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Sequence sensitivity of breathing dynamics in heteropolymer DNA

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Tobias Ambjornsson, Suman K. Banik, Oleg Krichevsky, Ralf Metzler

Biomolecules · Submitted 24 Aug 2006

abstract compiled · 2026-09-23 · no language-model review

The authors' main claim A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a biological sequence of the T7 bacteriophage.

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arXiv IDq-bio/0608036 (version 1)
Pith IDI7YX5C5Y, Pith's permanent record of this paper and its review
CitationOleg Krichevsky, Ralf Metzler, Suman K. Banik, Tobias Ambjornsson. "Sequence sensitivity of breathing dynamics in heteropolymer DNA." arXiv:q-bio/0608036 (2006). https://pith.science/paper/I7YX5C5Y
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The compiled record

The paper's own sentences, arranged. Each label is drawn from a closed vocabulary; the number beside it is the probability the classifier gave that label. Numbers in the tables are the authors', checked by code. No sentence in this record was written by a model.

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Compiled by classifier-1.13.0 via TypeSafe API, question bank abstract-p1-20260923, 2026-09-23: 1 request, 2,927 input tokens.

What the abstract itself states, as probabilities: claims first 0.05 · states limitation 0.06 · human participants 0.02 · controlled comparison 0.06 · randomized assignment 0.01 · states quantitative result 0.20 · compares with prior results 0.86 · mentions code or data availability 0.03.

The abstract, sentence by sentence

arXiv listing abstract v1. Results and the main claim are underlined; .

We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a biological sequence of the T7 bacteriophage. Quantitative agreement with data from fluorescence correlation spectroscopy (FCS) is demonstrated.

background contribution method result interpretation main claim

What the classifier reports for each sentence. The number is the probability it gave the label.
#sentencerolethe authors' own workstates the main conclusionstrength
s0 We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. method 0.60 0.95 0.06 asserted 0.96
s1 A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a biological sequence of the T7 bacteriophage. result 1.00 0.94 0.80 asserted 1.00
s2 Quantitative agreement with data from fluorescence correlation spectroscopy (FCS) is demonstrated. result 0.97 0.86 0.10 asserted 1.00

What kind of paper the classifier reports this is: simulation study 0.98 · evidence from simulation or computation 1.00.

What was examined, and what was not

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not examined
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  • figures and tables
  • references and citing sentences
  • relations to other papers
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  • P abstract
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  • S sections
  • T body sentences
  • C citations
  • R cross-paper relations

Every quoted sentence on this record is the authors'. Every label is from Pith's closed vocabulary, with the probability shown beside it. Every number in the measurements table is the authors', checked by code. Record as JSON

The paper
Original abstract

We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a biological sequence of the T7 bacteriophage. Quantitative agreement with data from fluorescence correlation spectroscopy (FCS) is demonstrated.

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Found among the papers closest to this one by title and main claim. Pith's classifier compared each pair's main results and a second model family confirmed the relation; checked against two further families, shown conflicts agreed 118 times in 120 and shown same results 218 times in 239. The quoted sentence is the other paper's main claim.

States the same result 1 paper
  • The strong dependence on sequence, temperature and salt concentration for the breathing dynamics of DNA found here points at a good potential for nanosensing applications by utilizing short fluorophore-quencher dressed DNA constructs.

    Breathing dynamics in heteropolymer DNA · 0.80

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