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Titolo:
Enhanced loop DNA folding induced by thymine-CH3 group contact and perpendicular guanine-thymine interaction
Autore:
Chou, SH; Chin, KH; Chen, CW;
Indirizzi:
Natl Chung Hsing Univ, Inst Biochem, Taichung 40227, Taiwan Natl Chung Hsing Univ Taichung Taiwan 40227 chem, Taichung 40227, Taiwan Natl Chung Hsing Univ, Dept Chem, Taichung 40227, Taiwan Natl Chung Hsing Univ Taichung Taiwan 40227 Chem, Taichung 40227, Taiwan Natl Yang Ming Univ, Inst Genet, Taipei 112, Taiwan Natl Yang Ming Univ Taipei Taiwan 112 iv, Inst Genet, Taipei 112, Taiwan
Titolo Testata:
JOURNAL OF BIOMOLECULAR NMR
fascicolo: 1, volume: 19, anno: 2001,
pagine: 33 - 48
SICI:
0925-2738(200101)19:1<33:ELDFIB>2.0.ZU;2-F
Fonte:
ISI
Lingua:
ENG
Soggetto:
STABLE RNA HAIRPIN; CENTER-DOT-A; MOLECULAR-DYNAMICS; HETERONUCLEAR NMR; 3-DIMENSIONAL STRUCTURE; 5-METHYL CYTOSINE; DISTANCE GEOMETRY; CRYSTAL-STRUCTURE; DOUBLE HELIX; BASE-PAIRS;
Keywords:
minor groove folding; perpendicular guanine-thymine interaction; T-methyl hydrophobic interaction; TTTG loop; UUCG loop;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
68
Recensione:
Indirizzi per estratti:
Indirizzo: Chou, SH Natl Chung Hsing Univ, Inst Biochem, Taichung 40227, Taiwan Natl Chung Hsing Univ Taichung Taiwan 40227 chung 40227, Taiwan
Citazione:
S.H. Chou et al., "Enhanced loop DNA folding induced by thymine-CH3 group contact and perpendicular guanine-thymine interaction", J BIOM NMR, 19(1), 2001, pp. 33-48

Abstract

A remarkable stabilizing effect induced by T-CH3 group and perpendicular guanine-thymine interactions in the DNA loop conformation has been demonstrated for the d(TTTG) loop structure using UV melting, high resolution NMR, distance geometry, and molecular dynamics studies. Contrary to the previously published d(TTCG) sequence that exhibits no specific inter-nucleotide interaction, we have found that d(TTTG), which differs only by one nucleotide with the d(TTCG) sequence (C7 --> T7), forms a rather stable and well-defined loop structure. Two characteristic structural features account for the stabilization of an otherwise flexible loop structure; the second loop T (T6) residue folds into the minor groove and engages in perpendicular interaction with the G8-NH2, while the third loop T (T7) residue stacks well upon the closing T5.G8 wobble base pair and exhibits good contacts with many of the loop T5 and T6 sugar protons, which may form a hydrophobic core in the loop region. The importance of the bulky T7-CH3 was also proved by the UV melting study; while d(TTCG) hairpin exhibits a lower melting point (74.5 degreesC ) than d(TTTG) hairpin (80.5 degreesC ), d(TT5-methylCG) hairpin resumes the same higher melting point (80 degreesC ). Similarly, the fact that the melting temperature (74 degreesC ) of d(TTTI) is lower than that of d(TTTG) indicates the critical role played by the G8-NH2 group. Our structuralstudies of the d(TTTG) loop indicate that DNA and RNA use a different strategy to establish stable tertiary folds. Comparison with several other pyrimidine-rich loop hairpins suggests that different minor-groove folding modes exist for the folding thymidine residue.

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Documento generato il 29/09/20 alle ore 22:57:16