Conformational analysis of a DNA triplet in aqueous solution. Thymidylyl-(3'-5')-thymidylyl-(3'-5')-2'-deoxyadenosine, d(T-T-A), studied by 1H nuclear magnetic resonance at 360 MHz

NMR studies of DNA single strands and DNA:RNA hybrids with and without 1-propynylation at C5 of oligopyrimidines

The 1-propynylation at C5 of consecutive pyrimidines in DNA can enhance DNA:RNA hybrid stability at 37 degrees C by over 1 kcal/mol of substitution [Barnes, T. W., III; Turner, D. H. J. Am. Chem. Soc.2001, 123, 4107-4118]. To provide information on the structural consequences of propynylation, two-dimensional NMR spectroscopy was used to study the structures of several oligonucleotides. Intraresidue nuclear Overhauser effect spectroscopy cross peaks were observed at 30 degrees C and a 200 ms mixing time in the H6-H1' region for 5'(dC(P)C(P)U(P)C(P)C(P)U(P)U(P)) (ssPrODN) but not for 5'(dCCUCCUU) (ssODN), suggesting preorganization of the propynylated single strand. NMR structures of the duplexes 5'(dC(P)C(P)U(P)C(P)C(P)U(P)U(P))3':3'(rGAGGAGGAAAU)5' (PrODN:RNA), 5'(dCC(P)U(P)C(P)C(P)U(P)U(P))3':3'(rGAGGAGGAAAU)5' (sPrODN1:RNA), and 5'(dCCUCCUU)3':3'(rGAGGAGGAAAU)5' (ODN:RNA) indicate that their global structures are almost identical. The NMR data, however, suggest that the 5'-end of sPrODN1:RNA is more dynamic than that of PrODN:RNA. In the propynylated duplexes, the propyne group stacks on the aromatic ring of the 5'-base and extends into the major groove. The results suggest that the increased stability of the propynylated duplexes is caused by preorganization of the propynylated single strand and different interactions in the double strand. The propynyl group provides volume exclusion, enhanced stacking, and possibly different solvation.

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.

Conformational analysis of the single-helical DNA fragment d(T-A-A-T) in aqueous solution. The combined use of NMR proton chemical shifts and coupling constants obtained at 300 MHz and 500 MHz

Proton NMR studies at 300 MHz and 500 MHz were carried out on the tetranucleoside trisphosphate d(T-A-A-T). The thermodynamics of the three stacking interactions, derived from chemical shift versus temperature profiles, were used to extrapolate the observed coupling constants, measured at a range of temperatures, to values appropriate to the fully stacked forms of the molecule. The data were interpreted in terms of N and S pseudorotational ranges [ Altona , C. and Sundaralingham , M. (1972) J. Am. Chem. Soc. 94, 8205-8212]. It is shown that the stacked state of the molecule cannot be described by one conformer, but consists of one major structure (60%) in which all sugar rings have S-type geometry and another structure (30%) in which residue dT(4) has an N-type sugar. The remainder of the stacked states consists of one or more conformers with two or three sugar residues in the N-type pseudorotational range. Detailed geometrical models are proposed for the major stacked conformers encountered in aqueous solution.

A nuclear magnetic resonance study of the ribotrinucleoside diphophate UpUpC

500 MHz 1H, 67.89 MHz 13C and 80.97 MHz 31P-NMR studies are reported on the ribotrinucleoside diphosphate UpUpC, the triplet codon corresponding to the amino acid phenylalanine. Complete spectral assignments are given and conformational parameters for the backbone and the furanose rings are determined. All three nucleotide units show a near-balance for the N/S equilibrium with a slight preference for the N-type ribose (approximately 60%). The backbone conformation around the C3'-03' bonds show a preference for the trans domain, while the orientation around the C5'-05' bonds is predominantly trans.

Conformational analysis of the single-stranded ribonucleic acid A-A-C-C. A one-dimensional and two-dimensional proton NMR study at 500 MHz

Proton NMR studies at 300 MHz and 500 MHz are reported on the ribotetranucleotide A-A-C-C. The complete 1H-NMR spectral assignment at 20 degrees C is given. Two-dimensional NMR was used to elucidate spin multiplets in 'crowded' regions. Nuclear Overhauser enhancement (NOE) experiments made an unambiguous spectral assignment possible and yielded information on interproton distances. The N/S equilibrium of the riboses and the rotamer populations around some backbone torsion angles are presented. A large preference for N-type ribose and gamma+ and beta t backbone torsions is observed, in particular in the central A-C unit of A-A-C-C. Information on distances between protons of different nucleotide units, obtained from NOE experiments, constitutes a probe of base-base stacking. It is concluded that A-A-C-C offers a good model for RNA single-strand conformation.

