| 0 |
Direction |
Structural |
degree |
In DNA, direction signifies the orientation of the DNA strands. DNA typically runs in a 5' to 3' direction, which is important for processes like DNA replication and transcription. |
8402210 |
| 1 |
Enthalpy |
Thermodynamic |
kcal/mol |
Enthalpy is the total heat content in a system. In DNA studies, it's vital for understanding the heat energy involved in processes like DNA melting, where hydrogen bonds holding the strands together are broken. |
15139820 |
| 2 |
Entropy |
Thermodynamic |
e.u. |
Entropy quantifies the level of disorder or randomness in a system. In DNA thermodynamics, it reflects how chaotic or structured the DNA molecule is, which influences DNA melting and other reactions. |
15139820 |
| 3 |
Free energy |
Thermodynamic |
kcal/mol |
Free energy combines enthalpy and entropy to predict whether a reaction will occur spontaneously. In DNA, it helps determine the stability of DNA structures and whether DNA strands will separate during processes like denaturation. |
15139820 |
| 4 |
Major Groove Clash size |
Structural |
Å |
The major groove of DNA is a wide gap between the two strands. Major groove clash size measures the available space in this region, important for understanding how molecules interact with DNA and fit into this region. |
7897660 |
| 5 |
Major Groove Distance |
Structural |
Å |
Major groove distance measures how far apart the two DNA strands are within the major groove. It tells us about the width of this structurally significant feature. |
7897660 |
| 6 |
Melting Temperature |
Thermodynamic |
°C |
Melting temperature (Tm) is the temperature at which DNA strands separate due to the breaking of hydrogen bonds. It's a crucial parameter for studying DNA stability and denaturation. |
7897660 |
| 7 |
Minor Groove Clash size |
Structural |
Å |
The minor groove of DNA is narrower than the major groove. Minor groove clash size measures the available space in this region, relevant for molecular interactions with DNA. |
7897660 |
| 8 |
Minor Groove Distance |
Structural |
Å |
Minor groove distance measures the separation between the two DNA strands within the narrower minor groove. It gives insight into the width of this structural feature. |
7897660 |
| 11 |
Propeller Twist |
Structural |
degree |
Propeller twist characterizes the twisting or rotation of DNA base pairs within the double helix. It reveals how the base pairs deviate from a flat, planar alignment. |
33621338 |
| 12 |
Rise |
Structural |
Å |
Rise measures the vertical distance between adjacent base pairs in the DNA helix. It shows how the DNA molecule "steps up" as it extends along its length. |
15562006 |
| 13 |
Rise stiffness |
Mechanical |
kcal/mol Å |
Rise stiffness quantifies how resistant DNA is to changes in the vertical rise between base pairs. It indicates how flexible or rigid DNA is regarding vertical displacement. |
18072969 |
| 14 |
Rise rise force constant |
Physicochemical |
kcal/mol angstroem^2 |
Rise rise force constant relates to the force constant associated with changes in the vertical rise between base pairs. It quantifies the energy required to alter the vertical spacing of base pairs. |
14581192 |
| 15 |
Roll |
Structural |
degree |
Roll is a structural parameter that quantifies the rotational orientation of base pairs within the DNA double helix. It describes how the base pairs twist or roll around the helix axis. |
15562006 |
| 16 |
Roll stiffness |
Mechanical |
kcal/mol degree |
Roll stiffness is a property of DNA that measures its resistance to changes in the roll angle. In other words, it tells us how difficult it is to twist the DNA molecule. |
18072969 |
| 17 |
Roll-rise force constant |
Physicochemical |
kcal/mol degree Å |
Roll-rise force constant is associated with the force constant required to simultaneously alter the roll angle and the vertical rise of base pairs. It quantifies the energy needed for changes in both roll and vertical displacement. |
14581192 |
| 18 |
Roll-roll force constant |
Physicochemical |
kcal/mol degree^2 |
Roll-roll force constant quantifies the energy needed to change the roll angle of DNA. It reflects how DNA resists alterations in its rotational orientation. |
14581192 |
| 19 |
Roll-shift force constant |
