Visualizing Poloidal Orientation in DNA Minicircles

Harold D. Kim; Tony Lemos

REVIEW 4 major objections 3 minor 48 references

Visualizing Poloidal Orientation in DNA Minicircles

T0 review · 4 major / 3 minor · reviewed 2026-08-05 · deepseek-v4-flash

Challenge this review Re-run · record.json Download PDF Read on arXiv ↗ Review JSON

Pith's one-line read This paper reports experimental confirmation of sequence-dependent poloidal orientation in DNA minicircles, using AFM to see whether a biotin label lands inside or outside the circle.

desk verdict Clever first experimental attack on a real prediction, but the label-carrying insert is a plausible confound that the available text doesn't rule out. read the letter →

arxiv 2508.15091 v1 pith:JP4NSCJY submitted 2025-08-20 physics.bio-ph q-bio.BM

Tony Lemos , Harold D. Kim This is my paper · ORCID

classification physics.bio-phq-bio.BM

keywords DNAminicirclepoloidalorientationatomicforcemicroscopysingle-moleculebiophysicssequence-dependentbending601nucleosomepositioningsequenceA-tractscoarse-grainedsimulation

verification ladder T0 review T1 audit T2 compute T3 formal

The pith

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The reading

Short DNA circles are predicted to bend unevenly because sequence-dependent energetics define a preferred side of the duplex to face inward—the poloidal orientation. The paper introduces an AFM-based single-molecule readout for that orientation: each minicircle carries a single biotin at one of seven positions along one helical turn, and bound NeutrAvidin marks whether that position sits inside or outside the circle. Applying this to two sequences predicted to have strong preferences—one derived from the 601 nucleosome positioning sequence, one from six in-phase A-tracts—the authors observe opposite phase shifts in the inside/outside position, and coarse-grained simulations reproduce narrowly distributed, sequence-specific orientations. If correct, these results give direct experimental evidence that poloidal orientation is real and sequence-dependent, supporting the view that nonuniform bending energetics shape the dynamics of circular DNA.

What carries the argument

The central object is poloidal orientation: the angle specifying which side of the DNA double helix faces the center of a minicircle versus facing outward. The readout machinery is a biotin ruler—seven constructs with a single biotin placed at successive positions along one helical turn—imaged by AFM through bound NeutrAvidin, which converts the unobservable bending-face angle into a binary inside/outside measurement. Coarse-grained simulations of the same sequences supply the predicted angular distributions that the AFM phases are compared against.

What would settle it

Repeat the same two core sequences with a set of biotin inserts whose sequences are permuted or reversed at the same positions: if the inside/outside phase follows the insert sequence rather than the core, the claim that the two cores have distinct poloidal orientations collapses. A simpler check is to place the same insert sequence in different registers along the core and see whether the phase shifts track the insert's own bend direction.

Watch

Extended reading notes

Core claim

The paper's central claim is that a short DNA minicircle adopts a preferred poloidal orientation—a sequence-determined choice of which face of the double helix bends toward the center of the circle. To test this, the authors made minicircles from an 85-nt core taken from either the left half of the 601 nucleosome positioning sequence or from six in-phase A-tracts, inserting a 20-nt biotin-tagged segment at seven positions spaced along one helical turn. AFM images scored whether the NeutrAvidin label appeared inside or outside the circle. For the two cores, the inside/outside position shifted with different phase as the insert moved around the helix, indicating distinct mean poloidal orientat

Load-bearing premise

The load-bearing premise is that the measured inside/outside position of the NeutrAvidin label reports the poloidal orientation of the 85-nucleotide core sequence, rather than being dominated by the bend preference of the 20-nucleotide biotin-tagged insert that carries the label.

Editorial extensions

If this is right

Poloidal orientation is measurable and sequence-specific, so a short DNA circle's shape is defined not only by its curvature but by which face of the helix bends inward.
Two known bending-relevant motifs, the 601 nucleosome positioning sequence and in-phase A-tracts, have opposite preferred orientations, meaning sequence identity controls how a minicircle presents its surface.
Coarse-grained simulations that include sequence-dependent bending can predict the orientation, giving a computational handle for designing circular DNA with intended inside/outside features.
The biotin-position ladder provides a general AFM assay for mapping the bending landscape of arbitrary roughly 85-bp sequences.
The result connects sequence-dependent DNA mechanics to topologically constrained DNA behavior such as looping, where the inward-facing side of a circle is the side most relevant for protein access.