Influence of the 2'-hydroxyl group and of 6-N-methylation on the conformation of adenine dinucleoside monophosphates in solution. A nuclear magnetic resonance and circular dichroism study

Proton NMR studies at 360 MHz are reported on the adenine dinucleoside monophosphates N6-dimethyladenyly(3'-5')-N6-dimethyladenosine (m(6)(2)Apm(6)(2)A), ApA, rApdA, dAprA and on the methyl phosphate esters of the monomers m(6)(2)Ap, pm(6)(2)A, Ap and pA. Complete 1H-NMR spectral assignments are given. The dimers were also investigated by means of circular dichroism to obtain accurate thermodynamic parameters of the stacking equilibrium. With the aid of the thermodynamic data NMR coupling constants are extrapolated to values appropriate to the stacked conformers. A modernized version of pseudorotation analysis is used to delineate the conformational behaviour of the ribose and 2'-deoxyribose rings. It is shown that the unmethylated dimers can be arranged in two groups (dApdA/dAprA vs ApA/rApdA) according to their melting temperatures. ApA and the fully N6-methylated dimer m(6)(2)Apm(6)(2)A prefer to adopt the classical right-handed N-N stacked conformation. Both dimers with a 2'-deoxyribose ring at the 5'-OH end (dApdA and dAprA) behave similarly and occur in solution as a 75:25 mixture of S-S and S-N stacked states. The fully stacked hybrid dimer rApdA displays an unexpectedly large amount of S conformers (greater than 40%) in both sugar rings. This finding is rationalized by the postulation of a right-handed helical S-S stacked state on the basis of NMR and circular dichroic data.

Complete assignment and conformational analysis of a deoxyribotetranucleotide. d(TAAT). A 360 and 500 Mhz NMR study

A proton NMR study at 360 MHz and 500 MHz was carried out on the tetranucleoside triphosphate d(TAAT) at a temperature of 27 degrees C. Extensive decoupling experiments allowed a complete and unambiguous spectral assignment. The data are interpreted in terms of the N and S deoxyribose pseudorotational ranges. From the observed proton-proton coupling constants it is calculated that (a) the populations of deoxyribose S-form are as follows: dT(1)-, 85%; -dA(2)-, 97%; -dA(3)-, 81%; -dT(4), 64%; and (b) the g+ populations (backbone notation) along the exocyclic C4'-C5' bond in -dA(2)-, -dA(3)- and dT(4) are 82%, 86% and 78%, respectively. From these values, combined with chemical shift considerations, it is concluded that the central -dA(2)-dA(3)- part of the molecule occurs preferentially as a mixture of two right-handed single-helical conformations, denoted S-S and S-N, in a ratio of approximately 8 : 2. This situation closely mimics that found for the 3'-end of d(A-A-A) (Olsthoorn, C.S.M., Bostelaar, L.J., Van Boom, J. H. and Altona, C. (1980) Eur. J. Biochem 112, 95--110). Similarly, the conformational behavior of the dT(1)-dA(2)- and -dA(3)-dT(4) terminals appears roughly identical to that displayed by the corresponding dinucleoside monophosphates. The molecules as a whole does not show signs of cooperatively of stacking.

Circular dichroism study of stacking properties of oligodeoxyadenylates and polydeoxyadenylate. A three-state conformational model

The temperature dependence of the circular dichroism (CD) spectra of a series of deoxyadenylates (dA)n, n = 2, 3, 6, 9, 12, infinity, in aqueous solution was studied. The data were interpreted on the basis of a new conformational model for the stacked state suggested by our previous proton NMR studies on (dA)2 and (dA)3 [C. S. M. Olsthoorn, L. J. Bostelaar, J. H. van Boom & C. Altona (1980) Eur. J. biochem. 112, 95-110]. In this model the stacked regions of the single-stranded oligomers consist of residues taking up a geometry resembling that of the B-DNA genus of structures (all sugars S or C2'-endo) except those residues at the 3' end that do not 'feel' a following stacking interaction. The deoxyribose rings in the latter residues retain (or regain when melting out removes a stacking interaction somewhere along the chain) the conformational freedom (S in equilibrium N, N = C3'-endo) that these rings possess in the monomers 2'-deoxyadenosine 5'-methylphosphate or in 2'-deoxyadenosine 3',5'-bis(methylphosphate), as the case may be. It is shown that this model allows (a) construction of the CD spectra of (dA)n, n = 3, 6, 9, 12, from those of the dimer and the polymer; (b) the separation of the weak CD displayed by the regular S-S stacking mode and the far stronger CD exhibited by the 3'-end S-N stacking (the latter CD resembles that of the A-DNA genus of structures); (c) delineation of the thermodynamics of stacking. The melting temperature remains constant and independent of chain length (about 50 degrees C) whereas delta H degrees and delta S degrees show a slight increase in absolute values on increasing n from 2 to infinity owing to small cooperativity effects. Near 0 degrees C the dimer occurs for about 90% in the stacked form, the oligomers attain even higher conformational purities. It is suggested that premelting phenomena observed in the CD spectra of double-helical DNAs may also involve local transitions from the normal B-like ----S-S-s---- stacking mode to an A-like ----S-S-N---- stacking geometry.

