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Current
Organic Chemistry
ISSN: 1385-2728
Current Organic
Chemistry
Volume 10, Number 4, March 2006
Contents
Thermodynamics and Kinetics of DNA-Protein
Interactions from Single Molecule Force Spectroscopy Measurements
Pp. 419-432
Mark C. Williams, Ioulia Rouzina and Richard L. Karpel
[Abstract]
What is Hidden Behind Peptide Bond Restriction and
α-Carbon
Asymmetry of Conserved Antigens? Peptide Bond Isosters and
Chirally Transformed Pseudopeptides as Novel Elements for
Synthetic Vaccines and Therapeutic Agents Against Malaria
Pp. 433-456
José Manuel Lozano, Luz Mary Salazar, Zuly Rivera and
Manuel Elkin Patarroyo
[Abstract]
Recent Uses of Iron (III) Chloride in Organic Synthesis
Pp. 457-476
David Díaz Díaz, Pedro O. Miranda, Juan I. Padrón
and Víctor S. Martín
[Abstract]
Progress in Spectroscopic Probes with Cleavable Active
Bonds Pp. 477-489
Xinqi Chen, Ming Sun and Huimin Ma
[Abstract]
Development and Applications of Fluorescent Oligonucleotides
Pp. 491-518
U. Asseline
[Abstract]
Abstracts
[Back to top]
Thermodynamics and Kinetics of DNA-Protein Interactions
from Single Molecule Force Spectroscopy Measurements
Mark C. Williams, Ioulia Rouzina and Richard L. Karpel
When single DNA molecules are stretched, the measurement
of the resulting force as a function of extension has yielded
new information about the physical, chemical, and biological
properties of these important molecules. It has been shown
that double-stranded DNA molecules undergo a force-induced
melting transition at high forces. Force-extension measurements
of single DNA molecules using optical tweezers allow us to
measure the stability of DNA under a variety of solution conditions
and in the presence of DNA binding proteins. Here we review
our studies of DNA force-induced melting in the presence of
the classical single-stranded DNA binding protein, gene 32
protein. Bacteriophage T4 gene 32 protein (gp32) is a well
studied representative of a large class of single-stranded
DNA binding proteins, which are essential for the replication,
recombination and repair of DNA. We have developed several
new single molecule methods, which when applied to gp32, have
led to significant new insights about this protein’s
structure-function relationships. We discuss a technique for
measuring Kss, the association
constant of these proteins to ssDNA, which we can determine
over a large range of salt concentrations not available to
bulk binding studies. In addition, we have measured the noncooperative
association constants (Kds) of the weak
but biologically-significant interaction with double-stranded
DNA as a function of salt concentration for full-length protein
and *I, a truncation of gp32 lacking the 48-residue C-terminal
domain. Our results have led to a quantitative model for the
salt dependence of protein binding, which we postulate to
be regulated by a salt-dependent conformational change within
the protein involving the C-terminal domain. With this new
force spectroscopy technique, we have obtained binding rates
and binding free energies for these interactions under a broad
range of conditions. Our methodologies should have useful
applications in many areas of DNA-protein interactions.
[Back to top]
What is Hidden Behind Peptide Bond Restriction
and α-Carbon
Asymmetry of Conserved Antigens? Peptide Bond Isosters and
Chirally Transformed Pseudopeptides as Novel Elements for
Synthetic Vaccines and Therapeutic Agents Against Malaria
José Manuel Lozano, Luz Mary Salazar, Zuly Rivera and
Manuel Elkin Patarroyo
In spite of the controversy regarding sugar and amino acid
mirror-image symmetry and nature, it has been demonstrated
that an intrinsic preference for left-handedness or right-handedness
would depend on weak energy responsible for stabilising L-amino
acids. A weak neutral current interaction involves an enantiomeric
energy difference for L-amino acids to have sufficient magnitude
to break open, non-equilibrium, racemic systems’ chiral
symmetry.
L-amino acid can form complex structural atom arrangements
when building proteins to allow specific chemical and molecular
interactions such as enzyme-substrate and antigen-antibody
complexes. Thus, pathogens can take advantage of higher vertebrates’
molecular immune system’s extremely well organised molecular
L-amino acid composition to establish efficient evasion mechanisms.
