Statistical method for A-RNA and B-DNA

Marco Zoli

REVIEW 3 major objections 4 minor 120 references

Statistical method for A-RNA and B-DNA

T0 review · 3 major / 4 minor · reviewed 2026-08-15 · deepseek-v4-flash

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

Pith's one-line read A three-dimensional base-pair model reproduces the opposite twist-stretch response of B-DNA and A-RNA and predicts short-DNA cyclization J-factors far above worm-like-chain values.

desk verdict A self-review of the author's own mesoscopic model—no new results, the cyclization comparison is calibrated to the same data, and the twist-stretch attribution lacks an ablation. read the letter →

arxiv 2505.05053 v1 pith:HPDC4DZE submitted 2025-05-08 cond-mat.soft cond-mat.mes-hallphysics.bio-phq-bio.BM

Marco Zoli This is my paper · ORCID

classification cond-mat.softcond-mat.mes-hallphysics.bio-phq-bio.BM

keywords nucleicacidspropertiesmesoscopicHamiltonianmodelspathintegralmethodsbasepairfluctuationstwist-stretchcouplingA-RNAB-DNAcyclizationJ-factor

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

This review article argues that a three-dimensional mesoscopic model, in which each nucleotide is a point and base pairs breathe through a finite ensemble of radial fluctuations, can reproduce two experimentally observed properties of short nucleic acids that elastic-rod models miss. First, under tension the model makes B-DNA overtwist and A-RNA untwist, tracing the opposite behavior to the helical-form geometry, base-pair tilt and slide in the A-form, rather than to sequence. Second, for roughly 100-base-pair DNA the model gives cyclization J-factors orders of magnitude larger than worm-like-chain predictions, in line with single-molecule FRET measurements. The author presents this as evidence that modeling flexibility at the level of individual base pairs is needed at short length scales.

What carries the argument

The load-bearing object is the three-dimensional mesoscopic Hamiltonian of Eq. (2.1): a Morse potential $V_1$ for each base pair's hydrogen bonds, a solvent barrier term, and a nonlinear stacking potential $V_2$ between adjacent base pairs that depends on the bending angle $\varphi_n$ and twist angle $\theta_n$ through the dimer distance $d_{n,n-1}$. The statistical method is the finite-temperature path integral: each radial coordinate is expanded in Fourier modes, and the integration cutoff on the Fourier coefficients is fixed by a first-passage probability benchmark, $P_j(R_0, 0) \simeq 1/2$, which also prevents the partition-function divergence that plagues untwisted one-dimensional models. For twist-stretch curves, the paper adds a force term $-F_{\rm ex}\, d_S \cos\varphi_n$, computes the free energy for a set of helical-repeat values $h$, and selects the equilibrium $\langle h \rangle^*$ by free-energy minimization. The A-form geometry enters as average tilt $\gamma = 15^\circ$ and slide $S$, which shorten the rise distance $d_S$ and, the calculation shows, drive untwisting under load.

What would settle it

Run the path-integral calculation for the A-form RNA parameter set with $\gamma = S = 0$ while keeping all other parameters fixed: the model must then produce B-DNA-like overtwisting. Any experiment or atomistic simulation showing that RNA-like untwisting persists in this geometric setting would refute the central claim that the opposite twist-stretch pattern follows from the helical-form tilt and slide.

Watch

Extended reading notes

Core claim

The central claim is that a discrete Hamiltonian with one radial coordinate per base pair, plus bending and twist angles between adjacent pairs, contains enough physics to explain the twist-stretch dichotomy and short-scale bendability of double-stranded nucleic acids. For the B-form (zero tilt and slide), the equilibrium helical repeat decreases as the applied force increases, meaning DNA overtwists; for the A-form, the same calculation with a base-pair tilt $\gamma = 15^\circ$ and a negative slide $S$ produces the opposite trend, meaning RNA untwists under tension. The same partition-function machinery, with a loop-closure constraint, yields J-factors for chains of 60 to 140 base pairs that stay appreciable down to about $10^{-12}$ mol/litre at $N = 80$, whereas the worm-like-chain model drives the looping probability toward zero at short lengths. The paper concludes that the mesoscopic Hamiltonian captures the experimentally observed bendability of about 100-base-pair fragments because it allows large bending angles and independent base-pair fluctuations at every site.

Load-bearing premise

The fragile premise is that the A-form versus B-form difference in twist-stretch response can be represented by two average geometric inputs, base-pair tilt $\gamma = 15^\circ$ and slide $S$, in a point-nucleotide Hamiltonian, even though the paper concedes that the true cause is the atomic-scale sugar-pucker conformation, which the model cannot represent.

Editorial extensions

If this is right

If the model is right, the opposite twist-stretch responses of double-stranded DNA and RNA are a structural consequence of helical form, not of base sequence or of fine atomic interactions.
The J-factor results imply that fragments around 80 to 100 base pairs are considerably more bendable than worm-like-chain estimates, supporting the idea that short DNA can wrap and loop with ease.
Open-end and fraying effects raise the equilibrium helical repeat and enhance flexibility under moderate loads, so terminal base pairs should be included when predicting short-fragment mechanics.
For channel confinement, the model predicts that reducing the channel diameter straightens the molecule, increasing the end-to-end distance by up to a factor of three at strong confinement.

Reading between the lines

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

One could test the geometric explanation directly by running the same path-integral calculation with $\gamma = S = 0$ while keeping all other RNA parameters fixed; the model would then predict DNA-like overtwisting, whereas experiments on genuine A-form duplexes with normal ribose pucker would still show untwisting if the atomic-scale sugar pucker is the true cause.
If tilt and slide are indeed sufficient effective coordinates, the same machinery could predict twist-stretch coupling for other helical forms, such as Z-DNA or DNA-RNA hybrids, simply by changing those average geometric inputs.
The first-passage cutoff method is a self-contained way to set fluctuation amplitudes, so it could in principle be transferred to other coarse-grained helical polymer models that suffer from unbounded phase spaces.

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

Colleague,

This is a self-review of Zoli's own mesoscopic Hamiltonian model for nucleic acids. The figures and equations are reprinted from his earlier papers; there is no new computation or independent validation. Take the headline claims with that frame.

What the paper does well: it gives a clear, compact account of the path-integral method and the fluctuation cutoff, and it is unusually honest about what the model cannot do. The limitation in Section 4.A that a point-nucleotide model cannot capture the ultimate sugar-pucker origin is stated plainly. The channel-stretching part is illustrative but self-consistent.