Physicochemical |
kcal/mol degree Å |
Roll-shift force constant measures DNA's resistance to changes in both roll and lateral displacement (shift) of base pairs. It characterizes how DNA maintains its rolling orientation while accommodating lateral shifts. |
14581192 |
| 20 |
Roll-slide force constant |
Physicochemical |
kcal/mol degree Å |
Roll-slide force constant represents the force constant associated with changes in both roll and slide angles of DNA. It quantifies how DNA resists changes in both rolling and lateral sliding between base pairs. |
14581192 |
| 21 |
Shift |
Structural |
Å |
Shift is a structural parameter that describes the lateral displacement of one base pair with respect to its neighboring base pairs within the DNA double helix. It characterizes local structural variations. |
15562006 |
| 22 |
Shift-stiffness |
Mechanical |
kcal/mol Å |
Shift stiffness is a property of DNA that indicates how resistant the molecule is to lateral shifting. It quantifies the rigidity of DNA concerning lateral displacement of base pairs. |
18072969 |
| 23 |
Shift-rise force constant |
Physicochemical |
kcal/mol Å^2 |
Shift-rise force constant relates to the force constant required to alter both the lateral shift and the vertical rise of base pairs. It quantifies the energy needed for changes in both lateral displacement and vertical spacing. |
14581192 |
| 24 |
Shift-shift force constant |
Physicochemical |
kcal/mol Å^2 |
Shift-shift force constant measures DNA's resistance to changes in the lateral displacement (shift) of base pairs. It characterizes how DNA maintains its lateral alignment. |
14581192 |
| 25 |
Shift-slide force constant |
Physicochemical |
kcal/mol Å^2 |
Shift-slide force constant represents the force constant associated with changes in both shift and slide angles of DNA. It quantifies how DNA resists changes in both lateral shifting and sliding between base pairs. |
14581192 |
| 26 |
Slide |
Structural |
Å |
Slide is a structural parameter that quantifies the relative lateral displacement of adjacent base pairs in the DNA double helix. It characterizes deviations from the regular stacking arrangement. |
15562006 |
| 27 |
Slide stiffness |
Mechanical |
kcal/mol Å |
Slide stiffness is a property that quantifies DNA's resistance to lateral sliding between base pairs. It indicates how rigid DNA is concerning lateral motion. |
18072969 |
| 28 |
Slide-rise force constant |
Physicochemical |
kcal/mol Å^2 |
Slide-rise force constant is related to the force constant required to alter both the lateral slide and the vertical rise of base pairs. It quantifies the energy needed for changes in both lateral sliding and vertical displacement. |
14581192 |
| 29 |
Slide-slide force constant |
Physicochemical |
kcal/mol Å^2 |
Slide-slide force constant measures DNA's resistance to changes in the lateral displacement (slide) of base pairs. It characterizes how DNA maintains its lateral arrangement. |
14581192 |
| 30 |
Stacking energy B DNA |
Structural |
kcal/mol |
Stacking energy in B-DNA refers to the energy associated with the attractive forces between adjacent base pairs in the DNA double helix. It's a critical structural feature that contributes to DNA stability, helping to hold the two strands together in the double helix. |
33621338 |
| 31 |
Tilt |
Structural |
degree |
Tilt refers to the angular deviation between adjacent base pairs in a DNA double helix. It's a structural parameter that characterizes the bending of DNA. |
15562006 |
| 32 |
Tilt stiffness |
Mechanical |
kcal/mol degree |
Tilt stiffness is a property of DNA that indicates how resistant the molecule is to changes in its tilt angle. It quantifies the rigidity of DNA concerning tilt. |
18072969 |
| 33 |
Tilt-rise force constant |
Physicochemical |
kcal/mol degree Å |
This physicochemical property represents the force constant associated with alterations in both tilt and rise of base pairs. It's a measure of the energy required to change the tilt and vertical displacement of base pairs. |
14581192 |
| 34 |
Tilt-roll force constant |
Physicochemical |
kcal/mol degree^2 |
Tilt-roll force constant quantifies the energy cost of changing both tilt and roll angles in DNA. It's a physicochemical characteristic reflecting DNA's resistance to twisting and bending. |
