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Abstract
By substitution of natural nucleotides by their abasic analogs (i.e., 1′,2′-dideoxyribose phosphate residue) at critically chosen positions within 27-bp DNA constructs originating from the first intron of N-myc gene, we hindered hybridization within the guanine- and cytosine-rich central region and followed formation of non-canonical structures. The impeded hybridization between the complementary strands leads to time-dependent structural transformations of guanine-rich strand that are herein characterized with the use of solution-state NMR, CD spectroscopy, and native polyacrylamide gel electrophoresis. Moreover, the DNA structural changes involve transformation of intra- into inter-molecular G-quadruplex structures that are thermodynamically favored. Intriguingly, the transition occurs in the presence of complementary cytosine-rich strands highlighting the inability of Watson–Crick base-pairing to preclude the transformation between G-quadruplex structures that occurs via intertwining mechanism and corroborates a role of G-quadruplex structures in DNA recombination processes.
Highlights
Non-canonical DNA structural motifs have been established as key biological elements [1,2,3].Particular attention goes to the two groups of four-stranded helical structures termed G-quadruplexes and i-motifs adopted by guanine (G)- and cytosine (C)-rich DNA, respectively [4,5]
This study focuses on structural specifics of G- and C-rich DNA oligonucleotides in equimolar mixture of complementary strands, while considering that they can fold into G-quadruplex or i-motif structures when studied alone
Upon addition of K+ ions into aqueous solution of mycG, new 1 H-NMR signals appear in the range from δ10.50 to 12.00 ppm, indicating that mycG adopts G-quadruplex structures (Figure 2a)
Summary
Non-canonical DNA structural motifs have been established as key biological elements [1,2,3].Particular attention goes to the two groups of four-stranded helical structures termed G-quadruplexes and i-motifs adopted by guanine (G)- and cytosine (C)-rich DNA, respectively [4,5]. Non-canonical DNA structural motifs have been established as key biological elements [1,2,3]. It is well established that availability of biologically relevant cations, such as K+ and Na+ ions greatly impacts structural characteristics of G-rich DNA [7,8,9,10,11]. In addition to i-motif, C+ ·C base-pairing is common to particular hairpin structures [12,13]. It is the delicate susceptibility of G- and C-rich DNA structural features to micro-environmental conditions that greatly contributes to consideration of these structures as biorecognition elements. Meaningful enrichment of G- and C-rich tracts exists within important genome
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