The soft spots are real. The cyclization 'prediction' is not independent: Section 4.C says rho_n and alpha_n are set by matching the model J-factor to the experimental looping probability at N~100, and the same data are then used in Fig. 6(b) to claim agreement. That is calibration, not validation. The twist-stretch attribution also has a load-bearing gap. The abstract says the opposite pattern follows from the different structural features, and the text calls base-pair inclination the primary cause. But the A-form inputs differ in three ways at once—R0=24 Å, gamma=15°, and S<0—and no calculation separates them. A curve with A-form radius and gamma=0 is never shown. So the sign change could be driven by the larger diameter or by the force-coupling term, not by tilt. The stress-test note is right about this. The limitation paragraph concedes the model can't represent the atomic source, which makes the 'explains it' language in the abstract stronger than what is actually demonstrated.

Who gets value: someone wanting a single-source summary of Zoli's model and its earlier results. But as a claim of explaining DNA/RNA mechanical differences, it is not there yet. A referee should ask for an ablation (gamma vs S vs R0) and for out-of-sample cyclization tests, ideally with code and data.

My call: it deserves a serious referee—it's a legitimate review with formal machinery, not a crackpot or a sloppy paper—but I would not cite it as independent evidence for the flexibility claims.

Referee Report

3 major / 4 minor

Summary. The manuscript presents a three-dimensional mesoscopic Hamiltonian model of double-stranded nucleic acids, treated by a finite-temperature path-integral method, and applies it to three problems: the twist-stretch response of B-DNA versus A-RNA, DNA stretching in a cylindrical nanochannel, and the cyclization J-factor of short DNA fragments. The paper claims that the model reproduces the experimentally observed opposite behavior (DNA overtwists, RNA untwists under tension) and attributes this to the different structural features of the two helical forms, in particular base-pair inclination. It also reports that the model yields cyclization J-factors at approximately 100 base pairs that are much larger than worm-like-chain predictions and consistent with FRET measurements. The manuscript is written as a review of the author's prior work, with the present version adding the A-RNA/B-DNA comparison and the cyclization discussion.

Significance. If the claims were fully supported, the model would be a useful coarse-grained alternative to worm-like-chain descriptions for short nucleic acid fragments, and the path-integral cutoff construction is a potentially valuable way to regularize base-pair fluctuation integrals. The cyclization calculation, however, is not an independent test because the parameters rho_n and alpha_n are calibrated to the experimental J-factor that the model then reproduces. The twist-stretch attribution is also not tested by an ablation of the structural parameters. The paper's strengths are the internally consistent computational framework and the explicit treatment of finite-size effects, but the central mechanistic claims need additional support before the results can be accepted as demonstrated.

major comments (3)

[Section 4.C, Eq. (4.2)] The cyclization prediction is not independent. The text states that rho_n and alpha_n are estimated by comparing the model J-factor with the experimentally available looping probability, with the J-factor order of magnitude at N approximately 100 used as a reference point and the choice 'not unique.' Consequently, the agreement in Fig. 6(b) is built into the parameter selection, and the claim that short fragments 'maintain a sizeable bendability in line with the experimental data' is not a test of the model. Please either present a parameter-free prediction, show a systematic sensitivity analysis over a physically justified range of (rho_n, alpha_n), or demonstrate that the order-of-magnitude enhancement over WLC survives without any calibration to the FRET data.
[Section 4.A, Fig. 3(b)] The assertion that base-pair inclination is the primary cause of RNA untwisting is not supported by the calculations shown. All A-form curves in Fig. 3(b) combine gamma = 15 degrees with R0 = 24 Angstrom, and no curve with gamma = 0 at the A-form radius is displayed; likewise, the effect of slide is only shown in the presence of tilt. The observed sign difference could therefore arise from the larger radius or from the modified force coupling d_S in the term -F_ex d_S cos(phi_n), rather than from tilt per se. Please provide an ablation varying gamma, S, and R0 independently, or a formal argument isolating the contribution of each parameter.
[Section 4.A, limitation paragraph] The paper's headline mechanism is weakened by its own stated limitation. The paragraph near the end of Section 4.A concedes that the ultimate origin of the DNA/RNA difference is the sugar-pucker conformation at atomic scale, which the point-nucleotide Hamiltonian cannot represent. If the model's (gamma, S, R0) inputs are merely effective proxies, then the conclusion that the opposite twist-stretch pattern 'follows from the different structural features' needs to be tempered: the model shows that certain geometric inputs produce the observed sign, but it does not establish that those inputs are the cause rather than a fitted representation of it. Please clarify what, precisely, is being claimed about causality in the twist-stretch relation.

minor comments (4)

[Section 2, Eq. (2.1)] In the definition of H_b, the kinetic term is written with the index i (mu/2 dot-r_i^2) while the sum runs over n; this should be dot-r_n^2 for consistency.
[Section 3.A, Eq. (3.2)] The bracket structure in Eq. (3.2) is difficult to parse, especially the product over n â‰ j and the single-trajectory integral. A clearer display separating the closed and open measures would help the reader verify the normalization and the role of the Heaviside constraint.
[Section 4.C, Fig. 6] The figure caption and text state that the calculation is performed at helical repeat h = 10, chosen as an input so N/h is an integer. This choice suppresses the twist-dependent oscillatory J-factor behavior that is standard in cyclization literature; the paper should note more prominently that the comparison to WLC in Fig. 6(b) is made under this special condition.
[Abstract and conclusions] The abstract describes the work as a review, while Sections 4.A and 4.C present new calculations. Please align the wording (for instance, 'we review and extend') so that the contribution is stated accurately.

Circularity Check

1 steps flagged · score 6.0 of 10

Cyclization J-factor validation is calibrated to the same FRET data it is then compared against; twist-stretch attribution is underdetermined but not itself circular.

fitted input called prediction [Section 4.C, Eq. (4.2) and Fig. 6 discussion]
"Then, the latter can be estimated by comparing the J- factor given by the model with the experimentally available looping probability. In particular, we have considered the cyclization of molecules yielding a J- factor ~ 10^-9 mol / liter for N ~ 100 as measured by FRET. ... That order of magnitude is assumed as a reference point in order to set a pair of values, e.g. alpha_n = 2.5 A^-1 and rho_n = 1.3 although this choice is not unique. The latter values are then taken to calculate the J- factor for various chain lengths as plotted in Fig. 6(a)."