Reading between the lines

Editorial extensions of the paper, not claims the author makes directly.

If the insert-position confound is controlled, the same ladder could map poloidal orientation across many sequence motifs, turning AFM into a readout for the direction, not just the magnitude, of sequence-dependent DNA bending.
Because the orientation determines which bases face inward, protein-binding sites on the inner face of a small circle could be sterically occluded, which would matter for DNA looping and chromatin studies.
The phase-shift method could be extended to detect orientation changes induced by protein binding, salt, or supercoiling, since such perturbations should rotate the phase of the inside/outside signal.
The close match with simulation suggests the models could predict the orientation of a new sequence before synthesis, enabling design of minicircles with labels or reactive groups deliberately placed on the inside or outside surface.

Share X Bluesky LinkedIn Reddit HN

Signed reviews

No signed human review yet.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, and a circularity audit.

Desk Editor's Note

read the letter

The premise is solid: theory has predicted sequence-dependent poloidal orientation for short DNA minicircles, and there's been no direct experimental test. The design is genuinely clever—biotin at different positions along a helical turn, AFM readout of inside/outside—and the abstract's claim is crisp: two sequences show different phases, and coarse-grained simulations match. If the data hold up, this is a real first.

The soft spot is load-bearing: the readout is on a 20-nt insert, not on the core sequence that is supposed to set the poloidal orientation. The insert is a sequence-specific piece of DNA with a biotin-dT, sitting at one of seven positions. If that insert has any intrinsic bend—or bends differently at the two core junctions—the observed inside/outside phase could report the insert's local orientation rather than the core's poloidal orientation. The abstract and the visible captions do not say whether the insert sequence is identical across constructs, whether the simulations include it, or whether there was any control for insert bending. Without that, the headline conclusion does not cleanly separate the label carrier from the thing being measured.

The full text is corrupted in the arXiv posting, so I can't check whether the authors addressed this in the main text. That's a practical problem for review but not a scientific one, assuming the authors have the real text. If they can show that the insert is explicitly modeled in the simulation and that the phase pattern is insensitive to its own bend, the paper is likely solid. As is, it's an unverified claim with a plausible confound.

Who's this for? Single-molecule biophysicists and DNA mechanics people. The technique itself could be useful even if the specific conclusion needs more work. If the full text is intact, send it to review, but ask the referee to scrutinize the insert handling. I wouldn't cite it yet.

Referee Report

4 major / 3 minor

Summary. The paper introduces an AFM-based single-molecule assay to visualize the poloidal orientation (the inside/outside face) of short DNA minicircles. A biotin within a 20-nt insert is placed at different positions along an 85-nt core, and the location of NeutrAvidin relative to the minicircle loop is measured. For two core sequences (the 601 half and an A-tract sequence), the inside/outside probability varies with insert position with different phases, which the authors interpret as distinct preferred poloidal orientations. Coarse-grained simulations are reported to show narrow poloidal distributions with different mean orientations, consistent with the AFM data. The paper claims the first experimental confirmation of sequence-dependent poloidal orientation in DNA minicircles.

Significance. If the interpretation is correct, this is the first direct experimental observation of a theoretically predicted but previously unseen phenomenon: sequence-dependent poloidal orientation in short DNA minicircles. The AFM readout is externally grounded: the position of a protein label does not presuppose the orientation it is used to infer, so the study is not circular. The agreement with coarse-grained simulations, if genuine, would be a valuable cross-validation. However, the version of the manuscript under review is not verifiable: the main text is largely unreadable due to character corruption, and the legible parts leave a potentially load-bearing confound unaddressed.

major comments (4)

