See: Article Principles and practice of nucleosome positioning in vitro

Would this be a single nucleosome at a specific place on 1000 bp or an array of nucleosomes with 1 positioned in a specific location? If a single nucleosome, would it be in the center or near one end?

a single nucleosome on 1000bp is preferred. but if that is not really possible then i have to put multiple target sequences in a row and place that number of nucleosomes like a nucleosome array.

it will be positioned in the centre if whether they are single or multiple nucleosomes.

Raul thank you, but I don't mean to use DNA sequence as a tool for nucleosome positioning

Is there a good reason not to use a 601 sequence here? This would be the easiest strategy. If your constraint is that you need to incorporate a specific DNA sequence within the nucleosome, the "601" can tolerate some sequence differences and can still have strong positioning power. I think the strategy to try will depend strongly on what you are trying to do with this positioned nucleosome. Our lab has built fusion chromatin remodeling proteins that can move nucleosomes onto "regular" DNA sequences, but the possibility to use these also will depend on how constrained you are in what sequences can be present in or near the centrally-positioned nucleosome. It is also important to know how well-positioned you need this nucleosome to be.

The target sequence where the nucleosome is positioned and the position of the nucleosome on the DNA are the key components. The sequences other than the part that incorporates into nucleosome can be anything for the experiment. Well, basically I want the nucleosome to be near the sequence of interest as much as possible, but I am not so sure about how feasible it is to position a nucleosome exactly at a specific location along the DNA. I am open to any idea. :)

Chanwoo Kim This is a tricky problem. One thing that comes to mind is the 5S array that Tom Owen-Hughes & Jerry Workman used herein: Article Remodeling the chromatin structure of a nucleosome array by ...

You can modify this to be 1000bp and incorporate flanking positioning sequences leaving enough room in the middle for a final nucleosome to sit on your site of interest. It might work, but it would require construction of a new array (601-based or 5S-based).

A second thought that comes to mind is to use a single 601 sequence on the 1000 bp fragment that is slightly off-center and place your sequence of interest adjacent to the 601 sequence. You can then incorporate your sequence of interest in the center and use "hybrid remodelers" to pull the nucleosome off the 601 sequence and onto or directly adjacent to your sequence. (see Article Extranucleosomal DNA Binding Directs Nucleosome Sliding By Chd1

If your sequence of interest is small, you probably will have reasonable flexibility in where you put the nucleosome with respect to your target sequence. It might take some tweaking to position the nucleosome appropriately.

If you can deal with small yields, it might be possible to reconstitute a nucleosome on a small DNA fragment that contains your sequence, then ligate larger fragments to each end and create a 1000bp DNA fragment with a nucleosome in the center.

There are probably simpler solutions, but I can't really think of any at the moment.

Thank you so much for your time. I am grateful. But I don't know how practically possible for me to use this approach. I hope there is an easier approach.

DNAse I footprinting - no?

Uwe Conrath Thank you for your help. As far as I understand, DNAse I footprinting locates a specific sequence that interacts with a protein of interest. However, in case of nucleosomes, they tend to localize to almost any sequences. But I want to localize histone octamer/nucleosome to a particular sequence, but just to any random sequences. I am therefore looking for a solution to this issue.