 So, we continue with the discussion of the DNA and the RNA structures and you see here as I said the ribose ring or the 5-membered ring is the important element, what are the elements of the DNA structure whether the phosphate backbone is one and the second thing is the sugar ring and the sugar ring as I said is a 5-membered ring here. Now we have to define the structure of the sugar ring so and that is an important element we have to define the structure of the phosphate backbone the various angles which are present here the torsion angles which are there we will come to that and then you have this sugar ring. The sugar ring structure is determined by these torsion angles which are indicated here so nu 0, nu 1, nu 2, nu 3, nu 4 not all of them are very independent the torsion angle is defined in this manner. So, the nu 0 torsion angle is defined as angle around this bond here rotation angle around this bond which defines the relative positions of C4 prime and C2 prime okay C4 prime O4 prime C1 prime C2 prime and the central around the central bond there is this torsion rotation angle these are also called as dihedral angles because this define the angle between the two planes formed by these groups C4 prime O4 prime C1 prime these atoms for one plane and O4 prime C1 prime C2 prime this form another plane and it is the angle between these two planes that defines the dihedral angle or it is also the torsion angle around this. So, likewise you have this nu 1 which is O4 prime C1 prime C2 prime C3 prime and then you have nu 2 which is C1 prime C2 prime C3 prime C4 prime and nu 3 C2 prime C3 prime C4 prime O4 prime and you have nu 4 C3 prime C4 prime O4 prime C1 prime but however notice that all these torsion angles are not independent they are dependent on each other because the ring is closed ring is closed and then there are also important you can see your physical chemistry calculations one can see how many degrees of freedom are there so you have you have the in a typical one you have four bonds and three three bond angles and you have two torsion angles typically two torsion angles are sufficient to describe this but then once you have the ring closure then you actually have only one torsion degrees of freedom left and that is what is indicated in this picture here you see these ones are all related all these torsion angles are related in a particular manner and the one degree of freedom which is there which is called as the P when one defines this P this is called as the pseudo rotation angle the pseudo rotation angle depending upon the value of the pseudo rotation angle so you have different kinds of new eyes here this new eye is the individual torsion angles is is given by tau m this defends the maximum distortion from the plane of the ring how much a particular item is going out so this is the kind of a quantity number which indicates how much is the a particular item going out of the plane what is the maximum value but this will have a certain constraint because of the bond angles and the bond distances are well fixed and they cannot be changed too much and therefore this actually is a kind of a well-defined element this is typically of the order of 38 degree okay and then the cosine the P is a value which can take values from 0 to 360 and I minus 2 delta delta is a fixed number like 144 you put for a put delta is equal to 2 and keep varying I to through different values then you will see by you get different kinds of sugar geometries you depending upon the value of P you get you different geometries and all of these are indicated in the kind of a circle because of the P can go from 0 to 360 or you can say it go from 0 to minus 180 or plus 180 and so on so forth okay and these are typically indicated how what is the kind of a structure that we will get these are all got certain labels that is what is the kind of a structure the sugar ring has got and here you see if you make a plane of a particular thing put the three items in a plane C1 prime O4 prime C4 prime if you put them in a particular plane what is the disposition of the 2 prime and the 3 prime items with respect to that plane and then you will get different and the C4 prime is always on one side so you get different kinds of structures for the sugar ring so in this case the 2 prime is above the plane of the ring and the 3 prime is below the plane of the ring and the O4 prime is here O4 prime is always there only and in this structure the 3 prime is above the plane of the ring and the 2 prime is below the plane of the ring so here you see both the things are above and below so you have the extent of the things which are above and below so you have the 3 prime above 2 prime below but the degree is more so 3 prime less 2 prime more the degree is less and therefore you get different kinds of structures which are indicated by typical Cn. This group of structures which are indicated where the 2 prime is above the plane of the ring these are called as S conformations or called the south and this is the south here. This is the south in this circle, this below this central line, this is the south and this is the north. So all those conformations which are below here these are called as the south conformations or S conformations and these are characterized by the 2 prime atom going above the plane of the ring and these are called as C2 prime endo. If it is above it is called as endo