[Figure S1 / Abstract] The central readout is the position of NeutrAvidin attached to a biotin-modified dT within a 20-nt insert. Figure S1 shows that every construct is an 85-nt core plus this insert, but the insert sequence is not given and no control for its own bend preference is described. If the insert has an intrinsic curvature or the biotin-dT perturbs local stacking, the inside/outside phase may be set by the insert rather than by the core; because the two cores differ, the core-insert junction also differs, so a differential phase between the 601 and A-tract series need not reflect the cores' poloidal orientations. The authors should state whether the insert sequence is identical in all constructs, include controls with alternate insert sequences, and/or show that simulations omitting the insert reproduce the same phase shift.
[Full text / Methods] The supplied main text is not readable: large portions consist of garbled characters, so the experimental protocol, the image-analysis procedure, the definition of the poloidal angle, and the simulation details cannot be checked. This is not a mere presentation issue; it makes verification of the central claim impossible in the version provided. A complete, readable manuscript with full Methods is required.
[Abstract / Coarse-grained simulations] The abstract states that coarse-grained simulations 'revealed' a narrow distribution and different mean orientation for each sequence, but no simulation parameters or fitting procedure are legible. If the sequence-dependent stiffness parameters were adjusted to reproduce the AFM phase shift, then the agreement is not independent confirmation. The authors must report whether the parameters are taken from prior work or fitted here, and must quantify the comparison (e.g., predicted vs measured phase for all seven insert positions).
[Figure S4] The histograms in Figure S4 are presented without sample sizes, fit functions, or statistical uncertainties. The claims of 'narrowly distributed' poloidal angles and of a significant phase difference between the 601 and A-tract series require a quantitative comparison (e.g., circular statistics, confidence intervals, or a permutation test). Without these, the quoted phase shift is not supported.

minor comments (3)

[Figure S4 caption] The caption says the insert position 'changes from 0 to 12', which is more than one helical turn (10.5 bp/turn). Please clarify whether the positions are along the 85-nt core or phasing relative to the helical repeat, and specify the exact total length of each minicircle (85+20 bp).
[Figure S1 / Table S1] Figure S1 refers to Table S1 for the full sequence list, but Table S1 is not legible in the supplied version. Please ensure all supplementary tables are included and readable.
[Abstract] The abstract uses 'short (<150 bp)' but the construct appears to be 105 bp. Stating the exact length and confirming the ligation product is a monomeric circle (e.g., by gel or AFM contour-length control) would strengthen the description.

Circularity Check

0 steps flagged · score 0.0 of 10

No significant circularity: AFM phase measurement is an external observable and the simulations are used for comparison, not fit to the data.

full rationale

I walked the claimed derivation chain. The experiment places a biotin at defined positions along one helical turn of each minicircle (Figure S1), images the bound NeutrAvidin with AFM, and reads out whether the label lies inside or outside the circle. The phase of that inside/outside signal across insert positions is a direct geometric observable, not a quantity defined by the poloidal-orientation claim. The coarse-grained simulations are described as revealing mean poloidal orientations for the two sequences and are compared with the AFM results; nothing in the legible text states that simulation parameters were fitted to the AFM inside/outside positions, and no equation or passage shows the predicted orientation being defined from the measured phase. The skeptic's insert-sequence confound is a possible experimental-control issue, but it is not circularity: even if the 20-nt insert controlled the phase, that would be an alternative explanation rather than a reduction of the conclusion to its own inputs. No load-bearing self-citation is evident. The paper is self-contained against the external AFM observable, so the circularity score is 0.

Assumptions & free parameters 1 free parameters · 3 assumptions · 0 invented entities

The full text is corrupted, so this ledger is reconstructed from the abstract and three legible figure captions. The central assumptions concern the AFM readout, the insert construct, and the simulation model. No new physical entities are introduced; the poloidal orientation concept predates this paper. The coarse-grained model's parameters are inherited from prior work and their provenance could not be verified.

free parameters (1)

Coarse-grained model sequence-dependent stiffness parameters
The simulation agreement is the corroborating evidence, but the model's bending and twist parameters are not stated in the abstract; they are presumably inherited from earlier fitted models. The corrupted full text hides their provenance.

