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Deoxyribonucleic acid, or DNA, is a nucleotide polymer that stores biological information in its nucleotide sequence. The crucial variable is order: two DNA molecules can contain the same numbers of each nucleobase yet carry different nucleotide sequences. This makes a physical molecule an inheritable record, rather than merely a mixture of ingredients. Genes are functional regions of that record; the whole DNA nucleotide sequence is not one long gene. See NHGRI: DNA fact sheet.

Each DNA strand has a backbone of alternating deoxyribose sugars and phosphate groups joined through covalent bonds. Attached nucleobases supply the familiar four-letter alphabet: adenine A, thymine T, guanine G, and cytosine C. In ordinary double-stranded DNA, base pairing matches A with T and G with C. The backbone connects successive nucleotides along a strand; base pairing connects partners across strands. Keeping these two connections distinct explains how strands can separate while each retains its own nucleotide sequence.

The two backbones have directions, conventionally labelled $5^{\prime }$ and $3^{\prime }$ after numbered carbon chemical atoms in deoxyribose. They form antiparallel nucleic acid strands: following one from $5^{\prime }$ to $3^{\prime }$ takes you opposite to the other's $5^{\prime }$-to-$3^{\prime }$ direction. For the chosen DNA nucleotide sequence $5^{\prime }\text{-}\mathrm{ATGCC}\text{-}{3}^{\prime }$, write its partner directly underneath as $3^{\prime }\text{-}\mathrm{TACGG}\text{-}{5}^{\prime }$. Now read that partner from its own $5^{\prime }$ end: its reverse complement is $5^{\prime }\text{-}\mathrm{GGCAT}\text{-}{3}^{\prime }$. Complementing letters and reversing their order are separate operations. See Alberts et al., Molecular Biology of the Cell: the structure and function of DNA.

The diagram's rails represent sugar–phosphate backbones and its coloured blocks represent nucleobases, not individual chemical atoms. Reading left to right gives five matched positions: A–T, T–A, G–C, C–G, C–G. There are two A–T-type base pairs and three G–C-type base pairs; the complete two-strand example contains ten nucleotides. Reversing the bottom row changes the reading convention, not the physical partners. Real double-stranded DNA winds into a nucleic acid double helix; the flattened ladder emphasizes base pairing and direction without pretending to show its three-dimensional geometry.

The motivating consequence is copying by a template. After strands separate, each existing DNA strand specifies which incoming nucleotides should accompany it through base pairing. DNA replication uses enzymes to build complementary strands, allowing the record to persist through successive biological cells. Base pairing supplies a selection rule, while enzymes perform the chemistry: a matching diagram alone is not a complete copying mechanism. The connection between structure and copying was already central to the model published by Watson and Crick on 25 April 1953. See Watson and Crick, Molecular Structure of Nucleic Acids, Nature 171, 737–738 (1953).

Stored information needs interpretation. Some DNA regions specify proteins through RNA; others contribute to functional RNA or regulate gene expression, and some have no known function. Non-coding DNA means sequence that does not specify a protein's sequence of amino acids, not automatically useless sequence. Nor does a DNA nucleotide sequence alone determine an organism's fate: phenotypes also depend on biological context and environment. See NHGRI: non-coding DNA. Its double-stranded form is often modeled mechanically as a worm-like chain, with elasticity and effective excluded volume depending on solvent conditions.

A strongly stretched inextensible worm-like chain has two small transverse tangent components. Its quadratic energy is $\frac{1}{2}\int [A|{\partial }_s{\mathbf{t}}_{\perp }{|}^2+f|{\mathbf{t}}_{\perp }{|}^2]ds-fL$. For a long bulk chain, the equipartition theorem assigns each Fourier mode covariance $k_{B}T/(A{q}^2+f)$. Integrating over $q$ and summing both components gives $⟨|{\mathbf{t}}_{\perp }{|}^2⟩=k_{B}T/\sqrt{Af}$, hence the extension deficit is half that value. With persistence length $L_p=A/(k_{B}T)$, the deficit is $\sqrt{k_{B}T/(4L_{p}f)}$. It requires small slopes and negligible stretching of the backbone.

The Kuhn length is the link length of an equivalent long ideal chain with the same contour length and mean squared end-to-end distance. A three-dimensional worm-like chain satisfies $⟨R^2⟩\sim 2l_{p}L$ for $L\gg l_p$, hence $b_K=2l_p$.

For a three-dimensional worm-like chain, the tangent correlation length is $l_p=B/(k_{B}T)$, where $B$ is the filament bending modulus. The measured persistence length therefore givesRepresent the actin filament as an isotropic solid circular cylinder with diameter $d=10^{-9}\mathrm{m}$. Its second moment of area is $I=\pi d^4/64=4.909\times 10^{-38}{\mathrm{m}}^4$. Since $B=EI$,This is an effective Young's modulus within the given continuum cross-sectional model; the numerical diameter and persistence length must not be replaced by unrelated typical biological values.

