24 research outputs found
A Quantum-mechanical Approach for Constrained Macromolecular Chains
Many approaches to three-dimensional constrained macromolecular chains at
thermal equilibrium, at about room temperatures, are based upon constrained
Classical Hamiltonian Dynamics (cCHDa). Quantum-mechanical approaches (QMa)
have also been treated by different researchers for decades. QMa address a
fundamental issue (constraints versus the uncertainty principle) and are
versatile: they also yield classical descriptions (which may not coincide with
those from cCHDa, although they may agree for certain relevant quantities).
Open issues include whether QMa have enough practical consequences which differ
from and/or improve those from cCHDa. We shall treat cCHDa briefly and deal
with QMa, by outlining old approaches and focusing on recent ones.Comment: Expands review published in The European Physical Journal (Special
Topics) Vol. 200, pp. 225-258 (2011
Engineering Terminal Disulfide Bonds Into DNA
This protocol presents a simple and general means of modifying nucleic acids with disulfide crossâlinks. These crossâlinks serve as powerful tools to probe the structure, dynamics, thermodynamics, folding, and function of DNA and RNA, much in the way that cystine crossâlinks have been used to study proteins. The chemistry described has been used to synthesize disulfideâcrossâlinked hairpins and duplexes, higherâorder structures such as triplexes, nonâgroundâstate conformations, and tRNAs. since the crossâlinks form quantitatively by mild air oxidation and do not purturb either secondary or tertiary structure, this modification should prove quite useful for the study of nucleic acids.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/152862/1/cpnc0507.pd
Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study
Kinetic analysis of specificity of duplex DNA targeting by homopyrimidine peptide nucleic acids
Determination of the helix-coil transition heats from the melting curves of deoxyribonucleic acid containing additional linkages
Theory of the helix-coil transition of deoxyribonucleic acid with additional interchain bonds
Kinetics and mechanism of polyamide ("peptide") nucleic acid binding to duplex DNA
To elucidate the mechanism of recognition of double-stranded DNA (dsDNA) by homopyrimidine polyamide ("peptide") nucleic acid (PNA) leading to the strand-displacement, the kinetics of the sequence-specific PNA/DNA binding have been studied. The binding was monitored with time by the gel retardation and nuclease S1 cleavage assays. The experimental kinetic curves obey pseudo-first-order kinetics and the dependence of the pseudo-first-order rate constant, kps, on PNA concentration, P, obeys a power law kps approximately P gamma with 2 < gamma < 3. The kps values for binding of decamer PNA to dsDNA target sites with one mismatch are hundreds of times slower than for the correct site. A detailed kinetic scheme for PNA/DNA binding is proposed that includes two major steps of the reaction of strand invasion: (i) a transient partial opening of the PNA binding site on dsDNA and incorporation of one PNA molecule with the formation of an intermediate PNA/DNA duplex and (ii) formation of a very stable PNA2/DNA triplex. A simple theoretical treatment of the proposed kinetic scheme is performed. The interpretation of our experimental data in the framework of the proposed kinetic scheme leads to the following conclusions. The sequence specificity of the recognition is essentially provided at the "search" step of the process, which consists in the highly reversible transient formation of duplex between one PNA molecule and the complementary strand of duplex DNA while the other DNA strand is displaced. This search step is followed by virtually irreversible "locking" step via PNA2/DNA triplex formation. The proposed mechanism explains how the binding of homopyrimidine PNA to dsDNA meets two apparently mutually contradictory features: high sequence specificity of binding and remarkable stability of both correct and mismatched PNA/DNA complexes