DNA-Directed Base Pair Opening
Strand separation is a fundamental molecular process essential for the reading of the genetic information during DNA replication, transcription and recombination. However, DNA melting in physiological conditions in which the double helix is expected to be stable represents a challenging problem. Cur...
| Main Author: | |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2012-10-01
|
| Series: | Molecules |
| Subjects: | |
| Online Access: | http://www.mdpi.com/1420-3049/17/10/11947 |
| _version_ | 1819210953477062656 |
|---|---|
| author | Youri Timsit |
| author_facet | Youri Timsit |
| author_sort | Youri Timsit |
| collection | DOAJ |
| description | Strand separation is a fundamental molecular process essential for the reading of the genetic information during DNA replication, transcription and recombination. However, DNA melting in physiological conditions in which the double helix is expected to be stable represents a challenging problem. Current models propose that negative supercoiling destabilizes the double helix and promotes the spontaneous, sequence-dependent DNA melting. The present review examines an alternative view and reveals how DNA compaction may trigger the sequence dependent opening of the base pairs. This analysis shows that in DNA crystals, tight DNA-DNA interactions destabilize the double helices at various degrees, from the alteration of the base-stacking to the opening of the base-pairs. The electrostatic repulsion generated by the DNA close approach of the negatively charged sugar phosphate backbones may therefore provide a potential source of the energy required for DNA melting. These observations suggest a new molecular mechanism for the initial steps of strand separation in which the coupling of the DNA tertiary and secondary interactions both actively triggers the base pair opening and stabilizes the intermediate states during the melting pathway. |
| first_indexed | 2024-12-23T06:19:22Z |
| format | Article |
| id | doaj.art-80cb3b02566d4ec7b2c9332a542176e6 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-12-23T06:19:22Z |
| publishDate | 2012-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-80cb3b02566d4ec7b2c9332a542176e62022-12-21T17:57:14ZengMDPI AGMolecules1420-30492012-10-011710119471196410.3390/molecules171011947DNA-Directed Base Pair OpeningYouri TimsitStrand separation is a fundamental molecular process essential for the reading of the genetic information during DNA replication, transcription and recombination. However, DNA melting in physiological conditions in which the double helix is expected to be stable represents a challenging problem. Current models propose that negative supercoiling destabilizes the double helix and promotes the spontaneous, sequence-dependent DNA melting. The present review examines an alternative view and reveals how DNA compaction may trigger the sequence dependent opening of the base pairs. This analysis shows that in DNA crystals, tight DNA-DNA interactions destabilize the double helices at various degrees, from the alteration of the base-stacking to the opening of the base-pairs. The electrostatic repulsion generated by the DNA close approach of the negatively charged sugar phosphate backbones may therefore provide a potential source of the energy required for DNA melting. These observations suggest a new molecular mechanism for the initial steps of strand separation in which the coupling of the DNA tertiary and secondary interactions both actively triggers the base pair opening and stabilizes the intermediate states during the melting pathway.http://www.mdpi.com/1420-3049/17/10/11947DNA-meltingstrand separationDNA condensationcrystal structurebase pair openingunstackingtranscription initiation |
| spellingShingle | Youri Timsit DNA-Directed Base Pair Opening Molecules DNA-melting strand separation DNA condensation crystal structure base pair opening unstacking transcription initiation |
| title | DNA-Directed Base Pair Opening |
| title_full | DNA-Directed Base Pair Opening |
| title_fullStr | DNA-Directed Base Pair Opening |
| title_full_unstemmed | DNA-Directed Base Pair Opening |
| title_short | DNA-Directed Base Pair Opening |
| title_sort | dna directed base pair opening |
| topic | DNA-melting strand separation DNA condensation crystal structure base pair opening unstacking transcription initiation |
| url | http://www.mdpi.com/1420-3049/17/10/11947 |
| work_keys_str_mv | AT youritimsit dnadirectedbasepairopening |