Polyamines stabilize left-handed Z-DNA: using X-ray crystallographic analysis, we have found a new type of polyamine (PA) that stabilizes left-handed Z-DNA.

There are many great reports of polyamine stabilization of the Z-DNA by bridge conformation between neighboring, symmetry-related Z-DNA in the packing of crystals. However, polyamine binding to the minor groove of Z-DNA and stabilizing the Z-DNA structure has been rarely reported. We proved that the synthesized polyamines bind to the minor groove of Z-DNA and stabilize the conformation under various conditions, by X-ray crystallographic study. These polyamines consist of a polyamine nano wire structure. The modes of the polyamine interaction were changed under different conditions. It is the first example that the crystals consisted of metal free structure. This finding provides a basis for clarifying B-Z transition mechanics.

Base and chain sense in d(CGCGCG)-BP and d(TATATATATATA). Analysis of CD measurements and x-ray crystal data.

We use CD spectra and x-ray crystal data to compare structures of d(CGCGCG)-BP, which is d(CGCGCG) modified on 2-amino group of guanine by (+)7R,8S-dihydroxy-9S,10R-expoxy-7,8,9,10-tetra hydroBenzo(a)Pyrene (7R-BPDE), with the d(TA)6 dodecamer which with increasing ionic strength of the buffer adopts CD spectrum similar to d(CGCGCG)-BP in 0.1M MgCl2 solution but opposite in sign. We indicates that DNA bases in both oligomers may be in a B-form however as a mirror image of stereo structure of right handed d(CGCGCG)-BP and left handed d(TA)6.

Strategies for crystallization of protein/DNA bound complex by in situ phosphorylation of aspartic residue using 5'-phosphorylated-DNA.

We explore an opportunities that lie at the interface of chemistry and biology to generate the processes with novel biological and chemical properties. Our goal is to create complex of DNA molecules in series of operation directed toward efficient protein phosphorylation beyond autophosphorylating kinases for protein/DNA complex formation. The NarL protein is a model of our studies. From crystal structure of NarL and one of its domain-NarLC/DNA complex it is suggested that upon phosphorylation of Asp(59), NarL must open compacted pair of domains, the NarLN and NarLC to receive DNA molecule in the pathway that is yet not elucidated. We try to understand such process using programmed 5'-phosphorylated DNA for simultaneous NarL protein phosphorylation and DNA binding.

The development of crystallization and X-ray crystallography method of long stem DNA.

We clarified stabilization mechanism of left-handed Z-DNA by X-ray crystal structure analysis. I was able to achieve it by burying big minor groove of Z-DNA because metal ion and polyamine connected it to minor groove of Z-DNA. On that occasion I understood that an electric charge and length of polyamine gave big influence to a combination brain very much. I succeeded in crystallization of Z-DNA of a long chain, X-ray crystal structure analysis by examining these combination ability.

Circular dichroism spectra of d(CGCGCGCGCGCG): evidence for intermediate models in the B-to-Z transition.

We analyze CD spectra of d(CGCGCGCGCGCG) to study the potential intermediate states produced during transition between both types of secondary structures of B- and Z-forms as ionic strength of PBS buffer increases. Decomposition of the CD spectra by linear superposition provides evidence for three intermediate states that distinct from B and Z-DNA. Intermediate states of B-form and Z-form found from CD spectra analysis are discussed in terms of early proposed by others the models for B- to Z-DNA transition and W-DNA model refined by molecular modelling program.

The X-ray crystallographic study of the conformation of Z-DNA which bound to polyamine for the minor groove at room temperature and low temperature.

We succeeded in x-ray crystal analysis of d(CG)3 with N1-{2-[(2-amino-ethylamino)-ethylamino]-ethyl}-ethane-1,2-diamine complex at three conditions (1: room temperature 2: low temperature 3: highly salt condition). At room temperature two polyamines took extended form and bound to minor groove of d(CG)3, at low temperature two polyamines took U-shape form and lied in minor groove of d(CG)3, at highly salt condition two polyamines took fishhook form and one polyamine lied in upper side of minor groove and the other polyamine lied in down side of minor groove of d(CG)3.

Function of AGCA tetrads in (CAG)n repeats.

We investigate the structural properties of d(CAG)n repeats in d[CG(CAG)4CG)]*d[CG(CTG)4CG]. The crystals diffract up to 3.5 A and completeness of data is only 60%. We also measure Tm-UV and CD spectra and gel electrophoresis of this oligomer.

The X-ray crystallographic study of long chain left handed Z-DNA and polyamine complex and structural chemistry study of effection by polyamine for the Z-DNA.

We cleared the stabilization mechanism of Z-DNA by using the molecular dynamics calculation and the grid map simulated annealing docking method. Then, we clarified Z-DNA was stabilized by the metal counter ions whose electrical charge and the number of electrons are too many and by polyamine to go into the minor groove. We succeeded in stabilizing Z-DNA of the long chain by using these methods, and succeeded in the crystallization and the data collection up to 1.7 A resolution.