The J-factor is said to depend strongly on the stacking parameters rho_n and alpha_n. Those parameters are set by requiring the model's J-factor at N ~ 100 to match the experimentally measured order of magnitude (~10^-9 mol/liter) from FRET. The same experimental data are then displayed in Fig. 6(b) as the validation of the model's short-length bendability. Thus the headline claim that ~100 bp DNA is much more bendable than WLC predicts is, at the anchor point, a restatement of the calibration condition rather than an independent prediction. The paper's own caveat that the parameter choice is not unique further confirms that the match at N ~ 100 is imposed, not derived.

full rationale

The strongest circularity is confined to the cyclization application. In Section 4.C, the nonlinear stacking parameters rho_n and alpha_n are estimated by matching the model J-factor to the FRET-measured looping probability at N ~ 100, and the same experimental points are then used in Fig. 6(b) to claim agreement. For that anchor length, the 'prediction' reduces to the fitting condition, so this is a fitted input presented as validation. The N < 100 and N > 100 points retain some independent content, but the central short-DNA bendability claim is partly calibrated into the model. The twist-stretch analysis is different: the A-form inputs (R0 = 24 A, gamma = 15 deg, finite S) are taken from X-ray diffraction and molecular dynamics studies, not fitted to the magnetic-tweezers twist-stretch data, so the model calculation is a forward exercise. However, the paper's attribution that base-pair inclination is the 'primary cause' of RNA untwisting is not supported by an ablation that isolates gamma from R0 and S, and Section 4.A concedes the ultimate origin is atomic-scale sugar pucker. That is an underdetermination/correctness issue rather than a circularity. Self-citations to the author's prior papers provide method details and reprinted figures, but the central equations are stated and no load-bearing uniqueness theorem is imported. Overall, one of the three headline predictions is partially circular, giving a score of 6.

Assumptions & free parameters 7 free parameters · 6 assumptions · 0 invented entities

The paper's central results rest on a coarse-grained Hamiltonian with Morse pairing, nonlinear stacking, twist and bend angles, a solvent barrier, and a path-integral cutoff fixed by a zero-time probability benchmark. For the A-form helix, tilt and slide are imposed as uniform averages. The cyclization agreement is partly produced by fitting rho_n and alpha_n to the target J-factor. No new physical entities are introduced; the load is carried by the potential form, the input structural parameters, and the prior parameter fits.

free parameters (7)

rho_n (nonlinear stacking constant) = 1.3 (1.25 in sensitivity case)
Set so the model J-factor matches the roughly 10^-9 mol/L FRET cyclization value at N about 100 (Section 4.C); not unique.
alpha_n (nonlinear stacking range) = 2.5 inverse Angstrom
Set together with rho_n to match the cyclization benchmark; affects J-factor magnitude and short-length looping.
gamma (A-form base-pair tilt angle) = 15 degrees
Input for ds-RNA helical structure, taken from X-ray and MD in ref. [95]; controls untwisting under load in Fig. 3(b).
|S|/d (slide ratio for A-form dimers) = 0, 0.066, 0.133, 0.2
Average slide of base pairs in A-form helix; larger slide increases untwisting in computed twist-stretch curves.
R0 (average helix diameter) = 20 Angstrom (B-DNA), 24 Angstrom (A-RNA)
Morse potential minimum and reference for radial fluctuations; structural inputs for the two helical forms.
U or Lambda_j(T) (fluctuation cutoff) = U=5.2 at h=10.5, Lambda_j=1.08 Angstrom
Chosen by requiring the zero-time first-passage probability P_j(R0,0) approximately 1/2; sets the amplitude of base-pair breathing and affects all computed quantities.
D_n, b_n, K_{n,n-1} (Morse and stacking force parameters) = D_n=50 meV, b_n=5 inverse Angstrom for Fig. 6; K not quoted in this paper
Base-pair dissociation energy, potential range, and harmonic stacking constant from prior thermodynamic fits; values used in J-factor and twist-stretch calculations.

assumptions (6)

standard math Base-pair radial fluctuations can be expanded in a Fourier series with periodic boundary conditions and integrated via the path-integral measure of Eq. (3.4).
Underlies the partition function and all computed averages; standard finite-temperature path integral formalism.
domain assumption The Morse potential plus solvent barrier V_Sol and the nonlinear stacking potential V2 adequately represent the forces stabilizing the double helix.
This is the model assumption in Section 2; the entire calculation inherits its validity from this coarse-grained representation.
ad hoc to paper The integration cutoff is fixed by the benchmark P_j(R0,0) approximately 1/2 (Section 3.A).
This calibration criterion is not derived from external data; the resulting fluctuation amplitude is the basis for the computed thermodynamic and elastic properties.
domain assumption For A-form RNA, tilt gamma and slide S are uniform average values along the chain.
Stated in Section 2; local sequence variations in tilt and slide are neglected.
domain assumption The equilibrium helical repeat is selected by minimizing free energy over a discrete set of input h values.
Used in Sections 4.A and 4.B; assumes the discrete set of trial conformations is sufficient to find the physical equilibrium twist.
ad hoc to paper For cyclization, the experimental J-factor at N about 100 provides a valid reference for setting rho_n and alpha_n.
The paper states the choice is not unique and is used as reference; this makes the subsequent comparison at that length non-independent.

how reviews work

0 comments

Cite this review

Pith. "Pith review of Statistical method for A-RNA and B-DNA." pith.science (2026). https://pith.science/paper/HPDC4DZE

@misc{pith2026250505053,
  author       = {Pith},
  title        = {Pith review of: Statistical method for A-RNA and B-DNA},
  year         = {2026},
  howpublished = {\url{https://pith.science/paper/HPDC4DZE}},
  note         = {Machine review of arXiv:2505.05053}
}

abstract

Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of order $\sim 100$ base pairs have revealed remarkable flexibility properties at short scales and called for theoretical approaches that emphasize the role of the bending fluctuations at single sites along the molecule stack. Here, we review a three dimensional mesoscopic Hamiltonian model which assumes a discrete representation of the double stranded (ds) molecules at the level of the nucleotides. The model captures the fundamental local interactions between adjacent sugar-phosphate groups and the pairwise interactions between complementary base pair mates. A statistical method based on the path integral formalism sets the ensemble of the base pair breathing fluctuations which are included in the partition function and permits to derive the thermodynamics and the elastic response of single molecules to external forces. We apply the model to the computation of the twist-stretch relations for fragments of ds-DNA and ds-RNA, showing that the obtained opposite pattern (DNA overtwists whereas RNA untwists versus force) follows from the different structural features of the two helices. Moreover, we focus on the DNA stretching due to the confinement in nano-pores and, finally, on the computation of the cyclization probability of open ends molecules of $\sim 100$ base pairs under physiological conditions. The mesoscopic model shows a distinct advantage over the elastic rod model in estimating the molecule bendability at short length scale.

