S.S. Wijmenga, B N.M. van Buuren/Progress in Nuclear Magnetic Resonance Spectroscopy 32(1998)287-387 293 Overview of short distances per residue L. constant 4. base-sugar 632 3000 0841 Inter-nucleotide 1. non-exchangeable I sequential sugar-base 2. sequential base-base 3. sequential sugar-sugar I. within base pair M: measurable distances <5 to 6 A[62]:A: tely conformation independent distances; B: distances that are conformation in within approximately +0.2 A; C: 'structural distances', i.e. confomation dependent distances with variation >0.2 A(see text):C:NMR accessible structural' distances: D: NMR accessible 'structural distances that are different in A- and B-helices. The intra-nucleotide distances: 1. The constant distances d 2: 2), d,(5, 5), dA(6, 5)and d(6, M); 2. the sugar-to-sugar distances, dA1'-4: 1-4); they all fall into group B, except for d, (2: 4)and d,(1, 4), which fall into groups C and C, while group d only contains d( 2: 43. the distances d(2-4, 5/ 5); group B contains the distances dA( 2/2.575); group C contains d(374, 575): none of them fall into groups C or D, 4. sugar-to-base distances d,(6/8: 1-5); they are subdivided according to: group B, d,(6/8: 4), group C, d( 6/8; 1-3, 575), group C, excluded d 6/8; 575), group D, dA6/8, 1-3). The distances d( S/M: 1-5)are not taken into account since they are larger than 5 A[62]. The inter-nucleotide distance (considered are the distances to and from Cytosine in a GCG trinucleotide sequence (see Fig. 2). I. Non-exchangeable protons: 1. sequential sugar-to-base distances, d(1-3; 8)and ds(1-3: 6/5); all of them fall into categories C, C and D; 2. base-to-base distances, ds(6/5; 8)and d, (8: 6/ 5); all of them fall into categories C, C and D; 3. sequential sugar-to-sugar distances, ds(1-2, 4, 5), ds(5",1-2,4), ds(2: 3), ds(3, 2), ds(2, 2)and ds (2, 2); all of them are conformation dependent (category C), but only dx2: 3)and d33, 2) are easily accessible tween A-type and B-type helices. Il. Inter-nucleotide distances involving exchangeable protons: 1. The distances within a bas d(NH2: NH); this distance depends on conformation(category C), is NMR accessible (C ), but does not differ between A-type helices; 2. the sequential distances are ds(NH2: NH)and ds NH; NH2); they both fall into category C and C, but not into category D: strand distances are d(NH2: NH2)s, and d(NH2: NH2)3, they fall into category C, Cand D(however, note that the NH2 resonances of G may be broadened making them inaccessible for NMR) ( 5-6 A)and categorized them into two main dependence on conformation is indicated(a to D). groups, intra-nucleotide and inter-nucleotide dis- with category A referring to conformation indepen- tances, with further subdivision to reflect more dent distances, category B to distances that can vary detailed conformational characteristics. The inter- by less than +0. 2 A, and category C to structural nucleotide distances fall into the two broad groups distances, i.e. distances that convey structural infor- of sequential and cross-strand distances involving mation since they can vary by more than +0.2 A non-exchanging protons and exchanging protons, Thestructural distances, category C, are subdivided respectively. The sequential distances involving into two further categories to indicate their usefulness non-exchanging protons are again subdivided into category C contains those structuraldistances that sugar-to-sugar distances, base-to-base distances and are reasonably well accessible by NMR, and category ugar-to-base distances. Within each category their D refers to NMR accessiblestructural'distances that( , 5–6 A˚ ) and categorized them into two main groups, intra-nucleotide and inter-nucleotide dis￾tances, with further subdivision to reflect more detailed conformational characteristics. The inter￾nucleotide distances fall into the two broad groups of sequential and cross-strand distances involving