I-motif

The hairpin (i motif occurs frequently in protein structures... 

There are numerous cases, where identical bases, mismatched bases, and even complementary bases in protonated states are involved in hydrogen bonding. Examples are as follows Protonated adenine (HA+) has been observed in DNA mismatches as well as in RNA in pairs such as HA 1 (antl) G(syn) and HA+(anti) C(anti) (70). Poly(A) forms HA+ HA+ self-pairs in a parallel strand fashion at pH <4 (21). Protonated cytosine (HC+) exists in hemiproto-nated polyC (i-motif) (32), in HC+(anti) G(syn) (71), in a HC+ C RNA... 

The most extensive studies on directed evolution have been carried out with Thermus aquaticus DNA Pol I (Taq Pol I). Motifs A and B have both been targeted for random mutagenesis by complementing the recA718polA12 temperature-sensitive Pol I muta-... 

The i-motif can be formed from a cytosine-rich strand with protonation of the intercalated C-C base pairs [Figure 13(a)]. In the case of duplex DNA the disassociation of the cytosine and guanine-rich strands is required before being refolded into a C-rich i-motif and a G-rich G-quadruplex motif. Under normal physiological cellular conditions the guanine and its complimentary sequences... 

J. Kondo, W. Adachi, S. Umeda, T. Sunami and A. Takenaka, Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats. Nucleic Acids Res., 2004, 32, 2541-2549. 

B. Pan, K. Shi and M. Sundaralingam, Base-tetrad swapping results in dimerization of RNA quadruplexes Implications for formation of the i-motif RNA octaplex, Proc. Natl. Acad. Sci. USA, 2006, 103, 3130-3134. 

Tetraplexes can also be formed fixim C-rich sequences at acidic pH. This tetraplex architecture is called the i-motif. It basically consists of two head-to-tail, intercalated, parallel-stranded duplexes held together by... 

LNA has been used in a variety of other biological applications. LNA, and its 2 -amino analogue, has been incorporated into aptamers (see section 2) for enhanced binding affinity." LNA has been substituted into i-motif structures, where it can have a significant effect on the structural stability. The presence of LNA in the structure alters the stability of the hemiprotonated cytosine base pairs, and as there is a sequence effect it is possible to tune the stability of the i-motif." Substituting LNA into quadruplex structures also has a sequence-dependent effect on stability, where in only certain positions are well-defined structures obtained." More recently the use of LNA nucleotides as polymerase substrates has been examined." KOD DNA polymerase has been shown to be a useful polymerase for the incorporation of LNA triphosphates into DNA, including its use as the polymerase in PCR reactions with LNA modifications." ... 

In addition to the G-quadruplex other motifs that have been solved include the i-motif, a pH-dependent poly dA helix which forms the basis of a molecular switch, the HIV-1 TAR DNA hairpin, and the B-Z transition in a GC-rich DNA sequence. There are also many protein/ peptide structures that have been solved that have DNA as part of the recognition domain, including a zinc sensor, MetJ repressor, lac repressor, Lambda integrase protein, protection of telomers (Potl)... 

---