Figures

Figures reproduced from arXiv: 2505.05053 by the authors.

**Figure 2.** FIG. 2: (Color online) Reprinted from ref.[81]. First-pass [PITH_FULL_IMAGE:figures/full_fig_p016_2.png] view at source ↗

**Figure 3.** FIG. 3: (Color online) Reprinted from ref.[47]. (a) Equilib [PITH_FULL_IMAGE:figures/full_fig_p018_3.png] view at source ↗

Figures from the paper (3 more)

**Figure 4.** Figure 4: FIG. 4: (Color online) Reprinted from ref.[98]. Schematic fo [PITH_FULL_IMAGE:figures/full_fig_p019_4.png]

**Figure 5.** Figure 5: FIG. 5: (Color online) Reprinted from ref.[98]. (a) Free ene [PITH_FULL_IMAGE:figures/full_fig_p021_5.png]

**Figure 6.** Figure 6: FIG. 6: (Color online) Reprinted from ref.[41]. (a) [PITH_FULL_IMAGE:figures/full_fig_p023_6.png]

Discussion (0). Continue with ORCID to comment.

Reference graph

Works this paper leans on

120 extracted references · 80 canonical work pages

[1]

Each nu- cleotide is composed of a sugar ring, a phosphate group and a nitrog enous base

Introduction Nucleic acids are polymeric chains whose building blocks are the nucleot ides. Each nu- cleotide is composed of a sugar ring, a phosphate group and a nitrog enous base. The bases are connected by (glycosidic) covalent bonds to the deoxyribose s ugar in DNA and to the ribose sugar in RNA. The sugar of one nucleotide is connected to the phospha...
[2]

These work s are based on a three dimensional model, whose schematic in shown Fig

Model Several studies produced over the last years have investigated d enaturation bubbles, ther- modynamics, ﬂexibility, force/stretching relations and length distr ibution functions of linear chains and loops with variable size and sequence [61–64]. These work s are based on a three dimensional model, whose schematic in shown Fig. 1(a), in which the rn’...
[3]

Method 13 3.A Fluctuations Cutoﬀ 13
[4]

Results and Discussion 16 4.A Twist - Stretch relations 17 4.B Stretching DNA in a channel 19 4.C Cyclization probability 21
[5]

Conclusions The mechanical properties of nucleic acids have been extensively ch aracterized over the past decades following the development of a broad range of techniq ues [108, 109] that al- low one to manipulate single molecules and probe their response to ext ernal forces. Double stranded (ds) nucleic acids display a remarkable rigidity against bend in...
[6]

Declarations 25 References 26 3
[7]

refs.[75–78]

Method The model, for a chain with N base pairs, is studied by the path integral computational method, discussed in a number of papers, see e.g. refs.[75–78]. In t he ﬁnite temperature path integral formalism, the base pair displacements rn’s are treated as dynamical quantities whose time evolution is deﬁned by functions rn(τ) whereby τ ∈ [0, β ] is the E...
[8]

Results and Discussion After settling the cutoﬀ issue, we apply the statistical model to an alyze the interplay between form and helical conformation of nucleic acids, performing a quantitative analysis of their twist-stretch properties. Moreover, we test the model by evaluating the stretching of a DNA chain that is forced to ﬂow through a cylindrical cha...

Show all 120 references

[9]

25 Funding: No funding was received for conducting this study

Declarations Conﬂict of Interest: The author has no conﬂicts to disclose. 25 Funding: No funding was received for conducting this study. Data availability: The data that support the ﬁndings of this study are available from t he corresponding author upon reasonable request
[10]

Calladine, H.R

C.R. Calladine, H.R. Drew, Understanding DNA , Academic Press, San Diego, USA, 1992

1992
[11]

Peters, L.J

J.P. Peters, L.J. Maher III, DNA curvature and ﬂexibilit y in vitro and in vivo. Q. Rev. Biophys. 43, 23-63 (2010)

2010
[12]

Flory, Principles of Polymer Chemistry , Cornell University Press, Ithaca, New York (1953)

P.J. Flory, Principles of Polymer Chemistry , Cornell University Press, Ithaca, New York (1953)

1953
[13]

Smith, L

S. Smith, L. Finzi, C. Bustamante, Direct mechanical mea surement of the elasticity of single DNA molecules by using magnetic beads. Science, 258, 1122-1126, 1992

1992
[14]

Bustamante, J.F

C. Bustamante, J.F. Marko, E.D. Siggia, S. Smith, Entrop ic elasticity of lambda-phage DNA. Science, 265, 1599-1601, 1994

1994
[15]

Kratky, G

O. Kratky, G. Porod. R¨ ontgenuntersuchung gel¨ oster Fadenmolek¨ ule.Rec. Trav. Chim. Pays- Bas 68, 1106 (1949)

1949
[16]

Kratky, X-ray small angle scattering with substances of biological interest in diluted solutions

O. Kratky, X-ray small angle scattering with substances of biological interest in diluted solutions. Progress in Biophysics and Molecular Biology 13, 105-173 (1963)

1963
[17]

Savelyev, Do monovalent mobile ions aﬀect DNA’s ﬂexibi lity at high salt content? Phys

A. Savelyev, Do monovalent mobile ions aﬀect DNA’s ﬂexibi lity at high salt content? Phys. Chem. Chem. Phys. 14, 2250-2254 (2012)

2012
[18]

Odijk, Polyelectrolytes near the rod limit

T. Odijk, Polyelectrolytes near the rod limit. J. Polym. Sci.: Polym. Phys. Ed. 15, 477 (1977)

1977
[19]

Skolnick, M

J. Skolnick, M. Fixman, Electrostatic persistence len gth of a worm like polyelectrolyte. Macromolecules, 10, 944–948 (1977)

1977
[20]

J. L. Barrat, J.-F. Joanny, Persistence Length of polye lectrolyte chains. Europhys. Lett. 24, 333 (1993)

1993
[21]

