Evidence map›Paper›PMID 39704950›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2025

Methods for Studying Motor-Driven Viral DNA Packaging in Bacteriophages phi29, Lambda, and T4 via Single DNA Molecule Manipulation and Rapid Solution Exchange.

Mounir Fizari, Brandon Rawson, Nicholas Keller, Damian delToro, Douglas E Smith

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
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

5 authors.

Mounir FizariDepartment of Physics, University of California San Diego, La Jolla, CA, USA.
Brandon RawsonDepartment of Physics, University of California San Diego, La Jolla, CA, USA.
Nicholas KellerDepartment of Physics, University of California San Diego, La Jolla, CA, USA.
Damian delToroDepartment of Physics, University of California San Diego, La Jolla, CA, USA.
Douglas E SmithDepartment of Physics, University of California San Diego, La Jolla, CA, USA. des@physics.ucsd.edu.

Funding

Structure and Function of Essential Nucleoprotein ComplexesAlong a Viral Genome Packaging PathwayR01GM127365 · NIGMS · UNIVERSITY OF COLORADO DENVER · PI Carlos Enrique Catalano, Marc Morais · 2018 to 2026
$3.5M
Mechanisms of Viral DNA Packaging: Biophysical, Biochemical, & Genetic AnalysisR01GM088186 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CATALANO, CARLOS ENRIQUE, FEISS, MICHAEL · 2011 to 2014
$2.9M
Linking Kinetics, Subunit Coordination & Structure of a Viral DNA Packaging MotorR01GM118817 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ARYA, GAURAV, CHEMLA, YANN R. · 2016 to 2019
$1.5M
NIGMS NIH HHS R01 GM088186NIGMS NIH HHS R01 GM118817NIGMS NIH HHS R01 GM127365NSF MCB-1158328NSF MCB-1716219NSF PHY-0848905
6 · The paper itself

Abstract

Viral DNA packaging is a required step in the assembly of many dsDNA viruses. A molecular motor fueled by ATP hydrolysis packages the viral genome to near crystalline density inside a pre-formed prohead shell in ~5 min at room temperature in vitro. We describe procedures for measuring the packaging of single DNA molecules into single viral proheads with optical tweezers. Additionally, we describe techniques for conducting rapid solution exchange measurements that can be used to probe nucleotide-dependent motor-DNA interactions, stall and restart the motor to probe DNA conformational relaxation, and to probe the dynamics of release of the DNA, akin to ejection, in conditions where the motor fully releases its grip. Three viral packaging systems are described in detail: bacteriophages phi29 (φ29), lambda (λ), and T4. Two different approaches are described: 1. With φ29 and T4, prohead-motor complexes can be pre-assembled in bulk and packaging can be initiated in the optical tweezers by "feeding" a single DNA molecule to one of the complexes; 2. with φ29 and λ, packaging can be initiated in bulk then stalled, and a single prohead-motor-DNA complex can then be captured with optical tweezers and restarted. In both cases, the prohead is ultimately attached to one trapped microsphere and the end of the DNA being packaged is attached to a second trapped microsphere such that packaging of the DNA pulls the two microspheres together and the rate of packaging and force generated by the motor is directly measured in real time. These protocols allow for the effect of many experimental parameters on packaging dynamics to be studied such as temperature, ATP concentration, ionic conditions, structural changes to the DNA substrate, and mutations in the motor proteins. Procedures for capturing microspheres with the optical traps and different measurement modes are also described.

Indexed as

Bacteriophage T4DNA PackagingDNA, ViralOptical TweezersVirus AssemblyBacteriophage lambdaBacteriophagesSingle Molecule ImagingDNA, ViralMolecular motorsOptical tweezersSingle-molecule manipulationSolution exchangeViral DNA packaging

Identifiers

PMID39704950

What OpenQuestion holds

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Registered trials

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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 OpenQuestion graph.