Evidence map›Paper›PMID 39313579›Full record

ArticleJournal of molecular evolution2024

High Nucleotide Skew Palindromic DNA Sequences Function as Potential Replication Origins due to their Unzipping Propensity.

Parthasarathi Sahu, Sashikanta Barik, Koushik Ghosh, Hemachander Subramanian

Abstract read
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Article in Journal of molecular evolution, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Parthasarathi SahuDepartment of Physics, National Institute of Technology, Durgapur, India.
Sashikanta BarikDepartment of Physics, National Institute of Technology, Durgapur, India.
Koushik GhoshDepartment of Physics, National Institute of Technology, Durgapur, India.
Hemachander SubramanianDepartment of Physics, National Institute of Technology, Durgapur, India. hsubramanian.phy@nitdgp.ac.in.ORCID 0000-0002-4869-5994

Funding

Science and Engineering Research Board, India CRG/2020/003555Science and Engineering Research Board, India MTR/2022/000086
6 · The paper itself

Abstract

Locations of DNA replication initiation in prokaryotes, called "origins of replication", are well-characterized. However, a mechanistic understanding of the sequence dependence of the local unzipping of double-stranded DNA, the first step towards replication initiation, is lacking. Here, utilizing a Markov chain model that was created to address the directional nature of DNA unzipping and replication, we model the sequence dependence of local melting of double-stranded linear DNA segments. We show that generalized palindromic sequences with high nucleotide skews have a low kinetic barrier for local melting near melting temperatures. This allows for such sequences to function as potential replication origins. We support our claim with evidence for high-skew palindromic sequences within the replication origins of mitochondrial DNA, bacteria, archaea and plasmids.

Indexed as

DNA ReplicationReplication OriginArchaeaBacteriaDNADNA, MitochondrialInverted Repeat SequencesMarkov ChainsNucleotidesPlasmidsDNADNA, MitochondrialNucleotidesAsymmetric cooperativityBubble formationDNA unzippingGC-skewKinetic asymmetryOrigin of ReplicationRY-skewSequence-dependent kinetics

Identifiers

PMID39313579

What Socratic holds

Textmetadata
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.