Marko, E.D

J.F. Marko, E.D. Siggia, Stretching DNA. Macromolecules, 28, 8759-8770, (1995)

1995
[22]

Bouchiat, M.D

C. Bouchiat, M.D. Wang, J.-F. Allemand, T. Strick, S.M. Block, V. Croquette, Estimating the Persistence Length of a Worm-Like Chain Molecule from Fo rce-Extension Measurements. Biophys J. 76, 409-413 (1999). 26

1999
[23]

Odijk, Stiﬀ chains and ﬁlaments under tension

T. Odijk, Stiﬀ chains and ﬁlaments under tension. Macromolecules, 28, 7016-7018 (1995)

1995
[24]

M.D. Wang, H. Yin, R. Landick, J. Gelles, S.M. Block, Str etching DNA with Optical Tweez- ers. Biophys. J. 72, 1335-1346 (1997)

1997
[25]

van Mameren, P

J. van Mameren, P. Gross, G. Farge, P. Hooijman, M. Modes ti, M. Falkenberg, G.J.L. Wuite and E.J.G. Peterman, Unraveling the structure of DNA d uring overstretching by using multicolor, single-molecule ﬂuorescence imaging. Proc. Natl. Acad. Sci. USA 106, 18231- 18236 (2009)

2009
[26]

Bosaeus, A.H

N. Bosaeus, A.H. El-Sagheer, T. Brown, S.B. Smith, B. ˚ Akerman, C. Bustamante, B. Nord´ en, Tension induces a base-paired overstretched DNA conformat ion. Proc. Natl. Acad. Sci. USA 109, 15179-15184 (2012)

2012
[27]

Kiianitsa, A

K. Kiianitsa, A. Stasiak, Helical repeat of DNA in the re gion of homologous pairing. Proc. Natl. Acad. Sci. U.S.A. 94, 7837-7840 (1997)

1997
[28]

Leger, J

J.F. Leger, J. Robert, L. Bordieu, D. Chatenay, J.F. Mar ko, RecA binding to a single double- stranded DNA molecule: A possible role of DNA conformationa l ﬂuctuations. Proc. Natl. Acad. Sci. U.S.A. 95, 12295-12299 (1998)

1998
[29]

Ragunathan, C

K. Ragunathan, C. Liu, T. Ha, RecA ﬁlament sliding on DNA facilitates homology search. eLife 1, e00067 (2012)

2012
[30]

Skoruppa, A

E. Skoruppa, A. Voorspoels, J. Vreede, E. Carlon, Lengt h-scale-dependent elasticity in DNA from coarse-grained and all-atom models. Phys. Rev. E 103, 042408 (2021)

2021
[31]

Segers, A

M. Segers, A. Voorspoels, T. Sakaue, E. Carlon, Mechani cal properties of nucleic acids and the non-local twistable wormlike chain model. J. Chem. Phys. 156, 234105 (2022)

2022
[32]

Guti´ errez Fosado, F

Y.A. Guti´ errez Fosado, F. Landuzzi, T.Sakaue, Coarse Graining DNA: Symmetry, Nonlocal Elasticity, and Persistence Length. Phys. Rev. Lett. 130, 058402 (2023)

2023
[33]

C. Yuan, H. Chen, X.W. Lou, L.A. Archer, DNA Bending Stiﬀn ess on Small Length Scales. Phys. Rev. Lett. 100, 018102 (2008)

2008
[34]

Shore, J

D. Shore, J. Langowski, R.L. Baldwin, DNA ﬂexibility st udied by covalent closure of short fragments into circles. Proc. Natl. Acad. Sci. USA 78, 4833-4837 (1981)

1981
[35]

Horowitz, J.C

D.S. Horowitz, J.C. Wang, Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J. Mol. Biol. 173, 75-91 (1984)

1984
[36]

Cloutier, J

T.E. Cloutier, J. Widom, Spontaneous Sharp Bending of D ouble-Stranded DNA. Mol. Cell. 14, 355-362 (2004). 27

2004
[37]

Vafabakhsh, T

R. Vafabakhsh, T. Ha, Extreme Bendability of DNA Less th an 100 Base Pairs Long Revealed by Single-Molecule Cyclization. Science 337, 1097-1101 (2012)

2012
[38]

T.T. Le, H.D. Kim, Measuring Shape-Dependent Looping P robability of DNA. Biophys. J. 104, 2068-2076 (2013)

2013
[39]

A. Noy, R. Golestanian, Length Scale Dependence of DNA M echanical Properties. Phys. Rev. Lett. 109, 228101 (2012)

2012
[40]

Garai, S

A. Garai, S. Saurabh, Y. Lansac, P.K. Maiti, DNA Elastic ity from Short DNA to Nucleosomal DNA. J. Phys. Chem. B , 119, 11146-11156, (2015)

2015
[41]

Zoli, J- factors of short DNA molecules J

M. Zoli, J- factors of short DNA molecules J. Chem. Phys. 144, 214104 (2016)

2016
[42]

Zoli, Twist-stretch proﬁles of DNA chains

M. Zoli, Twist-stretch proﬁles of DNA chains. J. Phys.: Condens. Matter 29 225101 (2017)

2017
[43]

Q. Du, A. Kotlyar, A. Vologodskii, Kinking the double he lix by bending deformation. Nucl. Acids Res. 36, 1120-1128 (2008)

2008
[44]

Sanchez, H

D.S. Sanchez, H. Qu, D. Bulla, G. Zocchi, DNA kinks and bu bbles: Temperature dependence of the elastic energy of sharply bent 10-nm-size DNA molecul es. Phys. Rev. E 87, 022710 (2013)

2013
[45]

T.T. Le, H.D. Kim, Probing the elastic limit of DNA bendi ng. Nucleic Acids Res. 42, 10786- 10794 ( 2014)

2014
[46]

Salari, B

H. Salari, B. Eslami-Mossallan, S. Naderi, M.R. Ejteha di, Extreme bendability of DNA double helix due to bending asymmetry. J. Chem. Phys. 143, 104904 (2015)

2015
[47]

Y.Y. Wu, L. Bao, X. Zhang, Z.J. Tan, Flexibility of short DNA helices with ﬁnite-length eﬀect: From base pairs to tens of base pairs. J. Chem. Phys. 142, 125103 ( 2015)

2015
[48]

Zoli, Flexibility of short DNA helices under mechani cal stretching

M. Zoli, Flexibility of short DNA helices under mechani cal stretching. Phys. Chem. Chem. Phys. 18, 17666 (2016)

2016
[49]

