1q2t: Difference between revisions

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[[Image:1q2t.gif|left|200px]]<br /><applet load="1q2t" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:1q2t.gif|left|200px]]<br /><applet load="1q2t" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1q2t" />

'''Solution structure of d(5mCCTCTCC)4'''<br />

==Overview==

The i-motif is a four-stranded structure built by intercalation in, head-to-tail orientation of two parallel duplexes associated by, hemi-protonated C.C(+) pairs. Using NMR methods, we investigated the, structure, the base-pair opening kinetics and the internal motions of, three i-motif tetramers: [d(5mCCTCnTCC)](4) (n=1, 2, 3). These tetramers, cannot accommodate the intercalation of two T.T pairs in face-to-face, orientation. They are built by intercalation of two symmetrical duplexes, whose contacting T3/TM thymidine bases (M=5, 6, 7) are either base-paired, or unstacked. The arrangement of the unstacked/paired thymidine bases of, the two T/T groups results in the formation of two different, conformations. One, fully symmetric, whose thymidine bases T3 and TM are, unstacked and base-paired respectively. The other is the asymmetric, assembly of two duplexes: one where both thymidine bases are unstacked and, the other with two T.T pairs. The proportion of the symmetric conformer, increases from a value beyond the detection threshold for n=1, to 19% for, n=2 and up to more than 95% for n=3. The exchange cross-peaks connecting, together the intercalated duplexes of [d(5mCCTCTCC)](4) and, [d(5mCCTCCTCC)](4) reveal a structural interconversion induced by the, simultaneous opening/closing of the contacting T3/TM thymidine bases. In, [d(5mCCTCCTCC)](4) the motion of the T3/T6 groups triggers the, interconversion of the symmetric and asymmetric conformations. In, [d(5mCCTCTCC)](4) the intercalated duplexes exchange their structures in, an apparently concerted motion, suggesting the simultaneous, opening/closing of two distant T3/T5* and T5/T3* switching groups. The, spectrum of [d(5mCCTCCCTCC)](4) is fully symmetric and, for this reason, its spectrum gives no indication for duplex interconversion. Nevertheless, the imino proton exchange kinetics argues for a switching motion of the, T3/T7 group. Duplex interconversion is not detectable in that case, due to, the tetramer symmetry. The origin of the structural conflict hindering the, intercalation of two T.T pairs into the i-motif is discussed.

The i-motif is a four-stranded structure built by intercalation in head-to-tail orientation of two parallel duplexes associated by hemi-protonated C.C(+) pairs. Using NMR methods, we investigated the structure, the base-pair opening kinetics and the internal motions of three i-motif tetramers: [d(5mCCTCnTCC)](4) (n=1, 2, 3). These tetramers cannot accommodate the intercalation of two T.T pairs in face-to-face orientation. They are built by intercalation of two symmetrical duplexes whose contacting T3/TM thymidine bases (M=5, 6, 7) are either base-paired or unstacked. The arrangement of the unstacked/paired thymidine bases of the two T/T groups results in the formation of two different conformations. One, fully symmetric, whose thymidine bases T3 and TM are unstacked and base-paired respectively. The other is the asymmetric assembly of two duplexes: one where both thymidine bases are unstacked and the other with two T.T pairs. The proportion of the symmetric conformer increases from a value beyond the detection threshold for n=1, to 19% for n=2 and up to more than 95% for n=3. The exchange cross-peaks connecting together the intercalated duplexes of [d(5mCCTCTCC)](4) and [d(5mCCTCCTCC)](4) reveal a structural interconversion induced by the simultaneous opening/closing of the contacting T3/TM thymidine bases. In [d(5mCCTCCTCC)](4) the motion of the T3/T6 groups triggers the interconversion of the symmetric and asymmetric conformations. In [d(5mCCTCTCC)](4) the intercalated duplexes exchange their structures in an apparently concerted motion, suggesting the simultaneous opening/closing of two distant T3/T5* and T5/T3* switching groups. The spectrum of [d(5mCCTCCCTCC)](4) is fully symmetric and, for this reason, its spectrum gives no indication for duplex interconversion. Nevertheless, the imino proton exchange kinetics argues for a switching motion of the T3/T7 group. Duplex interconversion is not detectable in that case, due to the tetramer symmetry. The origin of the structural conflict hindering the intercalation of two T.T pairs into the i-motif is discussed.

==About this Structure==

1Q2T is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1Q2T OCA].

1Q2T is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q2T OCA].

==Reference==

T.T pair intercalation and duplex interconversion within i-motif tetramers., Leroy JL, J Mol Biol. 2003 Oct 10;333(1):125-39. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14516748 14516748]

[[Category: Protein complex]]

[[Category: Leroy, J.L.]]

[[Category: Leroy, J L.]]