assumptions (3)

domain assumption Inside/outside classification of NeutrAvidin from AFM images reflects the true 3D poloidal orientation of the minicircle before adsorption.
All conclusions come from locating the protein relative to the loop in 2D projections; if adsorption distorts the circle or its face orientation, the phase would be a flattening artifact.
domain assumption The 20-nt biotin-labelled insert does not override the core sequence's bending preference.
Seven constructs differ only by insert position; interpreting the phase differences across positions as the core's poloidal orientation requires the insert to be a passive marker. Figure S1.
domain assumption The coarse-grained simulation model is a faithful representation of sequence-dependent DNA bending for roughly 105 bp circles.
Agreement between simulation and AFM is cited as confirmation; that agreement inherits all model assumptions and parameters.

how reviews work

0 comments

Cite this review

Pith. "Pith review of Visualizing Poloidal Orientation in DNA Minicircles." pith.science (2026). https://pith.science/paper/JP4NSCJY

@misc{pith2026250815091,
  author       = {Pith},
  title        = {Pith review of: Visualizing Poloidal Orientation in DNA Minicircles},
  year         = {2026},
  howpublished = {\url{https://pith.science/paper/JP4NSCJY}},
  note         = {Machine review of arXiv:2508.15091}
}

read the original abstract

A short (<150 bp) double-stranded DNA (dsDNA) molecule ligated end-to-end forms a DNA minicircle. Due to sequence-dependent, nonuniform bending energetics, such a minicircle is predicted to adopt a certain inside-out orientation, known as the poloidal orientation. Despite theoretical and computational predictions, experimental evidence for this phenomenon has been lacking. In this study, we introduce a single-molecule approach to visualize the poloidal orientation of DNA minicircles. We constructed a set of DNA minicircles, each containing a single biotin located at a different position along one helical turn of the dsDNA, and imaged the location of biotin-bound NeutrAvidin relative to the DNA minicircle using atomic force microscopy (AFM). We applied this approach to two DNA sequences previously predicted to exhibit strongly preferred poloidal orientations. The observed relative positions of NeutrAvidin shifted between the inside and outside of the minicircle with different phases, indicating distinct poloidal orientations for the two sequences. Coarse-grained simulations revealed narrowly distributed poloidal orientations with different mean orientations for each sequence, consistent with the AFM results. Together, our findings provide experimental confirmation of preferred poloidal orientations in DNA minicircles, offering insights into the intrinsic dynamics of circular DNA.

Discussion (0). Continue with ORCID to comment.

Reference graph

Works this paper leans on

48 extracted references · 47 canonical work pages

[1]

author author R. E. \ Dickerson ,\ title title Dna bending: the prevalence of kinkiness and the virtues of normality ,\ @noop journal journal Nucleic acids research \ volume 26 ,\ pages 1906 ( year 1998 ) NoStop

work page 1906
[2]

Ma \ and\ author A

author author N. Ma \ and\ author A. van der Vaart ,\ title title Anisotropy of b-dna groove bending ,\ @noop journal journal Journal of the American Chemical Society \ volume 138 ,\ pages 9951 ( year 2016 ) NoStop

work page 2016
[3]

Basu , author D

author author A. Basu , author D. G. \ Bobrovnikov , author Z. Qureshi , author T. Kayikcioglu , author T. T. \ Ngo , author A. Ranjan , author S. Eustermann , author B. Cieza , author M. T. \ Morgan , author M. Hejna , et al. ,\ title title Measuring dna mechanics on the genome scale ,\ @noop journal journal Nature \ volume 589 ,\ pages 462 ( year 2021 ) NoStop

work page 2021
[4]

Jeong \ and\ author H

author author J. Jeong \ and\ author H. D. \ Kim ,\ title title Determinants of cyclization--decyclization kinetics of short dna with sticky ends ,\ @noop journal journal Nucleic acids research \ volume 48 ,\ pages 5147 ( year 2020 ) NoStop

work page 2020
[5]

Yoo , author S

author author J. Yoo , author S. Park , author C. Maffeo , author T. Ha ,\ and\ author A. Aksimentiev ,\ title title Dna sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of dna minicircles ,\ @noop journal journal Nucleic acids research \ volume 49 ,\ pages 11459 ( year 2021 ) NoStop

work page 2021
[6]