non-exchanging protons and exchanging protons, respectively. The sequential distances involving non-exchanging protons are again subdivided into sugar-to-sugar distances, base-to-base distances and sugar-to-base distances. Within each category their dependence on conformation is indicated (A to D), with category A referring to conformation indepen￾dent distances, category B to distances that can vary by less than 6 0.2 A˚ , and category C to ‘structural’ distances, i.e. distances that convey structural infor￾mation since they can vary by more than 6 0.2 A˚ . The ‘structural’ distances, category C, are subdivided into two further categories to indicate their usefulness; category C9 contains those ‘structural’ distances that are reasonably well accessible by NMR, and category D refers to NMR accessible ‘structural’ distances that Table 1 Overview of short distances per residue Type % M A B C C9 D Intra-nucleotide 1. constant 5 3 3 0 0 0 0 2. sugar–sugar 16 10 0 8 2 2 1 3. sugar–59/50 13 8 0 4 4 0 0 4. base–sugar 12 7 0 1 6 4 4 sum 46 28 3 13 12 6 5 Inter-nucleotide I. non-exchangeable 1. sequential sugar–base 20 12 0 0 12 12 12 2. sequential base–base 6 4 0 0 4 4 0 3. sequential sugar–sugar 20 12 0 0 12 2 2 4. cross-strand (3%) (2) 0 0 (2) (2) (2) sum 46 28 0 0 28 18 14 II. exchangeable (imino/amino) 1. within base pair 2 1 0 0 1 1 0 2. sequential 3 2 0 0 2 2 0 3. cross-strand 3 2 0 0 2 2 2 sum 8 5 0 0 5 5 2 Total 100 61 3 13 45 29 20 % 100 5 21 74 48 33 M: measurable distances , 5 to 6 A˚ [62]; A: completely conformation independent distances; B: distances that are conformation independent within approximately 6 0.2 A˚ ; C: ‘structural distances’, i.e. conformation dependent distances with variation . 0.2 A˚ (see text); C9: NMR accessible ‘structural’ distances; D: NMR accessible ‘structural’ distances that are different in A- and B-helices. The intra-nucleotide distances: 1. The constant distances di(29;20), di(59;50), di(6;5) and di(6;M); 2. the sugar-to-sugar distances, di(19-49;19-49); they all fall into group B, except for di(20;49) and di(19;49), which fall into groups C and C9, while group D only contains di(20;49); 3. the distances di(29-49;59/ 50); group B contains the distances di(29/20;59/50); group C contains di(39/49;59/50); none of them fall into groups C9 or D; 4. sugar-to-base distances di(6/8;19-50); they are subdivided according to: group B, di(6/8;49), group C, di(6/8;19-39, 59/50), group C9, excluded di(6/8;59/50), group D, di(6/8;19-39). The distances di(5/M;19-50) are not taken into account since they are larger than 5 A˚ [62]. The inter-nucleotide distances (considered are the distances to and from Cytosine in a GCG trinucleotide sequence (see Fig. 2). I. Non-exchangeable protons: 1. sequential sugar-to-base distances, ds(19-39;8) and ds(19-39;6/5); all of them fall into categories C, C9 and D; 2. base-to-base distances, ds(6/5;8) and ds(8;6/ 5); all of them fall into categories C, C9 and D; 3. sequential sugar-to-sugar distances, ds(19-20,49;50), ds(50;19-20,49), ds(29;39), ds(39;29), ds(29;20) and ds(29;20); all of them are conformation dependent (category C), but only ds(29;39) and ds(39;29) are easily accessible and differ between A-type and B-type helices. II. Inter-nucleotide distances involving exchangeable protons: 1. The distances within a base pair are dc(NH2; NH); this distance depends on conformation (category C), is NMR accessible (C9), but does not differ between A-type and B-type helices; 2. the sequential distances are ds(NH2;NH) and ds(NH;NH2); they both fall into category C and C9, but not into category D; 2. the cross￾strand distances are dc(NH2;NH2) 59 and dc(NH2;NH2) 39; they fall into category C, C9 and D (however, note that the NH2 resonances of G may be broadened making them inaccessible for NMR). S.S. Wijmenga, B.N.M. van Buuren/Progress in Nuclear Magnetic Resonance Spectroscopy 32 (1998) 287–387 293