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- The
thermodynamics
of
template-direc
ted DNA
synthesis:
base insertion
and extension
enthalpies.: Proceedings of
the National
Academy of
Sciences of
the United
States of
America, Vol.
100, No. 25.
(9 December
2003), pp.
14719-14724.We
used
stopped-flow
calorimetry to
measure the
overall
enthalpy
change
associated
with
template-direc
ted nucleotide
insertion and
DNA extension.
Specifically,
we used
families of
hairpin
self-priming
templates in
conjunction
with an
exonuclease-fr
ee DNA
polymerase to
study primer
extension by
one or more dA
or dT
residues. Our
results reveal
exothermic
heats between
-9.8 and -16.0
kcal/bp for
template-direc
ted enzymatic
polymerization
. These
extension
enthalpies
depend on the
identity of
the inserting
base, the
primer
terminus,
and/or the
preceding
base. Despite
the complexity
of the overall
process, the
sign,
magnitude, and
sequence
dependence of
these
insertion and
extension
enthalpies are
consistent
with
nearest-neighb
or data
derived from
DNA melting
studies. We
recognize that
the overall
process
studied here
involves
contributions
from a
multitude of
events,
including dNTP
to dNMP
hydrolysis,
phosphodiester
bond
formation, and
enzyme
conformational
changes. It is
therefore
noteworthy
that the
overall
enthalpic
driving force
per base pair
is of a
magnitude
similar to
that expected
for addition
of one base
pair or base
stack per
insertion
event, rather
than that
associated
with the
rupture and/or
formation of
covalent
bonds, as
occurs during
this catalytic
process. Our
data suggest a
constant
sequence-indep
endent
background of
compensating
enthalpic
contributions
to the overall
process of DNA
synthesis,
with
discrimination
expressed by
differences in
noncovalent
interactions
at the
template-prime
r level. Such
enthalpic
discrimination
underscores a
model in which
complex
biological
events are
regulated by
relatively
modest energy
balances
involving weak
interactions,
thereby
allowing
subtle
mechanisms of
regulation.Con
ceição
Minetti, David
Remeta, Holly
Miller, Craig
Gelfand, Eric
Plum, Arthur
Grollman,
Kenneth
Breslauer
Source: Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 25. (9 December 2003), pp. 14719-14724. - Science in
court: DNA's
identity
crisis: Nature, Vol.
464, No. 7287.
(18 March
2010), pp.
347-348.Natash
a Gilbert
Source: Nature, Vol. 464, No. 7287. (18 March 2010), pp. 347-348. - A phylogeny of
extant
penguins
(Aves:
Sphenisciforme
s) combining
morphology and
mitochondrial
sequences: Cladistics,
Vol. 21, No.
3. (2005), pp.
209-239.The
phylogenetic
relationships
among the
penguins have
received
little
attention,
despite their
well-known
anatomy and
the
conspicuous
nature of the
group.
Previous
attempts have
included
datasets
limited to
few, mostly
osteological
characters,
and one study
was based on
integumentary
and breeding
characters. We
developed a
morphological
matrix
comprising 159
morphological
characters of
osteology (70
characters),
myology (15),
digestive
tract (1),
integument
(66), and
breeding (7
characters),
scored in 18
extant forms
(all currently
recognized
species plus
one distinct
subspecies). A
gaviiform was
placed at the
root, and 11
species of
representative
procellariifor
m groups
completed the
outgroup. A
heuristic
parsimony
analysis under
equal weights
was performed.
We also
compiled DNA
sequences
available in
GenBank for
the
mitochondrial
genes 12S rDNA
and cytochrome
b. We included
the two data
partitions in
a combined
analysis under
direct
optimization.
Both analyses
recovered the
monophyly of
Sphenisciforme
s and all the
traditional
polytypic
genera.