anything which is below it is called as exo and therefore you have here in these structures then you have see when it is this calls in the south you have the C2 prime endo the C2 prime endo is this one here. So all of these are C2 prime endo and to the different degree how much is the 3 prime below? So you get what we will say here C2 prime endo C3 prime exo but the degree of the 3 prime which is below or the degree to which this one is above that determines the different positions along the in this circle here. You see here this is 0 to 180 on this side similarly what we have the north conformations it is the 3 prime which is above the central line and this is the 3 prime endo therefore this is the 3 prime endo here and if you take the p value how the p value is changing? So this goes from 0, 36, 72 this becomes 90 so at this 90 the O4 prime endo. Now the other things becomes the O4 prime is actually going out of the plane and that is there is not shown there okay so your O4 prime becomes above the plane and put the other 3 items in the plane of the in a plane in a particular plane and then you go you have the twisted conformations they are described as endo conformations twisted conformations twisted means both the things are above and below but to different extent it is not only one. So you have in one particular case then only one which is all the 4 items are in a plane and only one item is above the plane you can also think about that and those ones are these O4 prime endos O4 prime endo or O4 prime XO 4 items in a plane and one of them is above and all other ones are kind of twisted to a certain extent okay which is closer to this to 180 this is called a C2 prime endo and then you have C3 prime XO here and so on so forth. So you see P is an important parameter which determines the nature of the sugar ring and the sugar ring varies from one nucleotide unit to the second nucleotide unit it can vary it can vary in the DNA and RNA why it can vary because the C2 prime here in the case of DNA has two hydrogens here whereas in the RNA it has one hydrogen and one oxygen and therefore this can create a kind of steric differences and interaction differences between the oxygens here and between the one nucleotide unit to the next nucleotide unit. Therefore this sugar ring can have different confirmations indeed you will find as we will show later that in the case of DNA this sugar ring adopts the south confirmations by and large the C2 endo confirmations is called a C2 prime endo confirmations and in the RNA they adopt what is called as the C3 prime endo confirmations and that primarily comes because of the oxygen at this point. Okay so now you see what it reflects in the case of there are different kinds of structures and these are classified as A, B, C, D, E in the DNA. Now the previous the fiber diffraction data the fiber diffraction data could not give you any more detail about this. Now how do we get this information? So you can use tools like NMR or crystallography and people then actually synthesize small DNA segments to get more details into the structures of the individual nucleotide units or short segments of the DNA segments because there is a repetitive in it. So therefore you can say if you take a short segment of the DNA segment or RNA segment you might be able to think what is the kind of a structure which is propagating through the entire polymer and that is what was done and they came out with the different kinds of DNA structures and those ones are indicated here and this is the stereophilic 12 base pair of A DNA this is a particular kind of a DNA structure where it is a DNA okay and this is the structure of this molecule deoxy gg ta ta cc okay and this is the 5 prime end here and this is the 3 prime end here. The sequence goes as gg ta ta cc this is how the DNA sequences are written okay and here you see the structure has a certain kind of a fact is a fat structure and this the base pairs are tilted with respect to the axis of the DNA axis of the double helix the axis of the double helix may go like this and the base pairs are tilted in this half they are tilted like this in the top of they are tilted like this and that typically the fiber diffraction data had shown that one complete turn of the DNA so what is the complete turn so you go from here to here like this and then you come to the beginning and that is one complete turn from here to your one complete turn and the fiber diffraction data had said that there can be approximately 10 nucleotide 10 base pairs in a particular segment okay and depending upon the structures of course there can be slightly more and also in the later segments which have been discovered. Therefore, you have this a particular half and this particular half and this structure is called as the ADNA because this DNA molecule has the structures which are very reminiscent of the 3 prime endo sugar geometry and therefore this is called as the ADNA and normally what is present in the larger probability in your solution inside the cell is what is called as the BDNA and this is the BDNA and this is the structure obtained by a larger DNA sequence under the different conditions and depends upon the hydration level also inside your structure I mean inside your DNA crystal how much water molecules are there so it also depends upon those ones and this is the structure of a 12 mer DNA segments which has the base