Kuli \'c , author R

author author I. Kuli \'c , author R. Thaokar ,\ and\ author H. Schiessel ,\ title title Twirling dna rings—swimming nanomotors ready for a kickstart ,\ @noop journal journal Europhysics Letters \ volume 72 ,\ pages 527 ( year 2005 ) NoStop

work page 2005
[7]

Kim , author C

author author M. Kim , author C. C. \ Hong , author S. Lee ,\ and\ author J. S. \ Kim ,\ title title Dynamics of a dna minicircle: Poloidal rotation and in-plane circular vibration ,\ @noop journal journal Bulletin of the Korean Chemical Society \ volume 43 ,\ pages 523 ( year 2022 ) NoStop

work page 2022
[8]

author author T. E. \ Cloutier \ and\ author J. Widom ,\ title title Spontaneous sharp bending of double-stranded dna ,\ @noop journal journal Molecular cell \ volume 14 ,\ pages 355 ( year 2004 ) NoStop

work page 2004

Show all 48 references

[9]

Geggier \ and\ author A

author author S. Geggier \ and\ author A. Vologodskii ,\ title title Sequence dependence of dna bending rigidity ,\ @noop journal journal Proceedings of the National Academy of Sciences \ volume 107 ,\ pages 15421 ( year 2010 ) NoStop

2010
[10]

Du , author C

author author Q. Du , author C. Smith , author N. Shiffeldrim , author M. Vologodskaia ,\ and\ author A. Vologodskii ,\ title title Cyclization of short dna fragments and bending fluctuations of the double helix ,\ @noop journal journal Proceedings of the National Academy of S...

2005
[11]

Pasi , author D

author author M. Pasi , author D. Mornico , author S. Volant , author A. Juchet , author J. Batisse , author C. Bouchier , author V. Parissi , author M. Ruff , author R. Lavery ,\ and\ author M. Lavigne ,\ title title Dna minicircles clarify the specific role of dna structure ...

2016
[12]

Mills \ and\ author F

author author A. Mills \ and\ author F. Gago ,\ title title Atomistic insight into sequence-directed dna bending and minicircle formation propensity in the absence and presence of phased a-tracts ,\ @noop journal journal Journal of Computer-Aided Molecular Design \ volume 34 ,...

2020
[13]

Kim , author S

author author M. Kim , author S. Bae , author I. Oh , author J. Yoo ,\ and\ author J. S. \ Kim ,\ title title Sequence-dependent twist-bend coupling in dna minicircles ,\ @noop journal journal Nanoscale \ volume 13 ,\ pages 20186 ( year 2021 ) NoStop

2021
[14]

Kumar , author L

author author P. Kumar , author L. W. \ Dillon , author Y. Shibata , author A. A. \ Jazaeri , author D. R. \ Jones ,\ and\ author A. Dutta ,\ title title Normal and cancerous tissues release extrachromosomal circular dna (eccdna) into the circulation ,\ @noop journal journal M...

2017
[15]

author author H. D. \ M ller , author M. Mohiyuddin , author I. Prada-Luengo , author M. R. \ Sailani , author J. F. \ Halling , author P. Plomgaard , author L. Maretty , author A. J. \ Hansen , author M. P. \ Snyder , author H. Pilegaard , et al. ,\ title title Circular dna e...

2018
[16]

Paulsen , author Y

author author T. Paulsen , author Y. Shibata , author P. Kumar , author L. Dillon ,\ and\ author A. Dutta ,\ title title Small extrachromosomal circular dnas, microdna, produce short regulatory rnas that suppress gene expression independent of canonical promoters ,\ @noop jour...

2019
[17]

Mitchell , author C

author author J. Mitchell , author C. Laughton ,\ and\ author S. A. \ Harris ,\ title title Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled dna ,\ @noop journal journal Nucleic acids research \ volume 39 ,\ pages 3928 ( year 2011 ) NoStop

2011
[18]

author author J. S. \ Mitchell \ and\ author S. A. \ Harris ,\ title title Thermodynamics of writhe in dna minicircles from molecular dynamics simulations ,\ @noop journal journal Physical review letters \ volume 110 ,\ pages 148105 ( year 2013 ) NoStop

2013
[19]

Sutthibutpong , author C

author author T. Sutthibutpong , author C. Matek , author C. Benham , author G. G. \ Slade , author A. Noy , author C. Laughton , author J. P. \ K. Doye , author A. A. \ Louis ,\ and\ author S. A. \ Harris ,\ title title Long-range correlations in the mechanics of small dna ci...

