dorsal/arxiv
View SchemaMesoscopic modeling for nucleic acid chain dynamics
| Authors | M. Sales-Pardo, R. Guimera, A. A. Moreira, J. Widom, L. A. N. Amaral |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0506001 |
| URL | https://arxiv.org/abs/q-bio/0506001 |
| DOI | 10.1103/PhysRevE.71.051902 |
| Journal | Phys. Rev. E, 71 art. num. 051902 (2005) |
Abstract
To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a novel mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational bead motion and rotational pin motion. By performing a number of tests we first show that our model is physically sound. We then focus on the study of a the kinetics of a DNA hairpin--a single-stranded molecule comprising two complementary segments joined by a non-complementary loop--studied experimentally. We find that results from our simulations agree with experimental observations, demonstrating that our model is a suitable tool for the investigation of the hybridization of single strands.
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"abstract": "To gain a deeper insight into cellular processes such as transcription and\ntranslation, one needs to uncover the mechanisms controlling the\nconfigurational changes of nucleic acids. As a step toward this aim, we present\nhere a novel mesoscopic-level computational model that provides a new window\ninto nucleic acid dynamics. We model a single-stranded nucleic as a polymer\nchain whose monomers are the nucleosides. Each monomer comprises a bead\nrepresenting the sugar molecule and a pin representing the base. The bead-pin\ncomplex can rotate about the backbone of the chain. We consider pairwise\nstacking and hydrogen-bonding interactions. We use a modified Monte Carlo\ndynamics that splits the dynamics into translational bead motion and rotational\npin motion. By performing a number of tests we first show that our model is\nphysically sound. We then focus on the study of a the kinetics of a DNA\nhairpin--a single-stranded molecule comprising two complementary segments\njoined by a non-complementary loop--studied experimentally. We find that\nresults from our simulations agree with experimental observations,\ndemonstrating that our model is a suitable tool for the investigation of the\nhybridization of single strands.",
"arxiv_id": "q-bio/0506001",
"authors": [
"M. Sales-Pardo",
"R. Guimera",
"A. A. Moreira",
"J. Widom",
"L. A. N. Amaral"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1103/PhysRevE.71.051902",
"journal_ref": "Phys. Rev. E, 71 art. num. 051902 (2005)",
"title": "Mesoscopic modeling for nucleic acid chain dynamics",
"url": "https://arxiv.org/abs/q-bio/0506001"
},
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