sequence C, C, A, A, C, G, T, T, G, G okay notice here this is self complementary what is the meaning of self complementary so if I write here the sequence C, C, A, A, C, G, G, G now this is the 5 prime end and this is the 3 prime end now what I do I write the same sequence here back C, C, A, A, C, G then I have T, T, G, G so this is the 3 prime and this is the 5 prime you see I have written the same sequence twice so therefore this is called as the self complementary sequence and therefore one molecule which is there naturally it goes into the form of a double helical structure like this and this is easier to work with such molecules otherwise you will have to generate two different kinds of sequences and then to make a duplex structure so this molecule was chosen though it is automatically forms a duplex structure as a most stable form okay so this is self complementary okay and this molecule the structure showed was like this and it is little bit more elongated you can see compared to the RNA molecule and the ADNA this structure is called as the BDNA okay and it has clearly two different kinds of grooves one can identify two grooves there is one groove which goes like this which is called as the major groove and there is another groove which is the smaller groove which is called as the minor groove so there are two different kinds of grooves described for the DNA structure so the this amount depending upon the amount of space which is available and you have a groove which is defined okay the base pairs open in the two different grooves one side of the base pair opens in the major groove other side of the base pair opens in the minor groove okay so that is when you explicitly write the base pairs that is what one sees now this is the third type of DNA segment and in naturally okay now let us go behind here now you see these ones are right handed helices here you see this is one right handed helix the daily helix goes like this okay this is the right handed helix and the other one is coming in the opposite direction so that is also right handed helix two right handed helices are coming like this and then they are held together by this hydrogen bonds in the base pairs okay so in this BA DNA as well as in ADNA we have two right handed helices which are going into intertwined at two form base pairs and that is but there are differences in the structural elements how fast is the how much is the distance between one base pair to another base pair typically it is about 3.64 angstroms here so therefore if I take 10 base pairs you will have the one end of once complete this turn of the DNA is about 34 angstrom this is what I used earlier for the calculation so what is the total length of the DNA segment okay and therefore you have this the unit rise is 3.4 angstroms and then you have a 34 angstroms in the BA DNA in the case of RNA is slightly smaller and the number of units also is given the same the height is slightly smaller okay now this is another kind of a DNA structure which was discovered this actually came quite late this came somewhere in the 19 close to the 1980s 1979 and this is called as the Z DNA or the Z DNA and this actually is a left handed helix okay this is not right handed helix this is the left handed helix and this very characteristics feature of this is that this is it is not a monomer which is repeating here but it is a dimer so the dimer structure is the basic unit of this repeating unit and this is a left handed DNA structure and it occurs only in such point of a sequences which are rich in CG segments CG segments initially it was not clear whether they are actually biologically present or not this is called as the Zignac Zignac nature of the of the phosphorus phosphate residues that you can see so this is also that is why it is called as Z DNA it is zigzag nature it is not a proper helix as you can see in the in the case of B DNA or the A DNA but this is a zigzag zigzag nature and the dinucleotide is the repeating unit unlike the mononucleotide which is the repeating unit in the A and the B DNA and in the dinucleotide the two units are different structural features and that is an important factor how they become different and these are typically observed in very high concentration of whenever there is high concentration of salt and why did they do it of course just curiosity and they discovered this and then of course it became an important point. So here is the summary of all of these DNA segments the structures of the different DNA segment so here you have the A DNA then you have the B DNA and this is the crystal structure which are these are these are from the model okay A DNA the small a which is here this indicates from whatever the build model they built the Watson and Crick these are from fibers fiber diffraction data and these are from single crystal structure GGCCGCC this is also you notice is the self complementary sequence and this forms an A DNA the B DNA this form which is there CG CG A A T T CG CG this is also self complementary sequence because if you write in the similar reverse way you will find it is the duplex and the Z DNA is as I said C C G G that was a structure which was there and it is a dinucleotide which is repeating unit here you have the C residues and the G residues they have different structures the individual units are different structures now what are the structures here what are these alpha