1a83

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INTRAMOLECULAR I-MOTIF, NMR, 6 STRUCTURES

Overview

We present a high-definition structure of d(5mCCT3CCT3ACCT3CC), a DNA, sequence which resembles a four-times repeat of the C-rich strand of, telomeres and centromeres. The structure is monomeric. The CC stretches, form four hemi-protonated C.C base-pairs, belonging to two, parallel-stranded duplexes which intercalate head-to-tail into an i-motif, core. The four grooves of the core are similar to those observed, previously in i-motif tetramers, with P-P distances around 0.9 nm and 1.4, nm for the narrow and wide grooves, respectively. At 0 degrees C, the, structure is formed even at pH 7, despite the required protonation of, cytidine pairs, suggesting that it may be biologically relevant.The, intercalation topology of the i-motif core is read off the pattern of, inter-residue cross-peaks along each groove: between H1' protons across, the narrow grooves, and between amino and H2' protons across the wide, grooves. In the hemi-protonated C.C pairs, the imino proton is shared, equally between the two bases, as shown by the equal intensities of the, NOESY cross-peaks between the imino proton and the two cis amino protons, of the pair. Short inter-sugar distances and the direction of CH1' bonds, are consistent with CH1'...O4' hydrogen bonds across the narrow grooves, as suggested by Berger et al. (1996). Proc. Natl. Acad. Sci. USA, 93, 12116-12121. At one extremity of the i-motif core, the T3A linker loops, across one of the two wide grooves. It extends the core by stacking of, A11, which also forms a strongly propeller-twisted reverse-Hoogsteen pair, with T8. At the other extremity, the two T3 linkers loop side by side, across the two narrow grooves, extending the core by stacking of a T5.T16, pair which connects the two linkers. In this T.T pair between parallel, strands, the hydrogen bonds are from imino proton to O4, and the base-pair, lifetime is 6 ms at 0 degrees C. The structures of segments 1 to 7 and 12, to 18, which form the i-motif core and the T3 loops, are related by a, 2-fold pseudo-symmetry: the geometries and environment are so similar that, the NOESY spectra are barely resolved. These various interactions, illustrate how linker sequences may affect the stability, intercalation, topology and folding pattern of the intramolecular i-motif.

About this Structure

1A83 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

An intramolecular i-motif: the solution structure and base-pair opening kinetics of d(5mCCT3CCT3ACCT3CC)., Han X, Leroy JL, Gueron M, J Mol Biol. 1998 May 22;278(5):949-65. PMID:9600855

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