2016
[20]

author author J. D. \ Curuksu ,\ title title Spectral analysis of dna superhelical dynamics from molecular minicircle simulations ,\ @noop journal journal The Journal of Chemical Physics \ volume 159 ( year 2023 ) NoStop

2023
[21]

author author S. R. \ Khan , author S. Sakib , author M. S. \ Rahman ,\ and\ author M. A. H. \ Samee ,\ title title Deepbend: an interpretable model of dna bendability ,\ @noop journal journal Iscience \ volume 26 ( year 2023 ) NoStop

2023
[22]

author author J. D. \ Parvin , author R. J. \ McCormick , author P. A. \ Sharp ,\ and\ author D. E. \ Fisher ,\ title title Pre-bending of a promoter sequence enhances affinity for the tata-binding factor ,\ @noop journal journal Nature \ volume 373 ,\ pages 724 ( year 1995 ) NoStop

1995
[23]

Kim , author G

author author J. Kim , author G. De Haan , author A. M. \ Nardulli ,\ and\ author D. J. \ Shapiro ,\ title title Prebending the estrogen response element destabilizes binding of the estrogen receptor dna binding domain ,\ @noop journal journal Molecular and cellular biology \ ...

1997
[24]

Lohmann , author J

author author F. Lohmann , author J. Valero ,\ and\ author M. Famulok ,\ title title A novel family of structurally stable double stranded dna catenanes ,\ @noop journal journal Chemical Communications \ volume 50 ,\ pages 6091 ( year 2014 ) NoStop

2014
[25]

Ackermann , author T

author author D. Ackermann , author T. L. \ Schmidt , author J. S. \ Hannam , author C. S. \ Purohit , author A. Heckel ,\ and\ author M. Famulok ,\ title title A double-stranded dna rotaxane ,\ @noop journal journal Nature nanotechnology \ volume 5 ,\ pages 436 ( year 2010 ) NoStop

2010
[26]

Valero , author N

author author J. Valero , author N. Pal , author S. Dhakal , author N. G. \ Walter ,\ and\ author M. Famulok ,\ title title A bio-hybrid dna rotor--stator nanoengine that moves along predefined tracks ,\ @noop journal journal Nature nanotechnology \ volume 13 ,\ pages 496 ( ye...

2018
[27]

Valero , author M

author author J. Valero , author M. Centola , author Y. Ma , author M. S kugor , author Z. Yu , author M. W. \ Haydell , author D. Keppner ,\ and\ author M. Famulok ,\ title title Design, assembly, characterization, and operation of double-stranded interlocked dna nanostructur...

2019
[28]

Yu , author M

author author Z. Yu , author M. Centola , author J. Valero , author M. Matthies , author P. Sulc ,\ and\ author M. Famulok ,\ title title A self-regulating dna rotaxane linear actuator driven by chemical energy ,\ @noop journal journal Journal of the American Chemical Society ...

2021
[29]

Thibault , author J

author author T. Thibault , author J. Degrouard , author P. Baril , author C. Pichon , author P. Midoux ,\ and\ author J.-M. \ Malinge ,\ title title Production of dna minicircles less than 250 base pairs through a novel concentrated dna circularization assay enabling minicirc...

2017
[30]

Casas , author F

author author G. Casas , author F. Perche , author P. Midoux , author C. Pichon ,\ and\ author J.-M. \ Malinge ,\ title title Dna minicircles as novel stat3 decoy oligodeoxynucleotides endowed with anticancer activity in triple-negative breast cancer ,\ @noop journal journal M...

2022
[31]

Assenza \ and\ author R

author author S. Assenza \ and\ author R. P \'e rez ,\ title title Accurate sequence-dependent coarse-grained model for conformational and elastic properties of double-stranded dna ,\ @noop journal journal Journal of chemical theory and computation \ volume 18 ,\ pages 3239 ( ...

