Surface differentiation of ferritin and apoferritin with atomic force microscopic techniques

In the study reported herein, we differentiated the structure of ferritin from that of its demetalated counterpart, apoferritin, using field-effect-based atomic force microscopic (AFM) techniques. When ferritin was subjected to conductive-mode AFM analysis, the protein resembled a pancake with a diameter of 10 nm adsorbed on the indium-doped tin-oxide substrate with its fourfold channel perpendicular to the substrate, whereas a flat, empty cavity was revealed for apoferritin. We also attempted to verify the conformational difference with magnetic-mode AFM. However, the resulting phase images failed to differentiate the proteins due to interference from the fringe effect. Despite this, the ferritin analysis revealed a sound correlation between the surface conductivity profiles and the phase profiles. In contrast, apoferritin showed a chaotic relationship in this respect. These results not only suggest that the magnetic domain of ferritin is limited to the iron aggregate in the core, but also demonstrate that AFM is a useful tool for protein conformation analysis.

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Quantum transport anomalies in DNA containing mispairs

The effect of mispairs on charge transport in DNA of sequence (GC)(TA)(N)(GC)(3) connected to platinum electrodes is studied using the tight-binding model. With parameters derived from an ab initio density functional result, we calculate the current versus bias voltage for DNA with and without a mispair and for different numbers of (TA) basepairs N between the single and triple (GC) basepairs. The current decays exponentially with N under low bias but reaches a minimum under high bias when a multichannel transport mechanism is established. A (GA) mispair substituting a (TA) basepair near the middle of the (TA)(N) sequence usually enhances the current by one order due to its low ionization energy but may decrease the current significantly when an established multichannel mechanism is broken.

Electrical current through DNA containing mismatched base pairs

Mismatched base pairs, such as different conformations of the G.A mispair, cause only minor structural changes in the host DNA molecule, thereby making mispair recognition an arduous task. Electron transport in DNA that depends strongly on the hopping transfer integrals between the nearest base pairs, which in turn are affected by the presence of a mispair, might be an attractive approach in this regard. We report here on our investigations, via the I-V characteristics, of the effect of a mispair on the electrical properties of homogeneous and generic DNA molecules. The I-V characteristics of DNA were studied numerically within the double-stranded tight-binding model. The parameters of the tight-binding model, such as the transfer integrals and on-site energies, are determined from first-principles calculations. The changes in electrical current through the DNA chain due to the presence of a mispair depend on the conformation of the G.A mispair and are appreciable for DNA consisting of up to 90 base pairs. For homogeneous DNA sequences the current through DNA is suppressed and the strongest suppression is realized for the G(anti).A(syn) conformation of the G.A mispair. For inhomogeneous (generic) DNA molecules, the mispair result can be either a suppression or an enhancement of the current, depending on the type of mispairs and actual DNA sequence.

Detection of Point Mutation and Insertion Mutations in DNA Using a Quartz Crystal Microbalance and MutS, a Mismatch Binding Protein

MutS protein is a mismatch binding protein that recognizes mispaired and unpaired base(s) in DNA. In this study, we incorporate the MutS protein-based mutation recognition into quartz crystal microbalance (QCM) measurements for DNA single-base substitution mutation and 1-4 base(s) insertion (or deletion) mutation detection. The method involves the immobilization of single-stranded probe DNA on a QCM surface, the hybridization of target DNA to form homoduplex or heteroduplex DNA, and finally the application of MutS protein for the mutation recognition. By measuring the MutS binding signal, DNA containing a T:G mismatch or unpaired base(s) is(are) discriminated against perfectly matched DNA at target concentrations ranging from 1nM to 5 microM. Furthermore, the QCM damping behavior upon MutS-DNA complex formation is studied using a Network Analyzer. The measured motional resistance changes per coupled MutS unit mass (deltaR/deltaf) are found to be indicative of the viscoelastic or structural properties of the bound protein, corresponding to different binding mechanisms. In addition, the deltaR/deltaf values vary remarkably when the MutS protein binds at different distances away from the QCM surface. Thus, these values can be used as a "fingerprint" for MutS mismatch recognition and also used to quantitatively locate the mutation site.