Polymorphism and conformational flexibility of DNA: right and left handed duplexes Goutam Gupta, Manju Bansal and V. Sasisekharan Molecular Biophysics Unit, Indian Institute q[Science, Bangalore-560012, India (Received 4 February 1980; revised 4 March 1980) L~'fi handed duplexes are shown to be in agreement with the X-ray intensity data o/A-, B- and D-[orms qf DN A. The structures are stereochemically sati,~Jactory because they were ohtainedJbllowing a stereochemical guideline derived.JJ~om theory and single crystal structure data q[ nucleic acid components. The same stereochemical guideline also led to right handed duplexes jbr B- and D-[~rms qf D N A which hat~e stereochemically preJerred coJ!J~rmation and hence are superior to those given by Arnott and coworkers a o.l l Introduction Conformational flexibility of DNA plays an important role in deciding its three dimensional structure. Exploiting the conformational flexibility inherent in the molecule, both right and left handed DNA duplexes were found to be stereochemically possible for various polymorphous forms of DNA 1'1. It was also pointed out that right and left handed segments can be alternately joined to arrive at an alternative model of DNA 2--6. The model obtained, involves two types of stacking arrangementsT: (i) normal stacking which includes right stacking in the right helical segment and left stacking in the left helical segment and (ii) inverted stacking in the bend region where right and left helical segments are joined together. It was shown earlier that both the stacking arrangements are energetically stable and are observed in single crystals of bases, nucleosides and nucleotides 8. Because the alternative model has energetically favourable normal and inverted stacking arrangements, the possibility of double helical structures with both stacking arrangements was exam- ined for various polymorphous forms of DNA. It turned out that both right and left handed double helical structures with normal or inverted stacking are possible. In this paper, DNA duplexes which are stacked normally are investigated. It is shown that both right and left handed duplexes are possible for three polymorphous forms of DNA viz: A-form 01 = 1I, 11 =2.56 A): B-form (n = 10, h=3.40 A) and D-form 01=8, h =3.03 A) ~- 11 The refined models of A-, B- and D-forms of DNA reported in literature, are all right handed duplexes ~° ~-~. Fuller et al. 9 ruled out the possibility of left handed duplexes for A- and B-forms of DNA. A left handed duplex was found to be possible for B-DNA, but not for A- DNA. Hence, it was argued that a smooth A~B trans- sition demands that both A- and B-DNA need to be right handed duplexes. Mitsui et al. ~s proposed a left handed duplex model for poly(dI-dC).poly(dC ~dI) which gave an X-ray pattern very similar to the D-form of DNA observed for poly(dA~dT).poly(dT~:lA) ~. But such a model was discarded by Arnott et al. ~ because it had an unusual sugar puckering. It was also pointed out that the 0141 8130 80060368 13502.00 © 1980 IPC Business Press 368 Int. J. Biol. Macromol., 1980, Vol 2, December left helical model could not explain smooth B,~-D tran- sition because B-DNA was considered to be right handed. However, stereochemically even the right handed models of B- and D-DNA are not satisfactory (see the next section). This prompted us to make a systematic study of both right and left handed duplexes for different polymor- phous forms of DNA. Our approach to the problem consisted of two parts. Firstly, we examined whether by exploiting the conformational flexibility of DNA, it was possible to obtain a stereochemical guideline for mole- cular model building, Secondly, we investigated whether the models obtained, for A-, B- and D-forms of DNA were consistent with the observed X-ray data 9- : Molecular model building: a stereochemical guideline Molecular conformation of a given helical duplex de- pends upon the stereochemistry of the repeating unit. Base-paired dinucleoside monophosphate was chosen as the repeating unit as it contains all the major sources of conformational flexibility present in the polymeric DNA, viz., (i) sugar puckering, (ii) rotation around phosphodies- ter linkages (P-O bonds) and (iii) glycosyl torsion. Owing to the presence of this flexibility, a given helical duplex can be generated from a number of conformationally distinct dinucleoside monophosphates. Hence, a detailed analysis of the single crystal structure data of dinucleoside mono- phosphates and higher oligomers was made to select the most probable repeating unit. Crystal data indicated that the ring puckering of the sugar is broadly divided into two regions: C3'-endo and C2'-endo. The energy calculations on the flexibility of ring puckering 14 also led to double-well minima in the confor- mational space corresponding to CY-endo and C2'-endo puckering. The crystal data 6 of GpC, ApU, ApA +, UpA, dTpdT and A + pA + show that sugar puckering can either be in a C3'-endo or in a C2'-endo region, both for purines or pyrimidines. However, in (pdApdT) 2 and dCpdG(pdCpdG) 2 the purines (A and G) are attached to sugars with C3'-endo puckering while the pyrimidines (C and T) are attached to sugars with C2'-endo pucker- ing 16":6. Thus, all the possibilities as exhibited by single