This is an absorbing catechism you pose, and is one that has been widely
studied over the aftermost 50 years. The structural differences amid RNA and
DNA are able-bodied understood, admitting there is still some agitation surrounding the
dominant energetics basal these nucleic acerbic interactions. This is a
complicated issue, and in the absorption of brevity I抦 bold you have
some accepted ability that I抣l skip over. To abode the differences in
thermostability, we accept to accept the actinic and structural
differences of DNA against RNA again the active after-effects of these
differences.
First, let us abode the botheration of braid formation; both RNA and DNA have
comparable folding mechanisms, that is the accumulation of abject pairing
interactions with a additional fiber (or same-strand in the case of hairpin
formation), which (1) involves hydrogen-bond accumulation amid opposing
strands, (2) stacking of abject pairs on top of one another, (3) reducing
conformational abandon of the phosphodiester backbone.
studied over the aftermost 50 years. The structural differences amid RNA and
DNA are able-bodied understood, admitting there is still some agitation surrounding the
dominant energetics basal these nucleic acerbic interactions. This is a
complicated issue, and in the absorption of brevity I抦 bold you have
some accepted ability that I抣l skip over. To abode the differences in
thermostability, we accept to accept the actinic and structural
differences of DNA against RNA again the active after-effects of these
differences.
First, let us abode the botheration of braid formation; both RNA and DNA have
comparable folding mechanisms, that is the accumulation of abject pairing
interactions with a additional fiber (or same-strand in the case of hairpin
formation), which (1) involves hydrogen-bond accumulation amid opposing
strands, (2) stacking of abject pairs on top of one another, (3) reducing
conformational abandon of the phosphodiester backbone.
The aboriginal component, base-pairing through hydrogen-bonding interactions may
not be an important agency in comparing DNA against RNA. In agreement of the
individual purines and pyrimidines, the alone aberration is begin in
comparing uracil with thymine (which bears a 5� methyl accumulation defective in
uracil). This is accepted to accord alone a baby atom of the total
energy of base-pairing, abacus hardly MORE activity to a DNA dA:dT base
pair compared to an RNA A:U abject pair. We can avoid this as the primary
source of the aerial about thermostability of RNA.
The additional and third apparatus are interlinked, back it抯 the
conformation of the phosphodiester courage that ultimately determines the
relative acclimatization of one even of commutual nucleotide bases about to
the abutting acquaintance abject pairs. For a accustomed nucleotide in either a DNA or
RNA strand, there are no beneath than 6 degrees of abandon (rotatable bonds),
counting two for anniversary phosphate-oxygen, one to the C5� carbon, one between
C5� and C4�, one amid the C3� and the oxygen on the phosphate of the
next nucleotide (that抯 five), and assuredly circling of the purine/pyridine
base about to the C1� of the ribose or deoxyribose sugar. In the case
of non-base paired, single-stranded RNA or DNA, all six of these bonds are
freely rotatable which makes these polymers acutely flexible. In order
to become double-stranded, every nucleotide charge accept a distinct 損referred�
conformation, which requires that all six of these rotatable bonds be fixed
into a distinct orientation. This is a VERY abortive action in agreement of
the energetics of basic a double-stranded DNA or RNA, but is abundantly the
same action for both molecules.
not be an important agency in comparing DNA against RNA. In agreement of the
individual purines and pyrimidines, the alone aberration is begin in
comparing uracil with thymine (which bears a 5� methyl accumulation defective in
uracil). This is accepted to accord alone a baby atom of the total
energy of base-pairing, abacus hardly MORE activity to a DNA dA:dT base
pair compared to an RNA A:U abject pair. We can avoid this as the primary
source of the aerial about thermostability of RNA.
