dorsal/arxiv
View SchemaGeneralized Poland-Scheraga model for DNA hybridization
| Authors | Thomas Garel, Henri Orland |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0402037 |
| URL | https://arxiv.org/abs/q-bio/0402037 |
Abstract
The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the binding (or hybridization) of two complementary strands of DNA of equal length, with the restriction that only bases with the same index along the strands are allowed to bind. In this paper, we extend this model by relaxing these constraints: We propose a generalization of the PS model which allows for the binding of two strands of unequal lengths $N_{1}$ and $N_{2}$ with unrelated sequences. We study in particular (i) the effect of mismatches on the hybridization of complementary strands (ii) the hybridization of non complementary strands (as resulting from point mutations) of unequal lengths $N_{1}$ and $N_{2}$. The use of a Fixman-Freire scheme scales down the computational complexity of our algorithm from $O(N_{1}^{2}N_{2}^{2})$ to $O(N_{1}N_{2})$.The simulation of complementary strands of a few kbps yields results almost identical to the PS model. For short strands of equal or unequal lengths, the binding displays a strong sensitivity to mutations. This model may be relevant to the experimental protocol in DNA microarrays, and more generally to the molecular recognition of DNA fragments. It also provides a physical implementation of sequence alignments.
{
"annotation_id": "be23c384-572c-4a9b-bce1-c318d87cb651",
"date_created": "2026-03-02T18:01:32.181000Z",
"date_modified": "2026-03-02T18:01:32.181000Z",
"file_hash": "1e00c21a716362435c9b7d521a9d0b90a83d14ea59ba883d68f74553f721965a",
"private": false,
"record": {
"abstract": "The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers\nthe statistical mechanics of the binding (or hybridization) of two\ncomplementary strands of DNA of equal length, with the restriction that only\nbases with the same index along the strands are allowed to bind. In this paper,\nwe extend this model by relaxing these constraints: We propose a generalization\nof the PS model which allows for the binding of two strands of unequal lengths\n$N_{1}$ and $N_{2}$ with unrelated sequences. We study in particular (i) the\neffect of mismatches on the hybridization of complementary strands (ii) the\nhybridization of non complementary strands (as resulting from point mutations)\nof unequal lengths $N_{1}$ and $N_{2}$. The use of a Fixman-Freire scheme\nscales down the computational complexity of our algorithm from\n$O(N_{1}^{2}N_{2}^{2})$ to $O(N_{1}N_{2})$.The simulation of complementary\nstrands of a few kbps yields results almost identical to the PS model. For\nshort strands of equal or unequal lengths, the binding displays a strong\nsensitivity to mutations. This model may be relevant to the experimental\nprotocol in DNA microarrays, and more generally to the molecular recognition of\nDNA fragments. It also provides a physical implementation of sequence\nalignments.",
"arxiv_id": "q-bio/0402037",
"authors": [
"Thomas Garel",
"Henri Orland"
],
"categories": [
"q-bio.BM",
"cond-mat.soft"
],
"title": "Generalized Poland-Scheraga model for DNA hybridization",
"url": "https://arxiv.org/abs/q-bio/0402037"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "addf084d-e701-491e-b728-ace56595771e",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}