[[Category: dna solution structure; i-motif; protonated cytidine; hemiprotonated base-pairs]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Sun Nov 25 03~~:28:~~28 2007~~''

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@@ Line 1: / Line 1: @@
-[[Image:1q2t.gif|left|200px]]<br /><applet load="1q2t" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1q2t.gif|left|200px]]<br /><applet load="1q2t" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1q2t" />
 '''Solution structure of d(5mCCTCTCC)4'''<br />
 ==Overview==
-The i-motif is a four-stranded structure built by intercalation in, head-to-tail orientation of two parallel duplexes associated by, hemi-protonated C.C(+) pairs. Using NMR methods, we investigated the, structure, the base-pair opening kinetics and the internal motions of, three i-motif tetramers: [d(5mCCTCnTCC)](4) (n=1, 2, 3). These tetramers, cannot accommodate the intercalation of two T.T pairs in face-to-face, orientation. They are built by intercalation of two symmetrical duplexes, whose contacting T3/TM thymidine bases (M=5, 6, 7) are either base-paired, or unstacked. The arrangement of the unstacked/paired thymidine bases of, the two T/T groups results in the formation of two different, conformations. One, fully symmetric, whose thymidine bases T3 and TM are, unstacked and base-paired respectively. The other is the asymmetric, assembly of two duplexes: one where both thymidine bases are unstacked and, the other with two T.T pairs. The proportion of the symmetric conformer, increases from a value beyond the detection threshold for n=1, to 19% for, n=2 and up to more than 95% for n=3. The exchange cross-peaks connecting, together the intercalated duplexes of [d(5mCCTCTCC)](4) and, [d(5mCCTCCTCC)](4) reveal a structural interconversion induced by the, simultaneous opening/closing of the contacting T3/TM thymidine bases. In, [d(5mCCTCCTCC)](4) the motion of the T3/T6 groups triggers the, interconversion of the symmetric and asymmetric conformations. In, [d(5mCCTCTCC)](4) the intercalated duplexes exchange their structures in, an apparently concerted motion, suggesting the simultaneous, opening/closing of two distant T3/T5* and T5/T3* switching groups. The, spectrum of [d(5mCCTCCCTCC)](4) is fully symmetric and, for this reason, its spectrum gives no indication for duplex interconversion. Nevertheless, the imino proton exchange kinetics argues for a switching motion of the, T3/T7 group. Duplex interconversion is not detectable in that case, due to, the tetramer symmetry. The origin of the structural conflict hindering the, intercalation of two T.T pairs into the i-motif is discussed.
+The i-motif is a four-stranded structure built by intercalation in head-to-tail orientation of two parallel duplexes associated by hemi-protonated C.C(+) pairs. Using NMR methods, we investigated the structure, the base-pair opening kinetics and the internal motions of three i-motif tetramers: [d(5mCCTCnTCC)](4) (n=1, 2, 3). These tetramers cannot accommodate the intercalation of two T.T pairs in face-to-face orientation. They are built by intercalation of two symmetrical duplexes whose contacting T3/TM thymidine bases (M=5, 6, 7) are either base-paired or unstacked. The arrangement of the unstacked/paired thymidine bases of the two T/T groups results in the formation of two different conformations. One, fully symmetric, whose thymidine bases T3 and TM are unstacked and base-paired respectively. The other is the asymmetric assembly of two duplexes: one where both thymidine bases are unstacked and the other with two T.T pairs. The proportion of the symmetric conformer increases from a value beyond the detection threshold for n=1, to 19% for n=2 and up to more than 95% for n=3. The exchange cross-peaks connecting together the intercalated duplexes of [d(5mCCTCTCC)](4) and [d(5mCCTCCTCC)](4) reveal a structural interconversion induced by the simultaneous opening/closing of the contacting T3/TM thymidine bases. In [d(5mCCTCCTCC)](4) the motion of the T3/T6 groups triggers the interconversion of the symmetric and asymmetric conformations. In [d(5mCCTCTCC)](4) the intercalated duplexes exchange their structures in an apparently concerted motion, suggesting the simultaneous opening/closing of two distant T3/T5* and T5/T3* switching groups. The spectrum of [d(5mCCTCCCTCC)](4) is fully symmetric and, for this reason, its spectrum gives no indication for duplex interconversion. Nevertheless, the imino proton exchange kinetics argues for a switching motion of the T3/T7 group. Duplex interconversion is not detectable in that case, due to the tetramer symmetry. The origin of the structural conflict hindering the intercalation of two T.T pairs into the i-motif is discussed.
 ==About this Structure==
-Q2T is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Q2T OCA].
+Q2T is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q2T OCA].
 ==Reference==
 T.T pair intercalation and duplex interconversion within i-motif tetramers., Leroy JL, J Mol Biol. 2003 Oct 10;333(1):125-39. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14516748 14516748]
 [[Category: Protein complex]]
-[[Category: Leroy, J.L.]]
+[[Category: Leroy, J L.]]
 [[Category: dna solution structure; i-motif; protonated cytidine; hemiprotonated base-pairs]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:28:28 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:35:15 2008''