2022
[32]

Lowary \ and\ author J

author author P. Lowary \ and\ author J. Widom ,\ title title New dna sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning ,\ @noop journal journal Journal of molecular biology \ volume 276 ,\ pages 19 ( year 1998 ) NoStop

1998
[33]

author author H. S. \ Koo , author J. Drak , author J. A. \ Rice ,\ and\ author D. M. \ Crothers ,\ title title Determination of the extent of dna bending by an adenine-thymine tract ,\ @noop journal journal Biochemistry \ volume 29 ,\ pages 4227 ( year 1990 ) NoStop

1990
[34]

author author D. J. \ Hart , author J. Jeong , author J. C. \ Gumbart ,\ and\ author H. D. \ Kim ,\ title title Weak tension accelerates hybridization and dehybridization of short oligonucleotides ,\ @noop journal journal Nucleic Acids Research \ volume 51 ,\ pages 3030 ( year...

2023
[35]

author author P. J. \ Haynes , author K. H. \ Main , author B. Akpinar ,\ and\ author A. L. \ Pyne ,\ title title Atomic force microscopy of dna and dna-protein interactions ,\ in\ @noop booktitle Chromosome Architecture: Methods and Protocols \ ( publisher Springer ,\ year 20...

2022
[36]

author author C. A. \ Schneider , author W. S. \ Rasband ,\ and\ author K. W. \ Eliceiri ,\ title title Nih image to imagej: 25 years of image analysis ,\ @noop journal journal Nature methods \ volume 9 ,\ pages 671 ( year 2012 ) NoStop

2012
[37]

author author A. P. \ Thompson , author H. M. \ Aktulga , author R. Berger , author D. S. \ Bolintineanu , author W. M. \ Brown , author P. S. \ Crozier , author P. J. \ in 't Veld , author A. Kohlmeyer , author S. G. \ Moore , author T. D. \ Nguyen , author R. Shan , author M...

2021
[38]

author author B. E. \ Snodin , author F. Randisi , author M. Mosayebi , author P. S ulc , author J. S. \ Schreck , author F. Romano , author T. E. \ Ouldridge , author R. Tsukanov , author E. Nir , author A. A. \ Louis , et al. ,\ title title Introducing improved structural pr...

2015
[39]

author author D. M. \ Hinckley , author G. S. \ Freeman , author J. K. \ Whitmer ,\ and\ author J. J. \ De Pablo ,\ title title An experimentally-informed coarse-grained 3-site-per-nucleotide model of dna: Structure, thermodynamics, and dynamics of hybridization ,\ @noop journ...

2013
[40]

author author I. M. \ Kulic , author R. Thaokar ,\ and\ author H. Schiessel ,\ title title A dna ring acting as a thermal ratchet ,\ @noop journal journal Journal of Physics-Condensed Matter \ volume 17 ,\ pages S3965 ( year 2005 ) NoStop

2005
[41]

Song \ and\ author J

author author Y. Song \ and\ author J. S. \ Kim ,\ title title Structure and dynamics of double-stranded dna rotaxanes ,\ @noop journal journal Nanoscale \ volume 16 ,\ pages 4317 ( year 2024 ) NoStop

2024
[42]

Park , author G

author author J. Park , author G. Prokopchuk , author A. R. \ Popchock , author J. Hao , author T.-W. \ Liao , author S. Yan , author D. J. \ Hedman , author J. D. \ Larson , author B. K. \ Walther , author N. A. \ Becker , et al. ,\ title title Probing mechanical selection in...

2024
[43]

author author T. L. \ Higashi , author G. Pobegalov , author M. Tang , author M. I. \ Molodtsov ,\ and\ author F. Uhlmann ,\ title title A brownian ratchet model for dna loop extrusion by the cohesin complex ,\ @noop journal journal Elife \ volume 10 ,\ pages e67530 ( year 202...