Conformational analysis of a modified ribotetranucleoside triphosphate: m6(2)A-U-m6(2)A-U studied in aqueous solution by nuclear magnetic resonance at 500 MHz

The complete and unequivocal assignment of the 24 ribose proton signals of m6(2)A(1)-U(2)-m6(2)(3)-U(4) by means of 500 MHz NMR spectroscopy at 17 degrees C is given. this assignment is based on scrupulous decoupling experiments carries out at various temperatures. Analysis of the observed chemical shifts and coupling constants of the tetramer shows that the two fragments -m6(2)A(3)-U(4) comprising the 3'-end occur mainly in the classical right-handed stack conformation, whereas the 5'-end the -U(2)- residue appears bulged out in favour of a less well-defined stacking interaction between the bases m6(2)A(1)-and -m6(2)A(3)-. Conformational populations about each of the torsional degrees of freedom along the backbone are discussed. A modernized version of pseudorotation analysis is used to delineate the conformational behaviour of the four ribose rings.

Conformational characteristics of the trinucleoside diphosphate dApdApdA and its constituents from nuclear magnetic resonance and circular dichroism studies. Extrapolation to the stacked conformers

Proton NMR studies at 360 MHz were carried out on the trinucleoside diphosphate dApdApdA, the dinucleoside monophosphate dApdA and the methylphosphate esters of the monomers pdA, pdAp and dAp. The compounds were also investigated by means of circular dichroism at varying temperatures. Complete NMR spectral assignments are given. The thermodynamics of stacking derived from the circular dichroic spectra was used to extrapolate the observed coupling constants, measured at a range of temperatures, to values appropriate to the pure stacked states of the dimer and the trimer. The data were interpreted in terms of the N and S deoxyribose pseudorotational ranges [Altona, C. and Sundaralingam, M. (1972) J. Am. Chem. Soc. 94, 8205--8212] and it is shown that the right-handed single helix of the trimer occurs in two distinct forms: the major one corresponds to a B-DNA-like structure, S-S-S; the minor one (30%) has the sugar rings in a hitherto unsuspected S-S-N conformational sequence. The dimer behaves quite similarly, a mixture of 70% S-S and 30% S-N stacks being indicated. The detailed geometry of teh S-type sugar rings is not invariable but appears to undergo a slight shift when another base stacks on top of a given nucleotide unit. The backbone angles of the fully stacked B-DNA-like single helix in solution are (starting the notation at P) beta = 187 degrees, gamma = 50 degrees, delta = 138 degrees, epsilon = 186 degrees.

Loopstructures in synthetic oligodeoxynucleotides

A comparative nuclear magnetic resonance study of the hydrogen-bonded imino protons in a series of synthetic DNA fragments is presented. The fragments ATCCTA(Tn)TAGGAT are in principle capable of forming either a self-complementary hairpin loop structure (monomer form) or an interior loop structure (dimeric form). It has been shown, that for n = 1 only the dimer structure is present in aqueous solution, whereas the exclusive existence of the hairpin loop structure is indicated for n = 3, 4 & 5. Surprisingly, for n = 2 two different structures appear to be present in solution. Concentration studies show that both monomers and dimers exist side by side in this case. Hairpins as well as interior loops form extra "melting sites" in addition to the wellknown fraying phenomenon at the terminus of the double helix.

Local destabilisation of a DNA double helix by a T--T wobble pair

Nuclear magnetic resonance is a technique which permits direct observation of the Waton--Click hydrogen-bonded ring imino protons (guanine N1H and thymine N3H). As the formation and disruption of hydrogen bonds of double-helical RNA and DNA structures are key events during various biological processes, NMR thus provides a useful tool for studying the fluctuational mobility of the individual base pairs. Indeed, several NMR studies of oligo- and polynucleotides have been carried out to probe the structure and dynamics of nucleic acids in solution (for a review see ref. 1). The present study constitutes the first part of our attempt to assess the influence of non-complementary base pairs on the stability of nucleic acid double helices. We report the spectral assignment and temperature-dependent NMR profiles of the hydrogen-bonded imino protons of the two DNA fragments shown in Fig. 1. The assignment is based solely on experimental grounds using the principle of chemical modification. It will be demonstrated that the introduction of a non-complementary (wobble) base pair in a DNA duplex introduces an extra melting site in addition to the sequential melting which starts with the terminal base pairs in the double helix structure.