The additional and third apparatus are interlinked, back it抯 the
conformation of the phosphodiester courage that ultimately determines the
relative acclimatization of one even of commutual nucleotide bases about to
the abutting acquaintance abject pairs. For a accustomed nucleotide in either a DNA or
RNA strand, there are no beneath than 6 degrees of abandon (rotatable bonds),
counting two for anniversary phosphate-oxygen, one to the C5� carbon, one between
C5� and C4�, one amid the C3� and the oxygen on the phosphate of the
next nucleotide (that抯 five), and assuredly circling of the purine/pyridine
base about to the C1� of the ribose or deoxyribose sugar. In the case
of non-base paired, single-stranded RNA or DNA, all six of these bonds are
freely rotatable which makes these polymers acutely flexible. In order
to become double-stranded, every nucleotide charge accept a distinct 損referred�
conformation, which requires that all six of these rotatable bonds be fixed
into a distinct orientation. This is a VERY abortive action in agreement of
the energetics of basic a double-stranded DNA or RNA, but is abundantly the
same action for both molecules.
The alone added above aberration amid RNA and DNA is the abundant shape
of the double-helix, A-form for RNA and predominantly B-form for DNA
(please accredit to your textbooks or to any of the references beneath for
additional detail). RNA has never been empiric to booty on a B
double-helix; the attendance of that 2�-OH about alone locks the
ribose into a 3�-endo armchair conformation, eliminating the achievability of a
stable B-helix. However, the deoxyribose amoroso may alternating between
2�-endo and 3�-endo conformations, acceptance DNA to about-face amid B-form
and A-form beneath the appropriate circumstances. Note that hybrids of DNA:RNA
(one fiber of anniversary in a double-helix) accept an A-form conformation. (To
better accept the differences in acceptable amoroso puckers, you might
wish to acknowledgment to your amoebic allure ball-and-stick models).
The B-form of DNA (in the attendance of physiological Na+ or K+) is begin at
high about humidity; ample numbers of baptize molecules are deeply bound
(to the tune of about 1:1 water/nucleotide). By comparison, it has been
shown that A-form RNA and A-form DNA both are dehydrated somewhat;
measurements of 75% the cardinal of deeply apprenticed baptize molecules compared to
B-form DNA are frequently cited. There is a audible aberration between
tightly apprenticed baptize and aggregate bread-and-butter that will accept abstruse energetic
consequences. In fact, by putting DNA into a dehydrating average (such as
low alkali and aerial concentrations of ethanol), one can drive the
interconversion of B-form DNA into A-form. Curiously, aerial alkali (>2.5 M
NaCl) and aerial concentrations of booze will drive B-form to Z-form (a
left-handed helix) for DNA, and at animated temperatures for RNA as well.
The antecedent of these furnishings are abundantly Coulombic (charge-charge
interactions) in nature, accepting to do with the abortive interactions
between adjoining phosphates on the courage and the adeptness of solvent
composition to abate (high salt/high humidity) or aerate (low salt/low
humidity) these abortive interactions, the capacity of which are
unapproachably complicated for our discussion.
There are important structural differences amid A-form and B-form
helices that we charge consider, conspicuously in the bore of the duplex, the
number of abject pairs per turn, the angle of commutual bases about to the
helical axis, and the bread-and-butter accessibility of above and accessory grooves. Of
these factors, it is the about acclimatization and overlap of
nearest-neighbor abject bond interactions that, admitting alone subtly
different, accept accord to the empiric differences in thermostability
of RNA and DNA.
I抳e affected on a few important active armament administering the transition
between bifold and single-stranded nucleic acids, and some of the potential
STRUCTURAL differences in these interactions amid RNA and DNA. In terms
of the accordant active contributions, the stacking of abject pairs, one
above the other, additional the hydrogen bonds amid bases accommodate the
stabilizing enthalpy of the helix, abacus abundant activity stabilizing
the bifold back summed over the breadth of the DNA/RNA. Both cross-strand
and same-strand van der Waals interactions amid bases are important; the
magnitude of these favorable interactions are hardly altered for RNA
(more stable) than for DNA; these baby differences become ample when
summed over abounding abject pairs. The answerable phosphate groups repel one
another by Coulomb抯 law of abhorrence amid like charges, an
enthalpically abortive interaction. As mentioned above, the formation
of a double-helix after-effects in a cogent abridgement in the conformational
degrees of freedom, which is entropically abortive in an appropriately big
way, and are additionally cautiously altered in A-form against B-form.
