Direct observation of (H8,H6)-Hr J-coupling correlations in oligonucleotides for unambiguous resonance assignments: use of J-scaling in two-dimensional correlated spectroscopy

Four-bond H8/H6-H1 scalar coupling correlations in two-dimensional correlated spectroscopy have been observed directly for the first time by using the J-scaled COSY [(1985) Chem. Phys. Lett. 116, 105-108] technique in a dinucleotide, cytidylyl(2'-5')guanosine (CpG). Unambiguous resonance assignment of nonexchangeable protons in CpG has been obtained using these H8/H6-H1' 4-bond correlations and the various 3- and 4-bond sugar ring proton correlations observed in the COSY and SUPER COSY experiments

Two-dimensional NMR for three-dimensional structure of nucleic acids: new techniques and novel results

The principles and the variety of two-dimensional (2D) NMR techniques useful for structure determination of nucleic acids have been described. Three new techniques namely, SUPERCOSY, J-scaled COSY and COSS which have been recently developed to overcome the problems of sensitivity and resolution have been described in greater detail. The strategies of resonance assignments and structure determination of nucleic acids have been discussed and the experimental results on four oligonucleotides longer than a complete turn of nucleic acid helix have been presented. The data indicate O I' -endo sugar geometry in a majority of the nucleotide units in two oligonucleotides namely, d-GAATTCGAATTC and d-GAA TTCCCGAATTC

NMR studies on truncated sequences of human telomeric DNA: observation of a novel A-tetrad

The structure of the telomeric DNA has been a subject of extensive investigation in recent years due to the realization that it has important functional roles to play in vivo and the observations that truncated telomeric sequences exhibit a great variety of 3D structures in aqueous solutions. In this context, we describe here NMR structural studies on two truncated human telomeric DNA sequences, d-AG3T and d-TAG3T in solutions containing K+ ions. The G3 stretches in both the oligonucleotides were seen to form parallel-stranded quadruplexes. However, the AG3 segment as a whole, had different structural characteristics. The structure of d-AG3T revealed the formation of a novel A-tetrad, which was not seen in d-TAG3T. The A's in the tetrad had syn glycosidic conformation as opposed to the anti conformation of the G's in the G-tetrads. The A-tetrad stacked well over the adjacent G-tetrad and the twist angle at this step was smaller in d-AG3T than in d-TAG3T. These observations are expected to be significant from the point of view of structural diversity and recognition in telomeres

Refined procedures for accurate determination of solution structures of nucleic acids by two dimensional nuclear magnetic resonance spectroscopy

New procedures have been described for accurate determination of solution structures of nucleic acids. These are two fold; new two dimensional nuclear magnetic resonance techniques and better approaches for interpretation of nuclear magnetic resonance data for structure determination purposes. The significant development in two dimensional nuclear magnetic resonance techniques for this purpose are ω1 -scaling and recording of pure phase spectra. Use ofω1-scaled correlated and nuclear Overhauser effect spectra for estimation of interproton distances and 1H-1H coupling constants has been described. Computer simulation procedures for exact determination of structure have been described. Experimental spectra demonstrating the application of new procedures have been presented

Exploring 'unstructured proteins'

In the post genomic era, as more and more genome sequences are becoming known and hectic efforts are underway to decode the information content in them, it is becoming increasingly evident that flexibility in proteins plays a crucial role in many of the biological functions. Many proteins have intrinsic disorder, either wholly or in specific regions. It appears that this disorder may be important for regulatory functions of the proteins, on the one hand, or, may help in directing the folding process to reach the compact native state, on the other. Nuclear Magnetic Resonane (NMR) has over the last two decades emerged as the sole, most powerful technique to help characterize these disordered protein systems. In this review, we first discuss the significance of disorder in proteins and then survey the NMR methods available for their characterization. A brief description of the results obtained on several disordered proteins is presented at the end

NMR recipe for sequencing short DNA fragments

A new recipe has been described for determination of the base sequence in short DNA segments by two - dimensional NMR spectroscopy. The recipe is based on (i) A,T,G,C-distinguishing criteria obtained by analysis of chemical shifts of the non-exchangeable protons and (ii) cross-peak patterns in two-dimensional COSY and NOESY spectra. The base H8 and sugar H2" chemical shifts have been found to be characteristically dependent on the base type to which they belong and the patterns of H8-H2" cross-peaks in NOESY allow determination of sequence of bases in DNA segments

NMR observation of a novel A-tetrad in a telomeric DNA segment in aqueous solution

NMR studies on the telomeric DNA segment d-AG3T show that the molecule exists as a mixture of several multistranded structures whose stabilities are dependent on added salt concentrations. There is one major conformation which can be selectively studied at low salt concentration and the NMR data indicate that this is a parallel stranded quadruplex with a novel A-tetrad at the 5' -end, The A-bases adopt the syn glycosidic conformation as against the anti conformation adopted by the G - bases in the three G - tetrads

Molecular conformation of gonadoliberin using two-dimensional NMR spectroscopy

Complete resonance assignments of the proton NMR spectrum of gonadoliberin (in its native amide and free acid forms) have been obtained using two-dimensional nuclear magnetic resonance spectroscopy under three different environmental conditions, namely, dimethyl sulphoxide solution, aqueous solution and lipid-bound form in model membranes. The proton chemical shifts in the three cases have been compared to derive information about inherent conformational characteristics of the molecule. It has been inferred that the molecule possesses no short-range or long-range order under any of the three solvent conditions. However, there is a nonspecific increase in the linewidths when gonadoliberin is bound to model membranes, indicating a reduced internal motion in the molecule due to lipid-peptide interactions

Recognition schemes for protein-nucleic acid interactions

The molecular forces involved in protein-nucleic acid interaction are electrostatic, stacking and hydrogen-bonding. These interactions have a certain amount of specificity due to the directional nature of such interactions and the spatial contributions of the steric effects of different substituent groups. Quantum chemical calculations on these interactions have been reported which clearly bring out such features. While the binding energies for electrostatic interactions are an order of magnitude higher, the differences in interaction energies for structures stabilised by hydrogen-bonding and stacking are relatively small. Thus, the molecular interactions alone cannot explain the highly specific nature of binding observed in certain segments of proteins and nucleic acids. It is therefore logical to assume that the sequence dependent three dimensional structures of these molecules help to place the functional groups in the correct geometry for a favourable interaction between the two molecules. We have carried out 2D-FT nuclear magnetic resonance studies on the oligonucleotide d-GGATCCGGATCC. This oligonucleotide sequence has two binding sites for the restriction enzyme Bam H1. Our studies indicate that the conformation of this DNA fragment is predominantly B-type except near the binding sites where the ribose ring prefers a3E conformation. This interesting finding raises the general question about the presence of specificity in the inherent backbone structures of proteins and nucleic acids as opposed to specific intermolecular interactions which may induce conformational changes to facilitate such binding