Morphological
characters
performed
optimally at
the ordinal
and generic
nodes, also
providing
resolution and
varying
degrees of
support at
supra- and
intrageneric
nodes. The
comparison of
molecular and
morphological
results
indicated that
the most
significant
problem in the
phylogeny of
extant
penguins is
rooting the
ingroup. The
mutual
interaction of
molecular and
morphological
data decreases
the ambiguity
regarding the
placement of
the root, and
provides a
resolved,
relatively
well-supported
phylogeny of
extant
penguins.
Biogeographica
l patterns
based on
breeding
ranges and
derived from
the combined
analysis show
that the major
intercontinent
al vicariance
events
detected are
consistent
with cold
marine current
patterns of
the Southern
Hemisphere. ©
The Willi
Hennig Society
2005.Sara
Bertelli,
Norberto
Giannini
Source: Cladistics, Vol. 21, No. 3. (2005), pp. 209-239. - Energetic
signatures of
single base
bulges:
thermodynamic
consequences
and biological
implications.: Nucleic acids
research, Vol.
38, No. 1.
(January
2010), pp.
97-116.DNA
bulges are
biologically
consequential
defects that
can arise from
template-prime
r
misalignments
during
replication
and pose
challenges to
the cellular
DNA repair
machinery.
Calorimetric
and
spectroscopic
characterizati
ons of
defect-contain
ing duplexes
reveal
systematic
patterns of
sequence-conte
xt dependent
bulge-induced
destabilizatio
ns. These
distinguishing
energetic
signatures are
manifest in
three coupled
characteristic
s, namely: the
magnitude of
the
bulge-induced
duplex
destabilizatio
n
(DeltaDeltaG(B
ulge)); the
thermodynamic
origins of
DeltaDeltaG(Bu
lge) (i.e.
enthalpic
versus
entropic);
and, the
cooperativity
of the duplex
melting
transition
(i.e.
two-state
versus non-two
state). We
find
moderately
destabilized
duplexes
undergo
two-state
dissociation
and exhibit
DeltaDeltaG(Bu
lge) values
consistent
with
localized,
nearest
neighbor
perturbations
arising from
unfavorable
entropic
contributions.
Conversely,
strongly
destabilized
duplexes melt
in a
non-two-state
manner and
exhibit
DeltaDeltaG(Bu
lge) values
consistent
with
perturbations
exceeding
nearest-neighb
or
expectations
that are
enthalpic in
origin.
Significantly,
our data
reveal an
intriguing
correlation in
which the
energetic
impact of a
single bulge
base centered
in one strand
portends the
impact of the
corresponding
complementary
bulge base
embedded in
the opposite
strand. We
discuss
potential
correlations
between these
bulge-specific
differential
energetic
profiles and
their overall
biological
implications
in terms of
DNA
recognition,
repair and
replication.Co
nceição
Minetti, David
Remeta, Rian
Dickstein,
Kenneth
Breslauer
Source: Nucleic acids research, Vol. 38, No. 1. (January 2010), pp. 97-116. - DNA-Templated
Self-Assembly
of Protein and
Nanoparticle
Linear Arrays: Journal of the
American
Chemical
Society, Vol.
126, No. 2. (1
January 2004),
pp.
418-419.PMID:
14719910
Self-assemblin
g DNA tiling
lattices
represent a
versatile
system for
nanoscale
construction.
Self-assembled
DNA arrays
provide an
excellent
template for
spatially
positioning
other
molecules with
increased
relative
precision and
programmabilit
y. Here we
report an
experiment
using a linear
array of DNA
triple
crossover
tiles to
controllably
template the
self-assembly
of
single-layer
or
double-layer
linear arrays
of
streptavidin
molecules and
streptavidin-c
onjugated
nanogold
particles
through
biotinstreptav
idin
interaction.
The
organization
of
streptavidin
and its
conjugated
gold
nanoparticles
into periodic
arrays was
visualized by
atomic force
microscopy and
scanning
electron
microscopy.Han
ying Li, Sung
Park, John
Reif, Thomas
LaBean, Hao
Yan
Source: Journal of the American Chemical Society, Vol. 126, No. 2. (1 January 2004), pp. 418-419.
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