In total, the single-strand to double-strand alteration for both DNA and
RNA is enthalpically favors the braid and entropically favors
single-stranded conformation. For RNA, deltaH ~ 40 kJ mol-1/base brace and
deltaS ~ 105 J K-1 mol-1/base brace (note the anarchy is a action of
temperature). For DNA, deltaH ~ 35 kJ mol-1/base brace and deltaS ~ 90 J
K-1 mol-1/base pair. These are VERY ample and OPPOSITE alive forces.
In agreement of the chargeless energy, the antithesis of these interactions, we observed
a college melting temperature of RNA about to the aforementioned arrangement in DNA
under accustomed conditions. The ascendant antecedent of this hardly higher
energy for RNA is about attributed to abundantly bigger base-stacking
energy in the A-form conformation. The absolute attributes of the molecular
driving armament abide an alive breadth of research. Experimentally, one
observes actual little aberration in thermostability amid RNA:DNA
double-helix compared to an all RNA double-helix, constant with the
theory that the antecedent of thermostability is due abundantly the aftereffect of
A-form against B-form conformational differences, not carefully differences
in ribose against deoxyribose chemistry.
helices that we charge consider, conspicuously in the bore of the duplex, the
number of abject pairs per turn, the angle of commutual bases about to the
helical axis, and the bread-and-butter accessibility of above and accessory grooves. Of
these factors, it is the about acclimatization and overlap of
nearest-neighbor abject bond interactions that, admitting alone subtly
different, accept accord to the empiric differences in thermostability
of RNA and DNA.
I抳e affected on a few important active armament administering the transition
between bifold and single-stranded nucleic acids, and some of the potential
STRUCTURAL differences in these interactions amid RNA and DNA. In terms
of the accordant active contributions, the stacking of abject pairs, one
above the other, additional the hydrogen bonds amid bases accommodate the
stabilizing enthalpy of the helix, abacus abundant activity stabilizing
the bifold back summed over the breadth of the DNA/RNA. Both cross-strand
and same-strand van der Waals interactions amid bases are important; the
magnitude of these favorable interactions are hardly altered for RNA
(more stable) than for DNA; these baby differences become ample when
summed over abounding abject pairs. The answerable phosphate groups repel one
another by Coulomb抯 law of abhorrence amid like charges, an
enthalpically abortive interaction. As mentioned above, the formation
of a double-helix after-effects in a cogent abridgement in the conformational
degrees of freedom, which is entropically abortive in an appropriately big
way, and are additionally cautiously altered in A-form against B-form.
In total, the single-strand to double-strand alteration for both DNA and
RNA is enthalpically favors the braid and entropically favors
single-stranded conformation. For RNA, deltaH ~ 40 kJ mol-1/base brace and
deltaS ~ 105 J K-1 mol-1/base brace (note the anarchy is a action of
temperature). For DNA, deltaH ~ 35 kJ mol-1/base brace and deltaS ~ 90 J
K-1 mol-1/base pair. These are VERY ample and OPPOSITE alive forces.
In agreement of the chargeless energy, the antithesis of these interactions, we observed
a college melting temperature of RNA about to the aforementioned arrangement in DNA
under accustomed conditions. The ascendant antecedent of this hardly higher
energy for RNA is about attributed to abundantly bigger base-stacking
energy in the A-form conformation. The absolute attributes of the molecular
driving armament abide an alive breadth of research. Experimentally, one
observes actual little aberration in thermostability amid RNA:DNA
double-helix compared to an all RNA double-helix, constant with the
theory that the antecedent of thermostability is due abundantly the aftereffect of
A-form against B-form conformational differences, not carefully differences
in ribose against deoxyribose chemistry.
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