Reference health
Control of DNA Strand Displacement Kinetics Using Toehold Exchange
64/64 checkable references clean · checked 2026-07-24
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
9 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 64 checked references that resolve
resolves10.1038/nature06597
Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra
resolves10.1103/PhysRevLett.101.238101
Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion
resolves10.1038/nbt1155
Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes
resolves10.1038/171737a0
Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid
resolves10.1073/pnas.95.4.1460
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
resolves10.1529/biophysj.105.070904
Nucleic Acid Helix Stability: Effects of Salt Concentration, Cation Valence and Size, and Chain Length
resolves10.1021/bi702363u
Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations
resolves10.1023/A:1020954307319
Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides
resolves10.1093/nar/29.11.2303
Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips
resolves10.1081/NCN-200026071
The Influence of Nearest Neighbours on the Efficiency of Coaxial Stacking at Contiguous Stacking Hybridization of Oligodeoxyribonucleotides
resolves10.1016/S0301-4622(01)00222-8
Heat does not come in different colours: entropy–enthalpy compensation, free energy windows, quantum confinement, pressure perturbation calorimetry, solvation and the multiple causes of heat capacity effects in biomolecular interactions
resolves10.1126/science.277.5329.1078
Selective Colorimetric Detection of Polynucleotides Based on the Distance-Dependent Optical Properties of Gold Nanoparticles
resolves10.1002/anie.200700047
Design of Molecular Logic Devices Based on a Programmable DNA‐Regulated Semisynthetic Enzyme
resolves10.1006/jmbi.1993.1159
Formation of a Single Base Mismatch Impedes Spontaneous DNA Branch Migration
resolves10.1016/0022-2836(77)90273-X
Uptake of homologous single-stranded fragments by superhelical DNA
resolves10.1021/bi00063a022
Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution
resolves10.1093/nar/9.8.1905
Reassociation rate limited displacement of DNA strands by branch migration
resolves10.1093/nar/gkl422
Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison
resolves10.1038/nnano.2008.164
Self-assembled DNA nanostructures for distance-dependent multivalent ligand–protein binding
resolves10.1529/biophysj.103.020743
Prediction of Hybridization and Melting for Double-Stranded Nucleic Acids
resolves10.1093/nar/gnf121
Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes
resolves10.1007/s00706-008-0895-3
Beyond energy minimization: approaches to the kinetic folding of RNA
The 9 references without a DOI — listed, not checked
no DOI — not checkedPeyret, N.Prediction of Nucleic Acid Hybridization: Parameters and Algorithms, Doctoral thesis, Wayne State University, 2000.
no DOI — not checkedNucleic Acids: Structures, Properties, and Functions
no DOI — not checkedMaune, H. T., Han, S., Barish, R. D., Rothemund, P. W. K., Goddard, W. A., Bockrath, M., and Winfree, E.Nat. Nanotechnol. 2009, in press.
no DOI — not checkedref48/cit48
no DOI — not checkedCardelli, L.Proceedings of the 15th Annual Conference on DNA Computing, June 8−11, 2009; Fayetteville, AR, 2009.
no DOI — not checkedBiophysical Chemistry: Part III: The Behavior of Biological Macromolecules
no DOI — not checkedOn the basis of the dependence ofkf1on the sequence composition of the toehold, we believe thatkf2is likely closest in value tokf1= 3 × 106M−1s−1for inputs X(m, n) with toeholds containing both strong G-C pairs and weak A-T pairs. However, we have no way of knowing the actual value ofkf2without performing a new series of experiments on theβmtoehold, similar to those shown in Figure3.
no DOI — not checkedTo take a simple example, consider when the invading and incumbent toeholds are both 4 nt but the branch migration domain is 1000 nt long. Molecules will spend a significant amount of time in a three-stranded complex, with the branch migration junction vacillating near the middle of the branch migration domain. Our model, with the 2/(b − m) correction, will account for the high multiplicity of branch migration microstates.
no DOI — not checkedODEs used for fittingk{m, n}simulated the two reactions X(m, n) + S → Y + L(m, n) and Y + R → F. The reverse reaction Y + L(m, n) → S + X(m, n) is not included because (1) it is desireable to fit one parameter at a time and (2) because the value of the reverse rate constantκ{n, m}is constrained poorly by data from experiments of the type shown in Figure3A. Furthermore, the concentration of the reporter R is in 3× excess over that of the substrate S, and the rate constant of the reaction between Y and R is high; consequently, it is expected that the reaction between Y and R will dominate that between Y and L(m, n). Fittingk{m, n}to a full model including the reverse reaction with its rate constantκ{m, n}set to the value predicted by our model yielded values very similar to those presented in the paper (difference of no more than 10%).
What this badge says. CiteStamped means the CHECKABLE references of this
work were clean at the dated check: each resolved to a known work in a public registry, and none
carried a retraction notice at that time. It says nothing about the quality, findings,
or importance of the work itself, and nothing about references deposited without a DOI.
checked 2026-07-24 — re-checked daily as this page is visited; titles and statuses come from Crossref and DataCite and are not part of the signed record
Embed this badge
Both snippets point at the live badge image and link back to this page. The badge re-renders from the daily check, so an embed never goes stale by more than a day of visits.
<a href="https://citestamp.com/citestamped/10.1021/ja906987s"><img src="https://citestamp.com/citestamped/10.1021/ja906987s/badge.svg" alt="CiteStamped reference-health badge" width="460" height="64"></a>
[](https://citestamp.com/citestamped/10.1021/ja906987s)