beta gamma and delta epsilon these ones these are the torsion angles along the backbone of the DNA so you have this backbone phosphodiester linkages all over there and that is the various six torsion angles which are present along the phosphodiester backbone and this chi is the angle which connects the sugar ring to the base sugar ring to the base that is the C1 prime nitrogen that bond the torsion angle around the around that bond that actually defines what is the orientation of the base with respect to the sugar ring and that angle is called as chi torsion angle and you notice here these have certain ranges of values typical ranges of values by and large so these ones the alpha is around between minus 50 to minus 75 and bdna it has minus 41 this is slightly lower compared to these ones and the b the beta angle this is 172 to 175 and here in the bdna it is smaller 136 the gamma and delta these are along the backbone so along the polypeptide backbone you have this different torsion angles there so if I want to draw here this is the CH2 this is the 5 prime this goes to the oxygen here this is the 5 prime then I have the C4 prime the C3 prime then the O3 prime okay then you have the CH2 again this is the 5 of the other end okay and then you have the P here then you have the O here again and your sugar ring is here this goes to the O here C1 prime C2 prime and this is connected to this and this angle is the delta torsion angle there okay and this is the gamma and this is the beta and this is the alpha and this angle is the epsilon okay and this is your xi and the one which connects to the C1 prime to this on there that is the chi that one angle which is not there is no space here and this goes this is the this is the chi here okay this is the 5 prime again CH2 so therefore you have this alpha beta gamma delta epsilon and xi so these are the 6 torsion angles what you have in this here okay and how these values are changing and of course there is also people did a DNA RNA and Decamer and of course this is a mixture of the DNA RNA and this has different kinds of torsion angles here the values are indicated there and the ARNA is the sugar ring is more C3 prime into here there is a sharp contrast and what it reflects which angle reflects the sugar ring here this by and large it is in the delta because the delta is in the sugar ring C4 prime C3 prime that is part of the sugar ring and so this is reflected in the delta torsion angle how these ones are different okay you see here the ADNA has 7991 and the BDNA has 130 between 120 to 140 so therefore this is a quite characteristic and the GDNA has alternating this and this so you have the C residues has this C2 prime endo and the G residues has the so called C3 prime endo so if the delta is around the 7990 that is the C3 prime endo structure and if it is 120 to 140 that is the C2 prime endo structure so therefore in the GDNA you see the C residues and the G residues have different sugar geometries so one of them has a C2 prime endo kind of a thing other one has a C3 prime endo kind of a string okay and the beta torsion angle is mostly around the trans value and except for this particular one here it is 136 otherwise it is mostly around the 180 value roughly and similarly this is the gamma is roughly around the 40 between so called the Gauch confirmation except for here the G residues in the GDNA and this goes into the trans area so this is minus 169 is like the trans area all of these ones are so called Gauch confirmations here close to less or more and things like that okay so this is how the various structures now all this information has come from the single crystal structures of sort DNA segments okay now there is also one should describe and what about the base pairs base pairs are they all parallel to each other or they are different from one another the base pairs can differ to and you have to describe what is the relative orientations of the basis in the base pairs so you can define that in with different parameters here so these are the various parameters which are used to describe the base pairs I told you that the base pair which is there on one side of that is the minor group other side is the major group so typically the base pairs open on the two sides because these are in the interior of the double lx and they open on the two sides of the double lx so one side is the major group other side is a minor group okay so and now you see here it is a 5 prime to 3 prime it is going here this is 5 prime to 3 prime and the base pairs are held together like this okay and now are these in the same plane or they can be did are they parallel to the orientation with respect to the double helical axis or are they tilted with respect to each other various kinds of parameters can be described here what is the orientation with respect to the axis of this here it is perpendicular perpendicular to the helical axis here it is slightly tilted in one dimension one direction okay this tilted with respect to what so this particular axis along this now here it is tilted with respect to the other axis okay so there is a rotation here this is indicated by the rotation here you indicate a rotation consider this as a planar planar one and then the whole base pair is the plane and you take a rotation around this axis therefore this becomes like this now you take a rotation around this axis it becomes like this okay