Drozdetski, A

A.V. Drozdetski, A. Mukhopadhyay, A.V. Onufriev, Stro ngly Bent Double-Stranded DNA: Reconciling Theory and Experiment. Front. Phys. 7, 195 (2019)

2019
[50]

Zoli, Thermodynamics of Twisted DNA with Solvent Int eraction

M. Zoli, Thermodynamics of Twisted DNA with Solvent Int eraction. J. Chem. Phys. 135, 115101 (2011)

2011
[51]

Sulaiman, F.P

A. Sulaiman, F.P. Zen, H. Alatas, L.T. Handoko, The ther mal denaturation of the Peyrard–Bishop model with an external potential. Phys. Scr. 86, 015802 (2012)

2012
[52]

Zoli, Entropic Penalties in Circular DNA Assembly

M. Zoli, Entropic Penalties in Circular DNA Assembly. J. Chem. Phys. 141, 174112 (2014)

2014
[53]

Macedo, I

D.X. Macedo, I. Guedes, E.L. Albuquerque, Thermal prop erties of a DNA denaturation with 28 solvent interaction. Physica A 404, 234-241 (2014)

2014
[54]

Singh, N

A. Singh, N. Singh, Eﬀect of salt concentration on the sta bility of heterogeneous DNA. Physica A 419, 328-334 (2015)

2015
[55]

Ferreira, T.D

I. Ferreira, T.D. Amarante, G. Weber, DNA terminal base pairs have weaker hydrogen bonds especially for AT under low salt concentration. J. Chem. Phys. 143, 175101 (2015)

2015
[56]

Zoli, Twist-stretch relations in nucleic acids

M. Zoli, Twist-stretch relations in nucleic acids. Europ. Biophys. J. 52, 641-650 (2023)

2023
[57]

C.M. Joy, L. Kavitha, Dynamics of Soliton Collision in D NA Double Helix. Braz. J. Phys. 55, 8 (2025)

2025
[58]

Poland, H

D. Poland, H. Scheraga, Phase Transitions in One Dimens ion and the Helix-Coil Transition in Polyamino Acids. J. Chem. Phys. 45, 1456 (1966)

1966
[59]

Peyrard, A.R

M. Peyrard, A.R. Bishop, Statistical mechanics of a non linear model for DNA denaturation. Phys. Rev. Lett. 62, 2755-2758 (1989)

1989
[60]

Dauxois, M

T. Dauxois, M. Peyrard, A.R. Bishop, Entropy-driven DN A denaturation. Phys. Rev. E 47, R44-R47 (1993)

1993
[61]

Hillebrand, G

M. Hillebrand, G. Kalosakas, Ch. Skokos, A. R. Bishop, D istributions of bubble lifetimes and bubble lengths in DNA. Phys. Rev. E 102, 062114 (2020)

2020
[62]

Campa, A

A. Campa, A. Giansanti, Experimental tests of the Peyra rd-Bishop model applied to the melting of very short DNA chains. Phys. Rev. E 58, 3585-3588 (1998)

1998
[63]

Singh, T

A. Singh, T. Modi, N. Singh, Opening of DNA chain due to fo rce applied on diﬀerent loca- tions. Phys. Rev. E 94, 032410 (2016)

2016
[64]

Likhachev, V.D

I.V. Likhachev, V.D. Lakhno, The direct investigation of DNA denaturation in Peyrard- Bishop-Dauxois model by molecular dynamics method. Chem. Phys. Lett. 727, 55-58 (2019)

2019
[65]

Zoli, Anharmonic Stacking in Supercoiled DNA

M. Zoli, Anharmonic Stacking in Supercoiled DNA. J. Phys.: Condens. Matter 24 195103 (2012)

2012
[66]

Mondal, S

S. Mondal, S. Mukherjee, B. Bagchi, Melting and Bubble F ormation in a Double-Stranded DNA: Microscopic Aspects of Early Base-Pair Opening Events and the Role of Water. J. Phys. Chem. B 128, 2076-2086 (2024)

2024
[67]

Zhang, W.M

Y.L. Zhang, W.M. Zheng, J.X. Liu, Y.Z. Chen, Theory of DN A melting based on the Peyrard- Bishop model. Phys. Rev. E 56, 7100-7115 (1997)

1997
[68]

Olsen, J

K. Olsen, J. Bohr, The geometrical origin of the strain- twist coupling in double helices. AIP Advances 1, 012108 (2011). 29

2011
[69]

Marin-Gonzalez, J.G

A. Marin-Gonzalez, J.G. Vilhena, R. Perez, F. Moreno-H errero, Understanding the me- chanical response of double-stranded DNA and RNA under cons tant stretching forces using all-atom molecular dynamics. Proc. Natl. Acad. Sci. U.S.A. 114, 7049-7054 (2017)

2017
[70]

Zoli, Twisting and Bending Stress in DNA Minicircles

M. Zoli, Twisting and Bending Stress in DNA Minicircles . Soft Matter 10, 4304-4311 (2014)

2014
[71]

Zoli, Twisting short dsDNA with applied tension

M. Zoli, Twisting short dsDNA with applied tension. Physica A 492, 903-915 (2018)

2018
[72]

Zoli, End-to-end distance and contour length distri bution functions of DNA helices

M. Zoli, End-to-end distance and contour length distri bution functions of DNA helices. J. Chem. Phys. 148, 214902 (2018)

2018
[73]

Zoli, DNA size in conﬁned environments

M. Zoli, DNA size in conﬁned environments. Phys. Chem. Chem. Phys. 21, 12566 (2019)

2019
[74]

Dickerson et al., Deﬁnitions and nomenclature of n ucleic acid structure components

R.E. Dickerson et al., Deﬁnitions and nomenclature of n ucleic acid structure components. Nucleic Acids Res. 5, 1797 (1989)

1989
[75]

Tolstorukov, A.V

M.Y. Tolstorukov, A.V. Colasanti, D. McCandlish, W.K. Olson, V.B. Zhurkin, A Novel ‘Roll-and-Slide’ Mechanism of DNA Folding in Chromatin. Im plications for Nucleosome Po- sitioning. J. Mol. Biol. 371, 725-738 (2007)

2007
[76]

Zhang, M.A

F. Zhang, M.A. Collins, Model simulations of DNA dynami cs. Phys. Rev. E 52, 4217 (1995)

1995
[77]