The same measurement corrects the independent-link approximation: the Kuhn length is $b_K=2l_p=40\mathrm{nm}$, with $N_K=L/b_K=2.5\times 10^9$. Thus the long-chain entropic stiffness is $3k_{B}T/(2l_{p}L)=3.105\times 10^{-15}\mathrm{N}{\mathrm{m}}^{-1}$, and the root-mean-square end-to-end distance is $2\mathrm{mm}$. For comparison, the material axial stiffness is $EA/L=1.325\times 10^{-11}\mathrm{N}{\mathrm{m}}^{-1}$, using $A=\pi d^2/4$. The corrected coil response remains much softer than axial backbone stretching.

An optical tweezers force requires the change in optical momentum. Define the optical momentum efficiency $Q$ by $F=QP/c$, with all ray geometry and medium-index factors absorbed in $Q$ and $c$ the vacuum light speed. The specified relative refractive index does not determine $Q$ without bead size and the beam's convergence, waist, and ray directions. A unique exact force is therefore not supplied by these data.

Retaining the entropic stiffness from part (a), the parameterized answer isUsing the persistence-length-corrected worm-like chain instead gives $z=1.074Q\mathrm{m}$ in its small-force regime.

For a definite scale estimate, take the weak-contrast optical momentum change to be $Q\sim m_r-1=0.2$. This gives $F\sim 6.67\times 10^{-16}\mathrm{N}$, $z\sim 5.37\mathrm{cm}$ for part (a)'s model, or $z\sim 21.5\mathrm{cm}$ for the corrected chain. These are estimates with an explicitly chosen ray-momentum efficiency, not a universal formula for a transparent trapped sphere.

Another illustrative optical model makes the uncertainty visible: normal-incidence Fresnel reflectance is $\mathcal{R}=[(m_r-1)/(m_r+1){]}^2=1/121$. An effective reflector with $Q=2\mathcal{R}$ in the simple $P/c$ momentum convention gives $F=5.51\times 10^{-17}\mathrm{N}$ and extensions $4.44\mathrm{mm}$ or $17.7\mathrm{mm}$, respectively. A refracting bead in a focused beam is not just that reflector; entry and exit rays also transfer momentum. Neither estimate eliminates the missing optical geometry.

Use the arc length $s$ and the unit tangent $\mathbf{t}={\partial }_s\mathbf{r}$ of an inextensible filament. In the high-force state choose its positive longitudinal branch. The constraint givesThe extension is $z={\int }_0^L{t}_{z}ds=L-\frac{1}{2}{\int }_0^L|{\mathbf{t}}_{\perp }{|}^{2}ds+\cdots$. The curvature of a space curve obeys ${\kappa }^2=|{\partial }_s\mathbf{t}{|}^2$. Since ${\partial }_s{t}_z=-{\mathbf{t}}_{\perp }\cdot {\partial }_s{\mathbf{t}}_{\perp }+\cdots$ is second order in small fluctuations, its squared contribution is fourth order. Thus the worm-like chain energy through quadratic order isPositive force suppresses transverse orientation fluctuations, while the filament bending modulus penalizes their spatial variation.

To apply the equipartition theorem without missing either component or a mode-counting factor, expand each component in a real orthonormal basis of eigenfunctions of $-{\partial }_s^2$, $t_{\alpha }(s)={\sum }_q{a}_{\alpha q}{w}_q(s)$, with $\int w_q{w}_{q^{\prime }}ds={\delta }_{q{q}^{\prime }}$ and $\alpha =x,y$. The quadratic energy is $\frac{1}{2}{\sum }_{\alpha ,q}(A{q}^2+f)a_{\alpha q}^2$. Each real quadratic degree of freedom contributes $k_{B}T/2$, soFor a chain long compared with the force-dependent correlation length, the interior is translation invariant and the mode sum per length becomes $\int dq/(2\pi )$. Equivalently, for the Fourier transform ${\tilde{t}}_{\alpha }(q)=\int e^{-iqs}{t}_{\alpha }(s)ds$,The negative and positive wavenumbers here represent the real-field mode count consistently, rather than two independent complex modes. Summing both transverse components gives the high-force worm-like chain elasticitywhere the integral follows by setting $q=\sqrt{f/A}u$ and using ${\int }_{-\infty }^{\infty }(1+u^2{)}^{-1}du=\pi$. ThereforeHere $L_p$ is the three-dimensional zero-force persistence length. The result requires $f{L}_p\gg k_{B}T$, negligible backbone stretching, and a long-chain bulk approximation. It does not describe the eventual bond-stretching regime. For a continuum polymer description, the force-dependent length should also exceed the microscopic cutoff.