so therefore you can describe the orientation of these base pairs using this one one particular parameter that is when these are all parallel if they are parallel now but they whether they are all exactly in the same pair like this or there is a small opening here okay so you can again describe these ones here there is an opening with respect to this axis their two bases are like this or the two bases are like this or the two bases are like this so this is the different torsion this is the parameter which is called as the kappa here and you have different these are labeled by different parameters and you can describe this as within the same base pair how they are oriented with respect to each other the two bases are now you can also describe the relative orientation of two base pairs consecutive base pairs to continue to base pairs if you look at these two consecutive base pairs with the rotation around this particular bond at this particular axis will displace the two base pairs in this manner okay so therefore not exactly sitting on top of each other but slightly displace with respect to each other their planes okay now if they are angled like this then difference is called as the roll this is called as the twist this angle is called as the twist this angle is called as the roll and this angle is called as the tilt so you differentiate these different parameters with by different names so one of them you call as a twist this call as the roll this is called as the tilt and similarly here you call them as opening and this is the propeller and this is the buckle so here also these ones are called as tip this is inclination and this is the coordinate frame in the same indicating the coordinate frame and all of those ones are described here in a little bit more explicit manner so you have the summarized so you have the minor groove on this side and the major groove on this side so if the base pair is like this you draw an axis like this to through this through the center of the base pair and then you have a vertical one and you have an axis like this you define x y z these three axis with respect to the base pair and you can define the positions of all of these groups with this as rotations with respect to these three these three axis there and that is the call this called as the one is called as the slide and then you have the shift so how they are shifted with respect to the center so whether it is exactly going through the center or it is shifted with respect to that so this one is shifted so this is the kind of a slide and this is a shift so these are the different parameters which are used to describe the orientations of the base pairs in the same in the plane and so you have so many parameters to describe the structure of the DNA segment so you have the sugar geometry on one hand then you have the torsion angles along the polypeptide backbone and then you have the base pair orientations with respect to each other and whether they are in the same plane or they are slightly tilted with respect to each other and how are the stacking whether the base pairs are stacking exactly on top of each other or they are slightly different from one another so these are the various parameters all this information has come because one could obtain high resolution structures of small DNA segments and this is taken from this paper of R. R. Dickerson this was this published in 1989 so this is the description of the individual base pairs here average helix parameters for the major DNA confirmations okay we need not go into the details of these numbers here but this is a kind of an indicator as to what sort of values are there for the different parameters the characterizing the DNA structure in the different DNAs so depending upon the small variations which were present so different kinds of labels have been given for the different DNAs we talked about the A, DNA, B, DNA but there are also some variations which occurred and they led to what are called as the C, DNA, D, DNA, T, DNA then you also have the Z DNA which you also described in major detail and then you have the A, RNA and A prior RNA these ones are the RNA segments all those are the DNA segments these are only minor variations with respect to the major ones the ones which are by and large available in the natural sequences are the B, DNA and the A, DNA and even there the RNAs are mostly in the A form and the DNA is in the B form and this depends on also on the extent of hydration how much is the water content depending upon that you get slightly different structures okay and this is the continuation of the same so what sort of parameters are there for the base pairs orientations of the base pairs in the and this is for the Z DNA and those ones were for the A, B, D and C and D etc and since in the Z DNA you have different things for the two different steps the CG steps are different therefore you have different parameters here for the two things so in other words we need to characterize this kind of details for the structure when we want to calculate the structures of the molecules and crystallography has been used and NMR also has been used and we will see what kind of structures have been determined by the NMR data and these happen in the solution okay so this has become possible with various kinds of NMR experiments and certain algorithms which have been developed so I think I think we can stop here