Drukker, G

K. Drukker, G. Wu, G.C. Schatz, Model simulations of DNA denaturation dynamics. J. Chem. Phys. 114, 579-590 (2001)

2001
[78]

Owczarzy, Y

R. Owczarzy, Y. You, B.G. Moreira, J.A. Manthey, L. Huan g, M.A. Behlke, J.A. Walder, Eﬀects of Sodium Ions on DNA Duplex Oligomers: Improved Predi ctions of Melting Tem- peratures. Biochemistry 43, 3537-3554 (2004)

2004
[79]

van Eijck, F

L. van Eijck, F. Merzel, S. Rols, J. Ollivier, V.T. Forsy th, M.R. Johnson, Direct Determina- tion of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix. Phys. Rev. Lett. 107, 088102 (2011)

2011
[80]

Zoli, First-passage probability: a test for DNA Hami ltonian parameters

M. Zoli, First-passage probability: a test for DNA Hami ltonian parameters. Phys. Chem. Chem. Phys. 22, 26901 (2020)

2020
[81]

Zgarbov´ a, M

M. Zgarbov´ a, M. Otyepka, J. Sponer, F. Lankas, P. Jurec ka, Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA. J. Chem. Theory Comput. 10, 3177-3189 (2014)

2014
[82]

Ashwood, M.S

B. Ashwood, M.S. Jones, A.L. Ferguson, A. Tokmakoﬀ, Disr uption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site . Proc. Natl. Acad. Sci. U.S.A. 120, e2219124120 (2023)

2023
[83]

Zoli, Helix untwisting and bubble formation in circu lar DNA

M. Zoli, Helix untwisting and bubble formation in circu lar DNA. J. Chem. Phys. 138, 205103 (2013). 30

2013
[84]

Zoli, Path Integral Method for DNA denaturation

M. Zoli, Path Integral Method for DNA denaturation. Phys. Rev. E 79, 041927 (2009)

2009
[85]

Zoli, Denaturation Patterns in Heterogeneous DNA

M. Zoli, Denaturation Patterns in Heterogeneous DNA. Phys. Rev. E 81 051910 (2010)

2010
[86]

Zoli, Stacking Interactions in Denaturation of DNA F ragments

M. Zoli, Stacking Interactions in Denaturation of DNA F ragments. Eur. Phys. J. E 34, 68 (2011)

2011
[87]

Zoli, Twist versus Nonlinear Stacking in Short DNA Mo lecules

M. Zoli, Twist versus Nonlinear Stacking in Short DNA Mo lecules. J. Theor. Biol. 354, 95-104 (2014)

2014
[88]

Zoli, c-axis resistivity in high Tc superconductors

M. Zoli, c-axis resistivity in high Tc superconductors. Phys. Rev. B 56, 111 (1997)

1997
[89]

Zoli, Path Integral Description of a Semiclassical S u-Schrieﬀer-Heeger Model

M. Zoli, Path Integral Description of a Semiclassical S u-Schrieﬀer-Heeger Model. Phys. Rev. B 67, 195102 (2003)

2003
[90]

Zoli, Base pair ﬂuctuations in helical models for nuc leic acids

M. Zoli, Base pair ﬂuctuations in helical models for nuc leic acids. J. Chem. Phys. 154, 194102 (2021)

2021
[91]

Majumdar, Brownian functionals in physics and com puter science

S.N. Majumdar, Brownian functionals in physics and com puter science. Curr. Sci. 89, 2076 (2005)

2005
[92]

Duguet, The helical repeat of DNA at high temperature

M. Duguet, The helical repeat of DNA at high temperature . Nucleic Acids Res. 21, 463-468 (1993)

1993
[93]

Z. Wu, A. Ono, M. Kainosho, A. Bax, H ···N hydrogen bond lengths in double stranded DNA from internucleotide dipolar couplings. J. Biomol. NMR 19, 361–365 (2001)

2001
[94]

Peyrard, S

M. Peyrard, S. Cuesta-L´ opez, G. James, Modelling DNA a t the mesoscale: a challenge for nonlinear science ? Nonlinearity 21, T91 (2008)

2008
[95]

Slocombe, M

L. Slocombe, M. Winokan, J. Al-Khalili, M. Sacchi, Prot on transfer during DNA strand separation as a source of mutagenic guanine-cytosine tauto mers. Commun. Chem. 5, 144 (2022)

2022
[96]

Zoli, Fluctuations cutoﬀ in a 1D Hamiltonian model fo r DNA

M. Zoli, Fluctuations cutoﬀ in a 1D Hamiltonian model fo r DNA. Phys. Scripta 99, 095009 (2024)

2024
[97]

Zhang, L

Y. Zhang, L. He, S. Li, Temperature dependence of DNA ela sticity: An all-atom molecular dynamics simulation study. J. Chem. Phys. 158, 094902 (2023)

2023
[98]

Herrero-Gal` an E, Fuentes-Perez M E, Carrasco C, Valpu esta J M, Carrascosa J L, Moreno- Herrero F, Arias-Gonzalez J R, Mechanical Identities of RNA and DNA Double Helices Unveiled at the Single-Molecule Level. J. Am. Chem. Soc. 135, 122-131 (2013)

2013
[99]

Faustino, A

I. Faustino, A. P´ erez, M. Orozco, Toward a Consensus Vi ew of Duplex RNA Flexibility. Biophys. J. 99, 1876-1885 (2010). 31

2010
[100]

Dong, Chen Zhang, L

H.-L. Dong, Chen Zhang, L. Dai, Y. Zhang, X.-H. Zhang, Z. -J. Tan, The origin of diﬀerent bending stiﬀness between double-stranded RNA and DNA reveal ed by magnetic tweezers and simulations. Nucleic Acid Res. 52, 2519–2529 (2024)

2024
[101]

J. Gore, Z. Bryant, M. N¨ ollmann, M.U. Le, N.R. Cozzarel li, C. Bustamante, DNA overwinds when stretched. Nature 442, 836-839 (2006)

2006
[102]

Lipfert, G.M

J. Lipfert, G.M. Skinner, J.M. Keegstra, T. Hensgens, T . Jager, D. Dulin, M. K¨ ober, Z. Yu, S.P. Donkers, F.-C. Chou, R. Das, and N.H. Dekker, Double-st randed RNA under force and torque: Similarities to and striking diﬀerences from double -stranded DNA. Proc. Natl. Acad. Sc...