14581192 |
| 35 |
Tilt-shift force constant |
Physicochemical |
kcal/mol degree Å |
Tilt-shift force constant measures the resistance of DNA to simultaneous alterations in tilt and lateral displacement (shift) of base pairs. It relates to how DNA resists lateral shifting while maintaining its helical structure. |
14581192 |
| 36 |
Tilt-slide force constant |
Physicochemical |
kcal/mol degree Å |
This physicochemical property represents the force constant associated with changes in both tilt and slide angles. It quantifies how DNA resists changes in tilt and lateral sliding between base pairs. |
14581192 |
| 37 |
Tilt-tilt force constant |
Physicochemical |
kcal/mol degree^2 |
Tilt-tilt force constant describes the energy required to alter the tilt angle of DNA. It's a measure of how DNA responds to changes in its angular orientation. |
14581192 |
| 38 |
Twist |
Structural |
degree |
Twist refers to the rotational angle between the two strands of DNA in a double helix. It characterizes the coiling or twisting of the DNA molecule. |
15562006 |
| 39 |
Twist stiffness |
Mechanical |
kcal/mol degree |
Twist stiffness is a mechanical property indicating DNA's resistance to twisting forces. It quantifies the rigidity of DNA concerning its ability to maintain its helical twist. |
18072969 |
| 40 |
Twist-rise force constant |
Physicochemical |
kcal/mol degree Å |
This physicochemical property relates to the force constant associated with changes in both twist and vertical rise of base pairs. It quantifies the energy required for altering twist and vertical spacing. |
14581192 |
| 41 |
Twist-roll force constant |
Physicochemical |
kcal/mol degree^2 |
Twist-roll force constant quantifies the energy needed to change both twist and roll angles in DNA. It reflects the molecule's resistance to twisting and rolling motions. |
14581192 |
| 42 |
Twist-shift force constant |
Physicochemical |
kcal/mol degree Å |
Twist-shift force constant measures DNA's resistance to changes in both twist and lateral displacement (shift) of base pairs. It characterizes how DNA maintains its twist while accommodating lateral shifts. |
14581192 |
| 43 |
Twist-slide force constant |
Physicochemical |
kcal/mol degree Å |
This physicochemical property represents the force constant associated with alterations in both twist and slide angles. It quantifies how DNA resists changes in both its twist and lateral sliding between base pairs. |
14581192 |
| 44 |
Twist-tilt force constant |
Physicochemical |
kcal/mol degree^2 |
Twist-tilt force constant quantifies the energy required to change both twist and tilt angles in DNA. It reflects the molecule's resistance to simultaneous twisting and bending. |
14581192 |
| 45 |
Twist-twist force constant |
Physicochemical |
kcal/mol degree^2 |
Twist-twist force constant describes the force constant associated with changes in the twist angle of DNA. It quantifies the energy needed to alter the helical twist. |
14581192 |
| 46 |
Wedge |
Structural |
degree |
Wedge is a structural feature that denotes the relative displacement of one base pair with respect to its neighboring base pairs within the DNA double helix. It characterizes local structural distortions. |
8402210 |
| 47 |
B form to A form transition energy |
Thermodynamic |
kcal/mol |
The energy required or released during B form to A form DNA transition is known as the B-form to A-form DNA transition energy. The B-form to A-form DNA transition energy can be either positive or negative, depending on whether energy is absorbed or released during the transition. |
11721003 |
| 48 |
Protein induced DNA deformability |
Mechanical |
deg^3Å^3 |
Blank |
9736707 |
| 49 |
DNA denaturation energy |
Thermodynamic |
kcal/mol |
Blank |
9649614; 10366657 |
| 50 |
Nucleosomal Positioning |
Structural |
% |
Blank |
7816643 |
| 51 |
X Displacement |
Structural |
degree |
X Displacement is a parameter that characterizes the displacement of the base pairs along the x-axis.It describes how much the base pairs are shifted horizontally concerning each other in the DNA structure. |
33621338 |
| 52 |
Y Displacement |
Structural |
degree |
