相关论文: Duplex formation and secondary structure of {\gamm…
We present a base-pairing model of oligonuleotide duplex formation and show in detail its equivalence to the Nearest-Neighbour dimer methods from fits to free energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids containing…
Hydrogen bonding between nucleobases produces diverse DNA structural motifs, including canonical duplexes, guanine (G) quadruplexes and cytosine (C) i-motifs. Incorporating metal-mediated base pairs into nucleic acid structures can…
The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps of these transitions have not been quantitatively…
Dynamical equations for a polaron and bipolaron in a DNA duplex are obtained on the basis of Holstein-Hubbard Hamiltonian. It is shown that in a PolyA/PolyT duplex especially stable is a bipolaron state in which holes are localized on…
Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…
We have measured the temperature driven denaturing, or melting transition in poly d(A)-poly d(T) DNA oligomers of various lengths in different buffer conditions. Our findings are in clear disagreement with two state, reaction kinetics…
Peptide nucleic acids (PNAs) are artificial nucleic acids with a peptide backbone instead of sugar phosphate backbone of DNA or RNA. Their resistance to degradation, selectivity and greater binding affinity in comparison to usual nucleic…
While studying nucleic acids to reveal the weak interactions responsible for their three-dimensional structure and for their interactions with drugs, we also contributed to the field of biomolecular mass spectrometry, both in terms of…
The phase transition of $(PolyA/PolyT)_{100}$ duplex into the denaturated state is studied in the Peyrard-Bishop-Dauxois model by the method of direct molecular-dynamical modeling. The temperature dependencies of the total energy and heat…
Ultrafast laser experiments yield increasingly reliable data on warm dense matter, but their interpretation requires theoretical models. We employ an efficient density functional neutral-pseudoatom hypernetted-chain (NPA-HNC) model with…
We study numerically the dynamics of acetanilide (ACN) molecules placed on a flat surface of a multilayer hexagonal boron nitride structure. We demonstrate that the ACN molecules, being achiral in three dimensions, become chiral after being…
An analysis of the stability of a duplex containing G.A mispairs or G.A/A.G tandem during DNA melting has revealed that duplex stability depends on both DNA sequences and on the conformations of the G.A mispairs. The thermodynamics of…
We determined a full 3D atomic structure of a dumbbell-shaped Pt nanoparticle formed by a coalescence of two nanoclusters using deep learning assisted atomic electron tomography. Formation of double twin boundary was clearly observed at the…
Renaturation and hybridization reactions lead to the pairing of complementary single-stranded nucleic acids. We present here a theoretical investigation of the mechanism of these reactions in vitro under thermal conditions (dilute solutions…
RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
Recent studies have pointed the importance of polyelectrolyte assembly in the elaboration of innovative nanomaterials. Beyond their structures, many important questions on the thermodynamics of association remain to be answered. Here, we…
The MnAs compound shows a first-order transition at T$_C\approx42$ C, and a second-order transition at T$_t\approx120$ C. The first-order transition, with structural (hexagonal-orthorhombic), magnetic (FM-PM) and electrical conductivity…