Distinctive features in the structure and dynamics of the DNA repeat sequence GGCGGG q Neel S. Bhavesh, Prasanta K. Patel, S. Karthikeyan, and Ramakrishna V. Hosur * Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India Received 1 March 2004 Abstract G-rich DNA has been known to form a variety of folded and multistranded structures, with even single base modifications causing important structural changes. But, very little is known about the dynamic characteristics of the structures, which may play crucial roles in facilitating the structural transitions. In this background, we report here NMR investigations on the structure and dynamics of a DNA repeat sequence GGCGGG in aqueous solution containing Na þ ions at neutral pH. The chosen sequence d-TGGCGGGT forms a parallel quadruplex with a C-tetrad in the middle, formed by symmetrical pairing of four Cs in a plane via NH 2 -O2 H-bonds. 13 C relaxation measurements at natural abundance for C1 0 sugar carbons provided valuable insight into the sequence specific dynamism of G and C-tetrads in the quadruplex. The C4 tetrad seems to introduce high conformational dynamism at milli- to micro-second time scale in the quadruplex. Concomitantly, there is a decrease in the pico-second time scale dynamics. Interestingly, these effects are seen more prominently at the G-tetrads on the 3 0 end of C-tetrad than on its 5 0 end. These observations would have important implications for the roles the tetrads may play in many biological functions. Ó 2004 Elsevier Inc. All rights reserved. Keywords: DNA; Quadruplex; C-tetrad; NMR; Dynamics; Structure G-rich sequences are known to form multistranded DNA structures which have assumed great importance in recent years with the realization that they play im- portant roles in DNA recombination, replication, dis- ease control, etc. on the one hand, and DNA packaging inside a living cell on the other [1,2]. Pursuing this goal many DNA structures have been solved and they have added to the family of multistranded structures [3–7]. The structures have exhibited great variety, dependence on experimental conditions, especially the cations [8–14]. They have created new paradigms and under- scored the possibility of hitherto not understood roles for DNA function. The variability in the quadruplex structures is seen to be so large that given a repeat se- quence and the experimental conditions, it is hardly possible to predict the characteristics of the structure. The structures formed by G-rich sequences located at telomeres [15–19], immunoglobulin switch regions [20], and gene promoter regions [21] have been the most widely investigated and these have led to discoveries of many new structural motifs such as, G:C:G:C tetrad [22–24], U-tetrad [25], A-Tetrad [26], T-Tetrad [27], G:C:A:T tetrad [28], etc., to name a few. However, until date there have been no reports on the dynamic aspects of the structures, in general, though it may be well en- visaged that dynamics plays a crucial role in the variety of functions, DNA performs. There are many repeat sequences in which a C-nu- cleotide is sandwiched within G repeats. Among them the GGGCGG sequence (or equivalently GGCGGG, when multiple stretches are concerned) is biologically significant for several reasons; (i) it is a repeat sequence in Simian Virus (SV) 40, playing important roles in viral encapsidation [29,30], (ii) it is a target for many anti cancer drugs [29], (iii) it is the recognition sequence of the SP1 transcription factor [31], (iv) it is a very common sequence in CpG islands in vertebrate genomes [32], and q Abbreviations used: NMR, nuclear magnetic resonance; HSQC, heteronuclear single quantum coherence; SV40, simian virus 40; NOESY, nuclear Overhauser enhancement spectroscopy; TOCSY, total correlation spectroscopy. * Corresponding author. Fax: +91-22-2280-4610. E-mail address: hosur@tifr.res.in (R.V. Hosur). 0006-291X/$ - see front matter Ó 2004 Elsevier Inc. All rights reserved. doi:10.1016/j.bbrc.2004.03.095 Biochemical and Biophysical Research Communications 317 (2004) 625–633 BBRC www.elsevier.com/locate/ybbrc