Y Displacement is similar to X Displacement but refers to the vertical displacement of base pairs along the y-axis. It describes the vertical shift between adjacent base pairs in the DNA structure. |
33621338 |
| 53 |
Inclination |
Structural |
degree |
Inclination is a measure of the tilt or slant of base pairs with respect to the helical axis. It provides information about the angular orientation of base pairs in the DNA double helix. |
33621338 |
| 54 |
Tip |
Structural |
degree |
Tip is a parameter that characterizes the rotation of base pairs around the helical axis. It describes the twisting of base pairs in the DNA structure. |
33621338 |
| 55 |
Axis Bend |
Structural |
degree |
Axis-Bend measures the bending of the DNA helical axis. It describes the curvature or bending of the overall DNA structure. |
33621338 |
| 56 |
Shear |
Structural |
degree |
Shear is a parameter that characterizes the lateral shift between adjacent base pairs. It describes the sliding motion of one base pair relative to its neighboring pair in the DNA helix. |
33621338 |
| 57 |
Stretch |
Structural |
degree |
Stretch measures the extension or compression of base pairs along the helical axis. It provides information about the lengthening or shortening of the DNA structure. |
33621338 |
| 58 |
Stagger |
Structural |
degree |
Stagger is a parameter that describes the vertical displacement of consecutive base pairs. It provides information about the step-wise vertical arrangement of base pairs in the DNA double helix. |
33621338 |
| 59 |
Buckle |
Structural |
degree |
Buckle measures the bending or bending-related deformations of the base pairs. It characterizes the bending of base pairs towards the minor groove or major groove. |
33621338 |
| 60 |
Opening angle |
Structural |
degree |
It refers to the displacement or movement of one base pair relative to another within the same strand of the DNA double helix. |
33621338 |
| 61 |
Helix Rise |
Structural |
degree |
Opening refers to the separation or displacement between the complementary nitrogenous bases of a DNA base pair. |
33621338 |
| 62 |
Helix Twist |
Structural |
degree |
H-Rise is a backbone structural parameter that measures the rise or vertical displacement between consecutive base pairs in the DNA double helix. |
33621338 |
| 63 |
Alpha |
Structural |
degree |
H-Twist is a structural parameter that measures the angular rotation between consecutive base pairs in the DNA structure. |
33621338 |
| 64 |
Beta |
Structural |
degree |
Alpha (α) measures the rotation about the sugar-phosphate backbone axis, specifically involving the O3' atom of the sugar, the phosphate group, and the O5' atom of the adjacent sugar. |
33621338 |
| 65 |
Gamma |
Structural |
degree |
Beta (β) measures the rotation about the phosphodiester bond axis, involving the atoms P, O5', C5', and C4'. |
33621338 |
| 66 |
Delta |
Structural |
degree |
Gamma (γ) measures the rotation about the phosphodiester bond axis, involving the atoms O5', C5', C4', and C3'. |
33621338 |
| 67 |
Epsilon |
Structural |
degree |
Delta (δ) measures the rotation about the sugar-phosphate backbone axis, specifically involving the atoms C5', C4', C3', and O3'. |
33621338 |
| 68 |
Zeta |
Structural |
degree |
Epsilon(ε) is a dihedral angle parameter associated with the DNA backbone structure. Dihedral angles describe the rotation about chemical bonds. In the context of DNA, epsilon is one of the angles characterizing the twist of the DNA backbone. |
33621338 |
| 69 |
Chi |
Structural |
degree |
Zeta(ζ) is another dihedral angle parameter related to the DNA backbone structure. Zeta contributes to the description of the twist in the DNA structure. These dihedral angles help define the three-dimensional conformation of the DNA molecule. |
33621338 |
| 70 |
Phase |
Structural |
degree |
Chi(χ) is a dihedral angle associated with the rotation around the glycosidic bond in the DNA backbone. It specifically characterizes the orientation of the nucleotide base with respect to the sugar molecule. Different values of chi represent different conformations of the nucleotide base. |
33621338 |
| 71 |
Amplitude |
Structural |
degree |
The phase angle is related to the torsional angle between adjacent base pairs and contributes to the overall understanding of the spatial arrangement of bases in DNA. |
33621338 |