Nucleic acid structure: Difference between revisions
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** N is the number of nucleotides to reach the exact same point along the helix axis | ** N is the number of nucleotides to reach the exact same point along the helix axis | ||
** m is the number of helical turns to reach the exact same point along the helix axis | ** m is the number of helical turns to reach the exact same point along the helix axis | ||
* the axial rise is the distance along helical axis between nucleotides | * the '''axial rise''' is the distance along helical axis between nucleotides | ||
** If all bases were coplanar and the pairs perpendicular to the helix axis, the rise should equal the van der Waals distance of 3.4 Å | ** If all bases were coplanar and the pairs perpendicular to the helix axis, the rise should equal the van der Waals distance of 3.4 Å | ||
* | * The '''pitch''' is the distance along the helix axis for one complete helix turn | ||
** The pitch equls the number of nucleotides in one turn multipled by the axial rise | ** The pitch equls the number of nucleotides in one turn multipled by the axial rise | ||
* The unit twist is 360 divided by the number of nucleotides in one turn and is the rotation between neighboring nucleotides | * The unit '''twist''' is 360 divided by the number of nucleotides in one turn and is the rotation between neighboring nucleotides | ||
* The base-pair tilt is when | * The base-pair '''tilt''' is when the base pair plane is not exactly perpendicular to the helical axis. | ||
** 0° is the plane perpendicular to the helical axis | |||
** tilt is defined relative to looking at the base pair plane from the 1'-C/N linkage side. Tilting this plane clockwise is positive tilt and negative tilt is counterclockwise | |||
** There is a linear relationship between the tilt of an individual base with the axial rise per nucleotide | ** There is a linear relationship between the tilt of an individual base with the axial rise per nucleotide | ||
* '''Sugar puckering''' is the deviation from planarity for the 5 atoms of the sugar ring. The 5 atoms are never seen to be planar. It can be in an envelope form where 4 atoms are in a plane and the fifth is out by 0.5Å or in a twist form where two adjacent atoms are out of the plane made by the other three atoms. Atoms on the same side as the 5'-C are called endo and those on the opposite side are called exo. | * '''Sugar puckering''' is the deviation from planarity for the 5 atoms of the sugar ring. The 5 atoms are never seen to be planar. It can be in an envelope form where 4 atoms are in a plane and the fifth is out by 0.5Å or in a twist form where two adjacent atoms are out of the plane made by the other three atoms. Atoms on the same side as the 5'-C are called endo and those on the opposite side are called exo. | ||
* '''Dislocation''' is the displacement of base-pairs from the helix axis | |||
Except for the left-handed S/Z helices, the structures are broadly classified into A and B families. The essential distinction between A and B type helices is in the sugar puckering. In A helices, 3'-endo sugar puckering is seen and in B-type helices, 2'-endo (or 3'-exo) is seen. This leads to differences in distance between phosphates from 5.9Å in A-type to 7.0Å in B-type helices. Base-pair tilt is positive | Except for the left-handed S/Z helices, the structures are broadly classified into A and B families. The essential distinction between A and B type helices is in the sugar puckering. In A helices, 3'-endo sugar puckering is seen and in B-type helices, 2'-endo (or 3'-exo) is seen. This leads to differences in distance between phosphates from 5.9Å in A-type to 7.0Å in B-type helices. Base-pair tilt is positive in A-type (10-20°) and negative in B-type helices (-16.4 - -5.9°). | ||
In A-type double helices, the axial rise can vary from 2.59 to 3.29 Å but has small variation in rotation from 30.0° to 32.7°. In B-type helices, the axial rise only changes from 3.03 to 3.37 Å but the rotation varies from 36° to 45° | In A-type double helices, the axial rise can vary from 2.59 to 3.29 Å but has small variation in rotation from 30.0° to 32.7°. In B-type helices, the axial rise only changes from 3.03 to 3.37 Å but the rotation varies from 36° to 45° | ||
Typical parameters for | In B-DNA, the disolcation is about -0.2-1.8Å into the minor groove. In A-DNA, the helix axis is pushed into the major groove with the dislocation about 4.4-4.9Å | ||
==DNA== | |||
DNA can form a wide range of double helical structures. Random sequences are found in the A, B, and C forms. Designed repetitive sequences can form D, E, and Z forms. Native DNA adopts the B-form with 10 base-pairs per turn in its crystalline state. But in solution, the molecule underwinds, yielding 10.3-10.6 base pairs per turn. | |||
