Solution structure of the d(T-C-G-A) duplex at acidic pH: A parallel-stranded helix containing C(+) · C, G · G and A · A pairs Journal Article
| Authors: | Wang, Y.; Patel, D. J. |
| Article Title: | Solution structure of the d(T-C-G-A) duplex at acidic pH: A parallel-stranded helix containing C(+) · C, G · G and A · A pairs |
| Abstract: | The solution structure of the d(T-C-G-A) sequence at acidic pH has been determined by a combination of NMR and molecular dynamics calculations including NOE intensity based refinements. This sequence forms a right-handed parallel-stranded duplex with C+ · C (three hydrogen bonds along Watson-Crick edge), G · G (two symmetry related N2-H ·· N3 hydrogen bonds) and A · A (two symmetry related N6-H ·· N7 hydrogen bonds) homo base-pair formation at acidic pH. The duplex is stabilized by intra-strand base stacking at the C2-G3 step and cross-strand base stacking at the G3-A4 step. The thymine residues on partner strands are directed towards each other and are positioned over the C+ · C base-pair. All four residues adopt anti glycosidic torsion angles and C2′-endo type sugar conformations in the parallel-stranded d(T-C-G-A) duplex which exhibits large changes in twist angles between adjacent steps along the duplex. This study rules out previously proposed models for the structure of the d(T-C-G-A) duplex at acidic pH and supports earlier structural contributions, which established that d(C-G) and d(C-G-A) containing sequences at acidic pH pair through parallel-stranded alignment. We have also monitored hydration patterns in the symmetry related grooves of the parallel-stranded d(T-C-G-A) duplex. |
| Keywords: | ph; dna; double stranded dna; molecular sequence data; magnetic resonance spectroscopy; base sequence; dna structure; protons; solutions; nucleic acid conformation; computer graphics; nuclear magnetic resonance; hydrogen-ion concentration; phosphorus; oligodeoxyribonucleotides; base mispairing; base composition; nmr spectroscopy; priority journal; article; support, u.s. gov't, p.h.s.; solution structure; homo base mismatches; molecular dynamics refinement; parallel-stranded dna duplex |
| Journal Title: | Journal of Molecular Biology |
| Volume: | 242 |
| Issue: | 4 |
| ISSN: | 0022-2836 |
| Publisher: | Academic Press Inc., Elsevier Science |
| Date Published: | 1994-09-29 |
| Start Page: | 508 |
| End Page: | 526 |
| Language: | English |
| PROVIDER: | scopus |
| PUBMED: | 7932707 |
| DOI: | 10.1006/jmbi.1994.1770 |
| DOI/URL: | |
| Notes: | Export Date: 14 January 2019 -- Article -- Source: Scopus |
