S.S. Wimenga, B NM van Buuren/Progress in Nuclear Magnetic Resonance Spectroscopy 32(1998)287-387 295 and the x torsion angle. The distance d(4: 6/8) reproduced from Wijmenga et al. [62] gives the does not convey useful structural information sequential distances, ds(; r) cross-strand since its dependence on these parameters is weak distances, dc r)and d(l; r), found in A-DNA [62]. The distances di (2/2/3: 6/8)are on the other B-DNA and rna helices hand quite useful. Each of these distances defines The cross-strand distances, dcdl, r) and desc; r). the x torsion angle quite well, because of their involving exchangeable protons are indicative of quite strong dependence on the torsion angle x base pair formation. The sequential distances involv [62]. Their dependence on the sugar puckering is ing either exchanging or non-exchanging protons are rather weak, in particular for the distances di(2/ indicative of base stacking. However, only a limited 2; 6/8)[62]. Despite this weak dependence on the number depend on the type of helix conformation. In sugar puckering, a concerted use of d(2273: 6/8) both A- and B-type helices, short base-to-base dis- makes it possible to determine the percentage N- tances, d, (6/8/5/M: 6/8/5/M), are present, depending type or S-type pucker, but to achieve a reasonable on the sequence. Similarly, all distances involving level of precision requires that the uncertainty in exchanging pro otons are very sin their values should be less than +0.5A [62]. w B-type helices. The differences occur for the cross- finally note that Lane and co-workers[64] have shown strand and sequential distances involving H2 protons the improved reliability of sugar pucker determination d&(2; 1/2)3 and ds(2; 1), the sequential sugar-to- using these distances together with J-couplings base distances, ds(2/273: 6/8/5), and for a number The H5/H5"to base proton distances, di(/5: 6/8) of stances,d(2n2”;5 depend on three torsion angles, y, 8 and x. Their 5),d, (2 3),d, (22)and d(1: 5). Short cross- dependence on the sugar pucker(o), and on th strand, as well as sequential H2 to HI'distances glycosidic torsion angle (x) in the usual anti are present in A-type helices, but absent in B-type domain (180-240)is weak, but they depen helices. Short sequential H2 to H6/8 distances and quite strongly on the y torsion angle. In particular long h2" to H6/8 distances are seen in A-helices. ;6/8) while in B-helices the reverse is found. The sugar- to 4.5 A), while for y' the distance d,(5: 6/8) to-sugar distances show the following pattern: Short becomes short(2.5 to 2.9 A). As has been s o8) sequential H2/H2"to H5 /5"distances in A-helices, ith uncertainties in the distance estimates in the while in B-helices these distances are long, rather order of +0.2 A, they determine quite well the long, but measurable, sequential H2 to H3 distances torsion angle y[62]. The distances d (5 /5"; 6/8) In A-helices, which are over 7 A and thus not measur- can be quite useful in NOESY spectra of dNa able in B-helices; finally, long(>7 A)sequential H2 since the related NoE cross pea to h2 and hi to h5" distances in a-helices. which in a crowded spectral region. This does not hold are relatively short in B-helices. While the distances true for RNa where these cross peaks overlap with involving H2 and the h2 /2"to base distances are he other H6/8 to H2 /3'NOE cross peaks. On the quite accessible from NMR spectra, the sugar-to- other hand, the distances d;(3/4; 5/5) all sugar distances are difficult to determine since the relate to cross peaks in crowded spectral sugar proton resonances reside in quite crowded regions for both DNA and RNA and are thus spectral regions difficult to establish 4.4. Derivation of distances from NOESY spectra and structure characterization using distances 4.3. Overview of structurally important sequential and cross-strand distances We will discuss here the three aspects of NMr accessible distances that are of particular relevance Helical conformations form an important part of for structure determination. First, how precisely can nucleic acid structures. We therefore present an over- distances be derived from NOE data? Secondly, how iew of the distances in the two most commonly does this on affect the precision of the deter- found helix types, A-helices and B-helices. Fig. 2, mined structure? Thirdly, how does the spread andand the x torsion angle. The distance di(49;6/8) does not convey useful structural information since