Some parameters for B-DNA | |||
* minor groove angle: 137.5078° | |||
* Twist angle of 34.7° | |||
* frequency: 10.4 bases/turn | |||
* The roll and tilt angles vary by a few degrees depending on the basepairs. The dinucleotide AA (or TT) causes significant variations in the roll and tilt angles | |||
Typical parameters for DNA helices: | |||
{| border=1 | {| border=1 | ||
|- | |- | ||
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| -30.0 | | -30.0 | ||
|} | |} | ||
==RNA== | ==RNA== | ||
The extra 2'-OH usually prevents formation of the B-form helix found in DNA. Double-helical RNA is usually of the A or A' form: | The extra 2'-OH usually prevents formation of the B-form helix found in DNA. Double-helical RNA is usually of the A or A' form. At low ionic strength, the A-RNA double helix dominates, but with > 20% salt, A'-RNA is formed. Both are right-handed antiparallel helices. Some key parameters and differences are: | ||
{| border=1 | |||
|- | |||
!Type | |||
!Pitch (Å) | |||
!Bases/turn | |||
!Axial rise (Å) | |||
!Base-pair tilt | |||
|- | |||
|A-type | |||
|30 | |||
|11 | |||
|2.73-2.81 | |||
|16-19° | |||
|- | |||
|A'-type | |||
|36 | |||
|12 | |||
|3.0 | |||
|10° | |||
|} | |||
===Pseudoknots=== | ===Pseudoknots=== | ||
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| 13.6 | | 13.6 | ||
| 14.0 | | 14.0 | ||
| | | 1 | ||
Revision as of 13:54, 25 August 2007
General
- Different double helical structures can be seen called A, A', B, α-B', β-B', C, C', C'', D, E, and Z
- The letters denote structural differences, the α and β are associated with packing differences, and primers indicate small variations
- the symmetries of the various double helices are represented with two numbers [math]\displaystyle{ N_m }[/math] (from crystallography nomenclature)
- N is the number of nucleotides to reach the exact same point along the helix axis
- m is the number of helical turns to reach the exact same point along the helix axis
- the axial rise is the distance along helical axis between nucleotides
- If all bases were coplanar and the pairs perpendicular to the helix axis, the rise should equal the van der Waals distance of 3.4 Å
- The pitch is the distance along the helix axis for one complete helix turn
- The pitch equls the number of nucleotides in one turn multipled by the axial rise
- The unit twist is 360 divided by the number of nucleotides in one turn and is the rotation between neighboring nucleotides
- The base-pair tilt is when the base pair plane is not exactly perpendicular to the helical axis.
- 0° is the plane perpendicular to the helical axis
- tilt is defined relative to looking at the base pair plane from the 1'-C/N linkage side. Tilting this plane clockwise is positive tilt and negative tilt is counterclockwise
- There is a linear relationship between the tilt of an individual base with the axial rise per nucleotide
- Sugar puckering is the deviation from planarity for the 5 atoms of the sugar ring. The 5 atoms are never seen to be planar. It can be in an envelope form where 4 atoms are in a plane and the fifth is out by 0.5Å or in a twist form where two adjacent atoms are out of the plane made by the other three atoms. Atoms on the same side as the 5'-C are called endo and those on the opposite side are called exo.
- Dislocation is the displacement of base-pairs from the helix axis
Except for the left-handed S/Z helices, the structures are broadly classified into A and B families. The essential distinction between A and B type helices is in the sugar puckering. In A helices, 3'-endo sugar puckering is seen and in B-type helices, 2'-endo (or 3'-exo) is seen. This leads to differences in distance between phosphates from 5.9Å in A-type to 7.0Å in B-type helices. Base-pair tilt is positive in A-type (10-20°) and negative in B-type helices (-16.4 - -5.9°).
In A-type double helices, the axial rise can vary from 2.59 to 3.29 Å but has small variation in rotation from 30.0° to 32.7°. In B-type helices, the axial rise only changes from 3.03 to 3.37 Å but the rotation varies from 36° to 45°
In B-DNA, the disolcation is about -0.2-1.8Å into the minor groove. In A-DNA, the helix axis is pushed into the major groove with the dislocation about 4.4-4.9Å
DNA
DNA can form a wide range of double helical structures. Random sequences are found in the A, B, and C forms. Designed repetitive sequences can form D, E, and Z forms. Native DNA adopts the B-form with 10 base-pairs per turn in its crystalline state. But in solution, the molecule underwinds, yielding 10.3-10.6 base pairs per turn.
