Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)₂at 1.7 Å resolution

Abstract

We present here a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG) all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. However, in the presence of zinc, magnesium, and in the absence of any metal ion, it does not take up the junction structure, but forms an A-type double helix. This allowed us to study possible conformational changes in the double helix due to the presence of metal ions. Upon addition of the zinc ion, there is a change in the space group from P422 to P4. The overall conformation of the duplex remains the same. There are small changes in the interaction of the metal ions with the DNA. In the zinc-bound structure, there are two zinc ions that show direct interaction with the N7 atoms of terminal G bases at either end of the molecule. There are small changes in the interhelical contacts. The consequence of these differences is to break some of the symmetry and change the space group.

Self-Assembled Cationic β-Cyclodextrin Nanostructures for siRNA Delivery

“…In this study, we used state of the art molecular dynamics (MD) computer simulations to model the dynamic encapsulation of siRNA via templated self-assembly of β-cyclodextrin derivatives on the siRNA surface. 21-base pair siRNA molecular models were built using A-DNA PDB structures as templates (5IYE, 5MVT, 5MVQ, 5OKL, and 3V9D ), and the uracil nucleobases were modified to 2′- o -methyluridine at 4 positions. Click-propyl-amine cationic β-cyclodextrin models were generated from published molecular structures. ,, Each complex was solvated in TIP3P water in a cubic box of edge length 18 nm and any net charge was neutralized by adding background Na + and Cl – ions.…”

Crystal structure of d(CCGGGGTACCCCGG)2at 1.4 Å resolution

“…These sequences were all designed with the expectation that they would form four-way junctions with different helical structures for the arms. It has been reported (Eichman et al, 2000) that a sequence with the triplet 'ACC' in its central portion would favour the formation of a four-way junction structure, and this was incorporated (Karthik et al, 2017) and the present sequence all crystallize as A-type double helices, with slight variations in the structure and crystal packing. Thus, an important determinant of the structure of a DNA fragment in the crystal is apparently its length.…”

“…In 2011, our laboratory reported the first structure of a tetradecadeoxynucleotide, d(CGCGGGTACCCGCG) 2 , in the A-DNA conformation (Venkadesh et al, 2011). Following this, a series of tetradecamer sequences such as d(CCCCGGT-ACCGGGG) 2 (Mandal et al, 2012;Purushothaman et al, 2014), d(CCCGGGTACCCGGG) 2 (Karthik et al, 2017) and the present sequence have all been reported to crystallize as A-type double helices. These sequences have some common features.…”

Systematics for types and effects of DNA variations

“…Most common of the DNA double helix structures is the B-form, however, there are numerous others. They have different conformations, such as A DNA [120], D DNA [121] and Z DNA [122] (see Figs. 5a to d), defined by the geometry of the DNA helices including e.g.…”

“…Double helical structures. a A DNA (5iyg) [120], b B DNA (5f9i), c D DNA (5vy6) [121], and ( d ) Z DNA (4ocb) [122]. e Triple helix structure (1bwg) [125].…”