Plasmodium falciparum (the most lethal form of malaria)
clearly employs its protein ligands’ non-polymorphic
regions when binding to specific receptors on its target cells.
These sequences are normally poorly immunogenic and non-protection
inducing when used as immunogens. It has been shown that these
ligands’ native L-amino acid composition and their secondary
structure play a vital role in maintaining a code of silence
to avoid a host immune response. Our institute has established
two strategies for overcoming this problem; one consists of
replacing critical ligand-derived peptide binding residues
by others having similar side chain mass but opposite polarity
and the other consists of altering the peptide bond and the
nature of α-carbon
asymmetry.
This review summarises the most widely used pseudopeptide
approaches for novel immunogen synthesis, emphasising their
potential in peptide-based vaccines and as therapeutical agents
for infectious diseases such as malaria.
[Back to top]
Recent Uses of Iron (III) Chloride in Organic Synthesis
David Díaz Díaz, Pedro O. Miranda, Juan I. Padrón
and Víctor S. Martín
Iron (III) chloride is extensively used in organic synthesis
as an ideal Lewis acid since it is an inexpensive, efficient,
stable, environmentally friendly and a convenient agent for
several useful reactions such as; polymerisations, oxidations,
oxidative couplings, reductions, C—C bond formation,
Ferrier rearrangement, one-pot multicomponent condensations,
Friedel-Crafts reactions, cyclisations, glycosidation, Prins-type
cyclisation, deprotection of various functional groups, and
as a reagent in key steps of natural products synthesis. This
comprehensive review attempts to cover the advances in this
field, which have occurred in the last five years.
[Back to top]
Progress in Spectroscopic Probes with Cleavable Active
Bonds
Xinqi Chen, Ming Sun and Huimin Ma
Spectroscopic probes may be defined as the molecules that
can react with analytes (targets) accompanying the changes
of their spectroscopic (chromogenic, fluorescent, or chemiluminescent)
properties; based on such changes the targets can thus be
determined. Spectroscopic probes have been extensively investigated
and used widely in many fields because of their powerful ability
to improve analytical sensitivity and to offer greater temporal
and spatial sampling capability. In this review, special interest
is devoted to a new type of spectroscopic probe that is constructed
with a cleavable active bond as a linker. This type of spectroscopic
probe, developed greatly in the past few years, has opened
a novel alternate route to the specific determination of analytes
with high hydrolytic reactivity, e.g., from metal ions to
enzyme activity, and enabled many biological processes to
be monitored in situ and in real-time. Theoretically,
various photophysical processes, such as photoinduced electron
transfer, photoinduced proton transfer, and fluorescence resonance
energy transfer, can be used to design spectroscopic probes
with cleavable active bonds for selective detection of analytes.
Herein we review the progress and application of this type
of spectroscopic probe, including spectroscopic response mechanism
and the probes with active bonds cleavable by enzyme, metal
ion and reactive oxygen species.
[Back to top]
Development and Applications of Fluorescent Oligonucleotides
U. Asseline
Fluorescent oligonucleotides (FONs) are used in a wide variety
of areas such as molecular and mechanistics biological studies,
molecular diagnostics, therapeutic development, biotechnology
and nanotechnology. Ever since the post-genome era, there
has been an ever-increasing demand for more rapid and accurate
nucleic acid detection and quantification methods. Genetic
information analyses require highly sensitive and specific
detection of certain sequences, single nucleotide changes,
specific structures and varied reactions in different formats
in vitro, in living cells and, ultimately in animals
and in human beings. Ideally, a unique event could be detected
and quantified using the genomic information without amplification
of the nucleic acids to be analyzed. Recent developments enabling
detection at the single-molecule (SM) level have opened new
perspectives for applications. This review reports on the
development and applications of different families of FON
probes. Specific insight is given to those leading to an important
fluorescent signal change upon hybridization with their targets.
Applications of FON probes include real time polymerase chain
reaction (PCR) quantification, detection of single-nucleotide
polymorphisms (SNP), fluorescence in situ hybridization
(FISH) including detection of specific messenger RNAs in living
cells, analysis of gene expression, analysis of nucleic acid
structures and reactions, and in nanotechnology, the assessment
of molecular machine motion and functioning.
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