phase spectra, sufficient resolution was achieved to be able to assign all seventy of the non-exchangeable proton resonances in the self-complementary octamer duplex, including the H3' resonances which overlap with the solvent peak.