its dependence on these parameters is weak [62]. The distances di(29/20/39;6/8) are on the other hand quite useful. Each of these distances defines the x torsion angle quite well, because of their quite strong dependence on the torsion angle x [62]. Their dependence on the sugar puckering is rather weak, in particular for the distances di(29/ 20;6/8) [62]. Despite this weak dependence on the sugar puckering, a concerted use of di(29/20/39;6/8) makes it possible to determine the percentage N￾type or S-type pucker, but to achieve a reasonable level of precision requires that the uncertainty in their values should be less than 6 0.5 A˚ [62]. We finally note that Lane and co-workers [64] have shown the improved reliability of sugar pucker determination using these distances together with J-couplings. The H59/H50 to base proton distances, di (59/50;6/8), depend on three torsion angles, g, d and x. Their dependence on the sugar pucker (d), and on the glycosidic torsion angle (x) in the usual anti domain (180–2408) is weak, but they depend quite strongly on the g torsion angle. In particular, for gþ both di(59; 6/8) and di(50;6/8) are long (3.7 to 4.5 A˚ ), while for gt the distance di(50;6/8) becomes short (2.5 to 2.9 A˚ ). As has been shown, with uncertainties in the distance estimates in the order of 6 0.2 A˚ , they determine quite well the torsion angle g [62]. The distances di(59/50;6/8) can be quite useful in NOESY spectra of DNA, since the related NOE cross peaks do not reside in a crowded spectral region. This does not hold true for RNA where these cross peaks overlap with the other H6/8 to H29/39 NOE cross peaks. On the other hand, the distances di(39/49;59/50) all relate to cross peaks in crowded spectral regions for both DNA and RNA and are thus difficult to establish. 4.3. Overview of structurally important sequential and cross-strand distances Helical conformations form an important part of nucleic acid structures. We therefore present an over￾view of the distances in the two most commonly found helix types, A-helices and B-helices. Fig. 2, reproduced from Wijmenga et al. [62], gives the sequential distances, ds(l;r), and cross-strand distances, dci(l;r) and dcs(l;r), found in A-DNA, B-DNA and RNA helices. The cross-strand distances, dci(l;r) and dcs(l;r), involving exchangeable protons are indicative of base pair formation. The sequential distances involv￾ing either exchanging or non-exchanging protons are indicative of base stacking. However, only a limited number depend on the type of helix conformation. In both A- and B-type helices, short base-to-base dis￾tances, ds(6/8/5/M;6/8/5/M), are present, depending on the sequence. Similarly, all distances involving exchanging protons are very similar in A- and B-type helices. The differences occur for the cross￾strand and sequential distances involving H2 protons, dcs(2;19/2)39 and ds(2;19), the sequential sugar-to￾base distances, ds(29/20/39;6/8/5), and for a number of sequential sugar-to-sugar distances, ds(29/20;59/ 50), ds(29;39), ds(20;20) and ds(19;50). Short cross￾strand, as well as sequential H2 to H19 distances, are present in A-type helices, but absent in B-type helices. Short sequential H29 to H6/8 distances and long H20 to H6/8 distances are seen in A-helices, while in B-helices the reverse is found. The sugar￾to-sugar distances show the following pattern: Short sequential H29/H20 to H59/50 distances in A-helices, while in B-helices these distances are long; rather long, but measurable, sequential H29 to H39 distances in A-helices, which are over 7 A˚ and thus not measur￾able in B-helices; finally, long ( . 7 A˚ ) sequential H20 to H29 and H19 to H50 distances in A-helices, which are relatively short in B-helices. While the distances involving H2 and the H29/20 to base distances are quite accessible from NMR spectra, the sugar-to￾sugar distances are difficult to determine since the sugar proton resonances reside in quite crowded spectral regions. 4.4. Derivation of distances from NOESY spectra and structure characterization using distances We will discuss here the three aspects of NMR accessible distances that are of particular relevance for structure determination. First, how precisely can distances be derived from NOE data? Secondly, how does this precision affect the precision of the deter￾mined structure? Thirdly, how does the spread and S.S. Wijmenga, B.N.M. van Buuren/Progress in Nuclear Magnetic Resonance Spectroscopy 32 (1998) 287–387 295