1s88
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(New page: 200px<br /><applet load="1s88" size="450" color="white" frame="true" align="right" spinBox="true" caption="1s88" /> '''NMR structure of a DNA duplex with two INA n...)
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Revision as of 21:57, 24 November 2007
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NMR structure of a DNA duplex with two INA nucleotides inserted opposite each other, dCTCAACXCAAGCT:dAGCTTGXGTTGAG
Overview
The intercalating nucleic acid (INA) presented in this paper is a novel, 1-O-(1-pyrenylmethyl)glycerol DNA intercalator that induces high thermal, affinity for complementary DNA. The duplex examined contained two INA, intercalators, denoted X, inserted directly opposite each other:, d(C(1)T(2)C(3)A(4)A(5)C(6)X(7)C(8)A(9)A(10)G(11)C(12)T(13)):d(A(14)G(15)C(, 16)T(17)-T(18)G(19)X(20)G(21)T(22)T(23)G(24)A(25)G(26)). Unlike most other, nucleotide analogues, DNA with INA inserted has a lower affinity for, hybridizing to complementary DNA with an INA inserted directly opposite, than to complementary unmodified DNA. In this study we used, two-dimensional (1)H NMR spectroscopy to determine a high-resolution, solution structure of the weak INA-INA duplex. A modified ISPA approach, was used to obtain interproton distance bounds from NOESY cross-peak, intensities. These distance bounds were used as restraints in molecular, dynamics (rMD) calculations. Twenty final structures were generated for, the duplex from a B-type DNA starting structure. The root-mean-square, deviation (RMSD) of the coordinates for the 20 structures of the complex, was 1.95 A. This rather large value, together with broad lines in the area, of insertion, reflect the high degree of internal motion in the complex., The determination of the structure revealed that both intercalators were, situated in the center of the helix, stacking with each other and the, neighboring nucleobases. The intercalation of the INAs caused an unwinding, of the helix in the insertion area, creating a ladderlike structure. The, structural changes observed upon intercalation were mainly of local, character; however, a broadening of the minor groove was found throughout, the helix.
About this Structure
1S88 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR structure determination of a modified DNA oligonucleotide containing a new intercalating nucleic acid., Nielsen CB, Petersen M, Pedersen EB, Hansen PE, Christensen UB, Bioconjug Chem. 2004 Mar-Apr;15(2):260-9. PMID:15025521
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