Major and Minor Groove Widths.

[shasha]

Hi there.

I am an undergraduate student currently doing my final year project on structural analysis of nucleic acids sequence.
My project is mainly focus on the effect of major and minor groove of dna for dna-protein interaction.

I'm using w3dna server to analyse nucleic acid sequences.
My problem is I don't understand on how to interpret the result for major and minor groove widths.
I would like to know,based on the result that I've received,the major and minor groove widths,
does the width have any effect on protein binding.

Attach herewith is the results that I've received.

Thankyou Sir

[xiangjun]

Thanks for using 3DNA, and posting your questions on the Forum.

My problem is I don't understand on how to interpret the result for major and minor groove widths.
I would like to know,based on the result that I've received,the major and minor groove widths,
does the width have any effect on protein binding.

First, from the screenshot you provided, it appears that 3DNA has been run 3DNA properly. Your example structure seems to be in B-form, where the major-groove widths are larger than the minor-groove widths.

Second, the 3DNA software package is a toolkit to be used as users see fit. Applying 3DNA to a specific project and interpreting results derived therein are entirely up to the user.

Third, the topic on DNA-protein interactions is big, and I do not know of a straight answer as to the effects of DNA groove widths on protein binding. That said, there are some 'general principles' of recognition you can find in literature. Below are just two examples:

• "Protein-DNA recognition" by Pabo & Sauer (1984) -- "Some sequence-specific DNA-binding proteins, like RNA polymerase, do not have symmetrically related subunits and do not bind to symmetric recognition sequences. Cro, repressor, and CAP use alpha-helices for many of the contacts between side chains and bases in the major groove. An adjacent alpha-helical region contacts the DNA backbone and may help to orient the "recognition" helices."
• "The role of DNA shape in protein–DNA recognition" by Rohs et al. (2005) -- "By comprehensively analysing the three-dimensional structures of protein–DNA complexes, here we show that the binding of arginine residues to narrow minor grooves is a widely used mode for protein–DNA recognition."

HTH,

Xiang-Jun

[shasha]

Thank you for your kind reply on the question.The first article cannot be access.

From the result provided,from my understanding,the one in pink colour column is my DNA sequence.
What about the character in yellow colour column ?

[xiangjun]

The first article cannot be access.

You need to ask your library for access to the Pabo & Sauer (1984) review article. Alternatively, you may want to read some more recent reviews or primary publications.

From the result provided,from my understanding,the one in pink colour column is my DNA sequence.
What about the character in yellow colour column ?

Using the classic B-DNA Dickerson dodecamer (355d) as an example, the bases in the duplex structure is listed at the top of the 3DNA analyze output, as shown below.

RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

            Strand I                    Strand II          Helix
   1   (0.010) ....>A:...1_:[.DC]C-----G[.DG]:..24_:B<.... (0.010)     |
   2   (0.007) ....>A:...2_:[.DG]G-----C[.DC]:..23_:B<.... (0.012)     |
   3   (0.010) ....>A:...3_:[.DC]C-----G[.DG]:..22_:B<.... (0.006)     |
   4   (0.008) ....>A:...4_:[.DG]G-----C[.DC]:..21_:B<.... (0.010)     |
   5   (0.004) ....>A:...5_:[.DA]A-----T[.DT]:..20_:B<.... (0.014)     |
   6   (0.012) ....>A:...6_:[.DA]A-----T[.DT]:..19_:B<.... (0.008)     |
   7   (0.007) ....>A:...7_:[.DT]T-----A[.DA]:..18_:B<.... (0.006)     |
   8   (0.010) ....>A:...8_:[.DT]T-----A[.DA]:..17_:B<.... (0.011)     |
   9   (0.010) ....>A:...9_:[.DC]C-----G[.DG]:..16_:B<.... (0.009)     |
  10   (0.012) ....>A:..10_:[.DG]G-----C[.DC]:..15_:B<.... (0.006)     |
  11   (0.012) ....>A:..11_:[.DC]C-----G[.DG]:..14_:B<.... (0.009)     |
  12   (0.010) ....>A:..12_:[.DG]G-----C[.DC]:..13_:B<.... (0.009)     |

With 12 base pairs, there are 11 dinucleotide steps: the 1st one is CG/CG, and the 2nd is GC/GC, ... the 8th is TC/GA, etc, where the two bases along each strand are listed along the 5'--->3' direction.

HTH,

Xiang-Jun 

[shasha]

1) What is dinucleotide steps ?

2) From the results, there were P-P and Refined. can you explain on this ?

[xiangjun]

1) What is dinucleotide steps ?

Two consecutive base pairs in a duplex. The example I showed you in the previous reply has 12 base pairs, and thus 12-1 = 11 dinucleotide steps. Use PyMOL or Jmol to see them.

2) From the results, there were P-P and Refined. can you explain on this ?

The details are provided in the reference given in 3DNA output. I have already emailed you the appendix (in PDF) describing the method in the El Hassan and Calladine JMP paper. Read it carefully. You may again using a molecular visualization program to check the P-P distances.

Xiang-Jun
 

[shasha]

Thanks sir.

Can i have the user manual for description of each type of parameter because the manual is apparently not available from the link.

[xiangjun]

Can i have the user manual for description of each type of parameter because the manual is apparently not available from the link.

Check files in the $X3DNA/doc folder of 3DNA v2.2 distribution. The user manual is in file x3dna_v1.5.pdf: it may look dated, but commands described there are still relevant. An updated version for v2.2 is coming shortly.

Given your background, I'd highly recommend Calladine's book: "Understanding DNA (Third Edition)
The Molecule & How It Works".

Xiang-Jun