For comparison, a three-dimensional freely jointed chain has contour length $L=Nb$ and independent link orientations. At force $f$, a link of polar angle $\vartheta$ has Boltzmann factor $e^{x\cos \vartheta }$ with $x=fb/(k_{B}T)$. Its angular canonical partition function isThe total canonical partition function is $Z_1^N$. Differentiating with respect to force gives the force-extension of a three-dimensional freely jointed chain:ConsequentlyThe extension deficits scale as $f^{-1}$ and $f^{-1/2}$ respectively. Inverting them gives force divergences proportional to the first and second inverse powers of the deficit. Freely jointed link rotations cost no bending energy; the worm-like chain instead has a continuum of coupled bending modes whose contributing wavelengths change with force. Setting a long-wavelength coarse-grained link length $b=2L_p$ can match weak-force statistics, but does not make these high-force laws identical.

For the transverse tangent correlation of a stretched worm-like chain, use a separation $r$ consistently: the source writes $C(y)$ but integrates a separation denoted $r$. In the translation-invariant bulk the spatial average is redundant andTo evaluate the integral without an assumed decay law, let $G(r)$ be the inverse Fourier transform of $(A{q}^2+f{)}^{-1}$. Then $(-A{\partial }_r^2+f)G=\delta (r)$. Away from zero, decay at both infinities requires $G=B{e}^{-|r|/\xi }$ with $\xi =\sqrt{A/f}$. Integrating across zero yields $-A[G^{\prime }(0^{+})-G^{\prime }(0^{-})]=1$, so $B=1/(2\sqrt{Af})$. ThusAt $r=0$ this agrees with the two-component equipartition theorem calculation. The correlation length decreases with force and is distinct from the zero-force persistence length. The full tangent correlation has a nonzero aligned background; the exponentially decaying quantity here is specifically the transverse correlation.

For a finite open chain, the source's integral samples $s+r$ beyond $L$ and supplies no endpoint tangent conditions. An exact finite-length correlation is therefore not uniquely specified. The result above is the intended bulk form when $L\gg \xi$. As one explicit finite convention, periodically extending the tangent fluctuations gives the periodic finite-length tangent correlation of a stretched worm-like chainwhere $d_L(r)$ is the distance from zero around the periodic interval. Then $C_L(0)=(k_{B}T/\sqrt{Af})\coth [L/(2\xi )]$, and the extension formula acquires this same finite-length factor. The bulk law is recovered as $L/\xi \to \infty$. This makes the endpoint assumption explicit rather than claiming an unspecified finite-chain correlation is exactly translationally invariant.

In the small-slope approximation the worm-like chain bending energy isThe clamped end obeys $h(0)=h_x(0)=0$, while a force-free and torque-free tip has the natural conditions $h_{xx}(L)=h_{xxx}(L)=0$. A static transverse tip force $f$ produces the cantilever compliance $h(L)/f=L^3/(3A)$. The equipartition theorem, or equivalently the static fluctuation--response relation, therefore gives the exact tip variance

For the dynamics, resistive-force theory gives the transverse drag per lengthat logarithmic accuracy and the stochastic beam equationLet ${\varphi }_n$ be clamped--free bending modes with $q_{n}L={\alpha }_n$, whereWriting $N_n={\int }_0^L{\varphi }_n^{2}dx$, independent thermally driven modes giveThe first mode contains almost all of the tip variance, so

For a microtubule, $A=k_{B}T{L}_p$. With $L=10\mu \mathrm{m}$ and $L_p=3\mathrm{mm}$,Taking water at room temperature and $a=0.5\mu \mathrm{m}$ gives ${\zeta }_{\perp }\simeq 3.6\times 10^{-3}\mathrm{Pa}\mathrm{s}$ andwith an order-one uncertainty from the logarithmic slender-body drag approximation.

Quenched intrinsic curvature of an elastic filament is fixed during a mechanical experiment, although different filaments can have different random intrinsic shapes. Ensemble averaging is then over these shapes after mechanical minimization. It differs from averaging over time-dependent thermal bending fluctuations in a worm-like chain.

A three-dimensional ideal chain of $N$ independent segments of length $b$ has $⟨R^2⟩=N{b}^2=Lb$. The isotropic small-force susceptibility gives $⟨z⟩=F⟨R^2⟩/(3k_{B}T)$, so $k_s=3k_{B}T/(Lb)$. For a long worm-like chain, the statistical segment is $b=2l_p$. This stiffness describes entropic end-to-end extension, not axial stretching of the material backbone, whose spring constant is $EA/L$.