Some parameters for B-DNA
- minor groove angle: 137.5078°
- Twist angle of 34.7°
- frequency: 10.4 bases/turn
- The roll and tilt angles vary by a few degrees depending on the basepairs. The dinucleotide AA (or TT) causes significant variations in the roll and tilt angles
Typical parameters for DNA helices:
Structure | Pitch (Å) | Helical symmetry | Axial rise (Å) | Twist (°) | Minor groove width (Å) | Major groove width (Å) | Minor groove depth (Å) | Major groove depth (Å) |
---|---|---|---|---|---|---|---|---|
A | 28.2 | [math]\displaystyle{ 11_1 }[/math] | 2.56 | 32.7 | 11.0 | 2.7 | 2.8 | 13.5 |
B | 33.8 | [math]\displaystyle{ 10_1 }[/math] | 3.38 | 36.0 | 5.7 | 11.7 | 7.5 | 8.5 |
C | 31.0 | [math]\displaystyle{ 9.33_1 }[/math] | 3.32 | 38.6 | 4.8 | 10.5 | 7.9 | 7.5 |
B' | 32.9 | [math]\displaystyle{ 10_1 }[/math] | 3.29 | 36 | ||||
C' | 29.5 | [math]\displaystyle{ 9_1 }[/math] | 3.28 | 40 | ||||
C | 29.1 | [math]\displaystyle{ 9_1 }[/math] | 3.23 | 40 | ||||
D | 24.3 | [math]\displaystyle{ 8_1 }[/math] | 3.04 | 45 | 1.3 | 8.9 | 6.7 | 5.8 |
E | 24.35 | [math]\displaystyle{ 7.5_1 }[/math] | 3.25 | 48 | ||||
S | 43.4 | [math]\displaystyle{ 6_5 }[/math] | 3.63 | -30.0 | ||||
Z | 45 | [math]\displaystyle{ 6_5 }[/math] | 3.7 | -30.0 |
RNA
The extra 2'-OH usually prevents formation of the B-form helix found in DNA. Double-helical RNA is usually of the A or A' form. At low ionic strength, the A-RNA double helix dominates, but with > 20% salt, A'-RNA is formed. Both are right-handed antiparallel helices. Some key parameters and differences are:
Type | Pitch (Å) | Bases/turn | Axial rise (Å) | Base-pair tilt |
---|---|---|---|---|
A-type | 30 | 11 | 2.73-2.81 | 16-19° |
A'-type | 36 | 12 | 3.0 | 10° |
Pseudoknots
RNA is normally assumed by folding algorithms to fold without pseudoknots. A non-pseudoknotted structure in parenthesis format would close all parenthesis in order, i.e. [()]. A pseudoknot has the form [(]). In a pseudoknot, the knotted region the "()" pairing cannot exceed 9 or 10 basepairs. This constraint is because of the helical structure of RNA which forms 10 or 11 basepairs per turn. With a full turn, the two strands of the pseudoknot would form a true knot which is physically and biologically unrealistic.
Thermodynamics
[math]\displaystyle{ \Delta G^0 = -RT log K = \Delta H^0 - T\cdot\Delta S^0 }[/math] where [math]\displaystyle{ K=\frac{\rm [duplex]}{\rm [single-strand]^2} }[/math]
At the melting temperature, [math]\displaystyle{ T_m }[/math], [math]\displaystyle{ 2[{\rm duplex}] = [{\rm single-strand}] }[/math] and from conservation of total RNA, [math]\displaystyle{ 2[{\rm duplex}] + [{\rm single-strand}] = [{\rm RNA}]_{total} }[/math]. From this, we can derive that:
[math]\displaystyle{ T_m = \frac{\Delta H^0}{\Delta S^0 + R\cdot log[{\rm RNA}]_{total}} }[/math]
You can experimentally find the melting curve and extract the values of [math]\displaystyle{ \Delta H^0 }[/math] and [math]\displaystyle{ \Delta S^0 }[/math] from which you can get [math]\displaystyle{ \Delta G^0 }[/math]. The Freier-Turner rules shows the incremental [math]\displaystyle{ \Delta G^0 }[/math] of stacking another basepair to the end of another pair. The top row shows the 5' basepair, the left column shows the 3' basepair, and the values are in kcal/mol. For example, a GC basepair followed by a CG basepair has -3.4 kcal/mol. This data was calculated for the folding of RNA at 37°C.
GU | UG | AU | UA | CG | GC | |
GU | -0.5 | -0.6 | -0.5 | -0.7 | -1.5 | -1.3 |
UG | -0.5 | -0.5 | -0.7 | -0.5 | -1.5 | -0.9 |
AU | -0.5 | -0.7 | -0.9 | -1.1 | -1.8 | -2.3 |
UA | -0.7 | -0.5 | -0.9 | -0.9 | -1.7 | -2.1 |
CG | -1.9 | -1.3 | -2.1 | -2.3 | -2.9 | -3.4 |
GC | -1.5 | -1.5 | -1.7 | -1.8 | -2.0 | -2.9 |
To calculate the total energy of a RNA duplex, simply sum the contribution of each pair plus a nucleation term for the first pair, which has been experimentally determined to be 3.4 kcal/mol. It's positive because of entropic loss due to association of two strands.
Loops can be analyzed similarly. The Freier and Turner values for loops are:
Length | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 12 | 14 | 16 | 18 | 20 | 25 | 30 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Bulges | 3.3 | 5.2 | 6.0 | 6.7 | 7.4 | 8.2 | 9.1 | 10.0 | 10.5 | 11.0 | 11.8 | 12.5 | 13.0 | 13.6 | 14.0 | 1 |