2021
[44]

Dekker , author C

author author C. Dekker , author C. H. \ Haering , author J.-M. \ Peters ,\ and\ author B. D. \ Rowland ,\ title title How do molecular motors fold the genome? ,\ @noop journal journal Science \ volume 382 ,\ pages 646 ( year 2023 ) NoStop

2023
[45]

Biswas \ and\ author A

author author A. Biswas \ and\ author A. Basu ,\ title title The impact of the sequence-dependent physical properties of dna on chromatin dynamics ,\ @noop journal journal Current Opinion in Structural Biology \ volume 83 ,\ pages 102698 ( year 2023 ) NoStop

2023
[46]

Bonato , author J.-W

author author A. Bonato , author J.-W. \ Jang , author D.-G. \ Kim , author K.-W. \ Moon , author D. Michieletto ,\ and\ author J.-K. \ Ryu ,\ title title Spontaneously directed loop extrusion in smc complexes emerges from broken detailed balance and anisotropic dna search ,\ ...

2025
[47]

author author H. Bergwerf ,\ title title Molview: an attempt to get the cloud into chemistry classrooms ,\ @noop journal journal DivCHED CCCE: Committee on Computers in Chemical Education \ volume 9 ,\ pages 1 ( year 2015 ) NoStop

2015
[48]

author author M. D. \ Hanwell , author D. E. \ Curtis , author D. C. \ Lonie , author T. Vandermeersch , author E. Zurek ,\ and\ author G. R. \ Hutchison ,\ title title Avogadro: an advanced semantic chemical editor, visualization, and analysis platform ,\ @noop journal journa...

2012

Pith tools

Reviewed August 5, 2026 · model on record in the stance chip above.

[1] [1]

author author R. E. \ Dickerson ,\ title title Dna bending: the prevalence of kinkiness and the virtues of normality ,\ @noop journal journal Nucleic acids research \ volume 26 ,\ pages 1906 ( year 1998 ) NoStop

work page 1906

[2] [2]

Ma \ and\ author A

author author N. Ma \ and\ author A. van der Vaart ,\ title title Anisotropy of b-dna groove bending ,\ @noop journal journal Journal of the American Chemical Society \ volume 138 ,\ pages 9951 ( year 2016 ) NoStop

work page 2016

[3] [3]

Basu , author D

author author A. Basu , author D. G. \ Bobrovnikov , author Z. Qureshi , author T. Kayikcioglu , author T. T. \ Ngo , author A. Ranjan , author S. Eustermann , author B. Cieza , author M. T. \ Morgan , author M. Hejna , et al. ,\ title title Measuring dna mechanics on the genome scale ,\ @noop journal journal Nature \ volume 589 ,\ pages 462 ( year 2021 ) NoStop

work page 2021

[4] [4]

Jeong \ and\ author H

author author J. Jeong \ and\ author H. D. \ Kim ,\ title title Determinants of cyclization--decyclization kinetics of short dna with sticky ends ,\ @noop journal journal Nucleic acids research \ volume 48 ,\ pages 5147 ( year 2020 ) NoStop

work page 2020

[5] [5]

Yoo , author S

author author J. Yoo , author S. Park , author C. Maffeo , author T. Ha ,\ and\ author A. Aksimentiev ,\ title title Dna sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of dna minicircles ,\ @noop journal journal Nucleic acids research \ volume 49 ,\ pages 11459 ( year 2021 ) NoStop

work page 2021

[6] [6]

Kuli \'c , author R

author author I. Kuli \'c , author R. Thaokar ,\ and\ author H. Schiessel ,\ title title Twirling dna rings—swimming nanomotors ready for a kickstart ,\ @noop journal journal Europhysics Letters \ volume 72 ,\ pages 527 ( year 2005 ) NoStop

work page 2005

[7] [7]

Kim , author C

author author M. Kim , author C. C. \ Hong , author S. Lee ,\ and\ author J. S. \ Kim ,\ title title Dynamics of a dna minicircle: Poloidal rotation and in-plane circular vibration ,\ @noop journal journal Bulletin of the Korean Chemical Society \ volume 43 ,\ pages 523 ( year 2022 ) NoStop

work page 2022

[8] [8]

author author T. E. \ Cloutier \ and\ author J. Widom ,\ title title Spontaneous sharp bending of double-stranded dna ,\ @noop journal journal Molecular cell \ volume 14 ,\ pages 355 ( year 2004 ) NoStop

work page 2004