2014
[103]

X. Mou, K. Liu, L. He, S. Li, Mechanical response of doubl e-stranded DNA: Bend, twist, and overwind. J. Chem. Phys. 161, 085102 (2024)

2024
[104]

Liebl, T

K. Liebl, T. Drsata, F. Lankas, J. Lipfert, M. Zacharias , Explaining the striking diﬀerence in twist-stretch coupling between DNA and RNA: A comparative m olecular dynamics analysis. Nucleic Acid Res 43, 10143-10156 (2015)

2015
[105]

Dickerson, The DNA Helix and How It Is Read

R.E. Dickerson, The DNA Helix and How It Is Read. Scientiﬁc American 249, 94-111 (1983)

1983
[106]

E.T. Lam, A. Hastie, C. Lin, D. Ehrlich, S.K. Das, M.D. Au stin, P. Deshpande, H. Cao, N. Nagarajan, M. Xiao, P.-Y. Kwok, Genome mapping on nanocha nnel arrays for structural variation analysis and sequence assembly. Nat. Biotechnol. 30, 771-776 (2012)

2012
[107]

Zoli, Stretching DNA in hard-wall potential channel s

M. Zoli, Stretching DNA in hard-wall potential channel s. EPL - Europhysics Letters 130, 28002 (2020)

2020
[108]

J. Yan, R. Kawamura, J.F. Marko, Statistics of loop form ation along double helix DNAs. Phys. Rev. E 71, 061905 (2005)

2005
[109]

Czapla, D

L. Czapla, D. Swigon, W.K. Olson, Sequence-Dependent Eﬀects in the Cyclization of Short DNA. J. Chem. Theory Comput. 2, 685-695 (2006)

2006
[110]

Shin, A.G

J. Shin, A.G. Cherstvy, R. Metzler, Polymer Looping Is Controlled by Macromolecular Crowding, Spatial Conﬁnement, and Chain Stiﬀness. ACS Macro Lett. 4, 202-206 (2015)

2015
[111]

Jacobson, W.H

H. Jacobson, W.H. Stockmayer, Intramolecular Reacti on in Polycondensations. I. The Theory of Linear Systems. J. Chem. Phys. 18, 1600 (1950)

1950
[112]

Popov, A.V

Y.O. Popov, A.V. Tkachenko, Eﬀects of sequence disorde r on DNA looping and cyclization. Phys. Rev. E 76, 021901 (2007)

2007
[113]

Towles, J.F

K.B. Towles, J.F. Beausang, H.G. Garcia, R. Phillips, P.C. Nelson, First-principles calcula- 32 tion of DNA looping in tethered particle experiments. Phys. Biol. 6, 025001 (2009)

2009
[114]

Shimada, H

J. Shimada, H. Yamakawa, Ring-Closure Probabilities for Twisted Wormlike Chains. Appli- cation to DNA. Macromolecules 17, 689-698 (1984)

1984
[115]

Shore, R.L

D. Shore, R.L. Baldwin, Energetics of DNA Twisting I. R elation between Twist and Cycliza- tion Probability. J. Mol. Biol. 170, 957- 981 (1983)

1983
[116]

Zhang, D.M

Y. Zhang, D.M. Crothers, Statistical Mechanics of Seq uence-Dependent Circular DNA and Its Application For DNA Cyclization. Biophys. J. 84, 136-153 (2003)

2003
[117]

Chu, Laser manipulation of atoms and particles

S. Chu, Laser manipulation of atoms and particles. Science, 253, 861-866 (1991)

1991
[118]

Bustamante, S.B

C. Bustamante, S.B. Smith, J. Liphardt D. Smith, Singl e-molecule studies of DNA mechanics. Current Opinion in Structural Biology 10, 279-285 (2000)

2000
[119]

Saran, Y

R. Saran, Y. Wang, I.T.S. Li, Mechanical Flexibility o f DNA: A Quintessential Tool for DNA Nanotechnology. Sensors 20, 7019 (2020)

2020
[120]

Gusarova, N.A

E.B. Gusarova, N.A. Kovaleva, Molecular Dynamics Sim ulation of Melting of the DNA Du- plex with Silver-Mediated Cytosine–Cytosine Base Pair. Computation 12, 145 (2024). 33

2024

Pith tools

Reviewed August 15, 2026 · model on record in the stance chip above.

[1] [1]

Each nu- cleotide is composed of a sugar ring, a phosphate group and a nitrog enous base

Introduction Nucleic acids are polymeric chains whose building blocks are the nucleot ides. Each nu- cleotide is composed of a sugar ring, a phosphate group and a nitrog enous base. The bases are connected by (glycosidic) covalent bonds to the deoxyribose s ugar in DNA and to the ribose sugar in RNA. The sugar of one nucleotide is connected to the phospha...

[2] [2]

These work s are based on a three dimensional model, whose schematic in shown Fig

Model Several studies produced over the last years have investigated d enaturation bubbles, ther- modynamics, ﬂexibility, force/stretching relations and length distr ibution functions of linear chains and loops with variable size and sequence [61–64]. These work s are based on a three dimensional model, whose schematic in shown Fig. 1(a), in which the rn’...

[3] [3]

Method 13 3.A Fluctuations Cutoﬀ 13

[4] [4]

Results and Discussion 16 4.A Twist - Stretch relations 17 4.B Stretching DNA in a channel 19 4.C Cyclization probability 21

[5] [5]

Conclusions The mechanical properties of nucleic acids have been extensively ch aracterized over the past decades following the development of a broad range of techniq ues [108, 109] that al- low one to manipulate single molecules and probe their response to ext ernal forces. Double stranded (ds) nucleic acids display a remarkable rigidity against bend in...

[6] [6]

Declarations 25 References 26 3

[7] [7]

refs.[75–78]

Method The model, for a chain with N base pairs, is studied by the path integral computational method, discussed in a number of papers, see e.g. refs.[75–78]. In t he ﬁnite temperature path integral formalism, the base pair displacements rn’s are treated as dynamical quantities whose time evolution is deﬁned by functions rn(τ) whereby τ ∈ [0, β ] is the E...

[8] [8]

Results and Discussion After settling the cutoﬀ issue, we apply the statistical model to an alyze the interplay between form and helical conformation of nucleic acids, performing a quantitative analysis of their twist-stretch properties. Moreover, we test the model by evaluating the stretching of a DNA chain that is forced to ﬂow through a cylindrical cha...